Date / DatabasesFiles / Description
2017/09/20: system kegg Added support for the new DBLINKS field in lreaction
icarus/db/href.i
icarus/db/lcommon.is
icarus/db/lreaction.i
icarus/db/lreaction.is
web/WEB-INF/jsp/views/lreactionentry/lreactionentry.jsp
2017/09/11: emboss Corrected a configuration mistake which would have needleall not do an all against all comparison for the input sequences, but only do the first sequences against the other sequences
icarus/lion/emboss/needlealln.i
icarus/lion/emboss/needleallp.i
2017/09/06: ensembl_mysql Update for some minor schema changes in EnsEMBL 90
icarus/db/ensemblRDB.i
icarus/db/ensembl_compara_schema.i
icarus/db/ensembl_funcgen_schema.i
icarus/db/ensemblcore_schema.i
2017/09/04: system Added support for the new elm (Eukaryotic Linear Motif resource for Functional Sites in Proteins) references in UniProt
icarus/db/dbxref.i
icarus/db/href.i
2017/08/10: genpept Fix to prevent errors caused by the disappearance of GI numbers (they are discontinued by the NCBI) in the the data. After applying this update please re-index genpept (genpeptrelease and genpeptnew)
icarus/db/genpept.is
2017/08/04: kegg Update to support the new Created field in the Kegg genome database
icarus/db/kegggenome.i
icarus/db/kegggenome.is
web/WEB-INF/jsp/views/kegggenomeentry/kegggenomeentry.jsp
2017/07/03: ccds system Change to give the mouse section of CCDS its onw databases (CCDSNUCMUS and CCDSNUCPROT. CCDSNUC and CCDSPROT now only contain human sequences. This is needed as the download area at the ncbi ftp site is configured in such a way that it is no longer possible for SRS Prisma to download both human and mouse data as a single database
icarus/db/ccds.i
icarus/db/ccdsnuc.it
icarus/db/ccdsprot.it
icarus/db/srsdb.i
2017/07/03: epd Change to make it easier to control which parts of epdnew is being downloaded by SRS Prisma. Please make sure your SRS Prisma files are up to date when you install this file
icarus/db/epd.i
icarus/db/epd.it
2017/07/03: prisma Fix for a problem with recursive mirroring if multiple remote directories are specified
icarus/lion/prisma/remoteConnection.i
2017/06/23: kegg Inproved stability of the unpacking of Kegg pathway images
icarus/db/pathwaytar.it
2017/06/23: prisma Removed the escaping of backticks in unpackcommands, as this was causing instability. You may have to review unpackCommands which use backticks in an environment where you also use a batch queue system to ensure that they work as expected
icarus/lion/prisma/pretransPhase.i
2017/06/14: chembl Update for some minor schema changes in ChEMBL 23
icarus/db/chembl_mysql_schema.i
icarus/db/chembl_oracle_schema.i
2017/06/13: ensembl_mysql update for EnsEMBL 89
icarus/db/ensemblRDB.i
icarus/db/ensembl_compara_schema.i
icarus/db/ensembl_funcgen_schema.i
icarus/db/ensemblcore_schema.i
2017/06/06: epd Update for EPD (Eukariatic Promotor Database) so it also includes the EPDnew datasets
icarus/db/epd.i
icarus/db/epd.is
icarus/db/epd.it
2017/05/31: prisma srscheck A number of fixes/improvements for SRS Prisma: Improved stability when using batch queues, Fixed a reporting issus for the check phase, where remote site check problems weher not reported in the Prisma Reports, Fixed a number of problems which where Prisma would show error messages, where actually nothing was wrong
icarus/lion/prisma/checkRemoteFiles.i
icarus/lion/prisma/configUpdate/srssection_off
icarus/lion/prisma/dbSync.i
icarus/lion/prisma/generateCalendar.i
icarus/lion/prisma/moveLibs.i
icarus/lion/prisma/movePrismaData.i
icarus/lion/prisma/pretransPhase.i
icarus/lion/prisma/prismaCheckClasses.i
icarus/lion/prisma/prismaCheckMain.i
icarus/lion/prisma/prismatime.is
icarus/lion/prisma/reformatPhase.i
icarus/lion/prisma/remoteConnection.i
icarus/lion/prisma/setReportPhase.i
icarus/workflows/buildPhase.i
icarus/workflows/coreCheckClasses.i
icarus/workflows/getSystemLibs.i
icarus/workflows/linkPhase.i
2017/05/22: geneseq Added support for the new Kind Code field in geneseq supplements and fastalert
icarus/db/geneseqsupp.is
icarus/db/geneseqsuppcommon.i
2017/05/22: pdbfinder Fixes for some problems with entry boundaries and sorting in prbfinder
icarus/db/pdbfinder.i
icarus/db/pdbfinder.is
2017/05/15: genbank refseq ddbj Change to make the genbank parser more tolerant for missing division information. Entry MF002601 in the nc0508.flat genbank updates file is missing the division information and causes srs indexing to hang on that file
icarus/db/genbank.is
2017/05/08: uniprot Increased the number of parts in which the links between Uniprot Trembl and Interpro and GO are build
icarus/db/uniprot_trembl.i
2017/05/08: genbank refseq ddbj Made the method used for not including contigs in RefSeq Updates more specific, so it also works if the refseqfiles library is not enabled
icarus/db/genbank.is
2017/04/18: genbank refseq ddbj Added a mechanism to exclude contigs (CON division) from the RefSeq and GenBank updates, as these entries are creating problems building the virtual datasets for the full RefSeq and GenBank databases
icarus/db/genbank.is
2017/04/06: ensembl_mysql update for Ensembl release 88
icarus/db/ensemblRDB.i
icarus/db/ensembl_compara_schema.i
icarus/db/ensembl_funcgen_schema.i
icarus/db/ensemblcore_schema.i
2017/03/30: genpept As GI numbers are being phased out by the NCBI, we can no longer us it as the primary identifier for GenPept. This update makes the ID field the primary identifier. After applying this update you will have to re-index GenPept (GENPEPTRELEASE and GENPEPTNEW), during which time these datasets will not be accessible to the users
icarus/db/genpept.is
icarus/db/genpeptcommon.i
icarus/db/genpeptnew.i
2017/03/30: blast fasta Change so Fasta and Blast results are linking to GenPept using the ID field in GenPept rather than the now phased out GI field
icarus/db/alipsiblast.i
icarus/db/blastp.i
icarus/db/blastx.i
icarus/db/contpsiblast.i
icarus/db/fasta.i
icarus/db/fastsmf.i
icarus/db/ggsearch.i
icarus/db/glsearch.i
icarus/db/psiblast.i
icarus/db/ssearch.i
2017/03/30: pdb Change so PDB is linked to GenPept using the Protein ID field rather than the GI field (which is being phased out)
icarus/db/pdb.i
2017/03/14: genbank refseq ddbj Some tweaking of sort sets and links to inprove indexing performance
icarus/db/genbankcommon.i
icarus/db/refseqnew.i
icarus/db/refseqpnew.i
icarus/db/refseqprelease.i
icarus/db/refseqrelease.i
2017/02/24: medline Fix for a problem extracting Mesh Qualifiers
icarus/db/medline.is
2017/02/22: system Update for the changed URL for imgt links in UniProt
icarus/db/dbxref.i
icarus/db/href.i
2017/02/20: system Update for the new Araport link in UniProtKB
icarus/db/dbxref.i
icarus/db/href.i
2017/02/08: geneseq Added two useful parsing elements fro GeneSeq - no functional changes
icarus/db/geneseq.is
icarus/db/geneseqsupp.is
2017/02/08: genbank refseq ddbj Change needed to allow for the fact that the dbxref index in RefSeqP is now larger than 4GB. After appying this update, please re-index All RefSeqP databases. If you have upgraded to SRS8.4 then you will not need this fix !
icarus/db/genbankcommon.i
2017/02/08: uniprot Split the indexing of the link between UNIPROT_TREMBL and TAXONOMY in parts to improve performance
icarus/db/uniprot_trembl.i
2017/02/06: prosite Correction for an error in the realier update for the new format of the date field in Prosite
icarus/db/prosite.is
2017/02/02: entrezgene Change to build the links between EntrezGene and RefSeq in parts in order to improve indexing performance
icarus/db/entrezgene.i
2017/02/02: prosite Fix for some changes in the data field in Prosite
icarus/db/prosite.is
2017/01/23: system Added support for the new SFLD link in UniProt
icarus/db/dbxref.i
icarus/db/href.i
2017/01/17: entrezgene Fix for a problems with chromosome coordinates, and removed the Pathway field, as it is no longer populated
icarus/db/entrezgene.i
icarus/db/entrezgene.is
icarus/db/entrezgene_dm.i
web/WEB-INF/jsp/views/entrezgeneentry/entrezgeneentry.jsp
2017/01/16: refseq Increased the number of parts in which the link between REFSEQNEW and REFSEQPRELEASE is build to improve indexing performance
icarus/db/refseqnew.i
2017/01/13: ensembl_mysql Fixes for some problems displaying Ensembl transcripts
icarus/db/ensemblcommon.i
icarus/db/ensemblcore_schema.i
icarus/db/ensembldatamodel.i
icarus/db/ensemblproteinmodel.i
2017/01/13: genbank refseq ddbj iprmatches Removed some srs 8,4 specific code which has crept in some files
icarus/db/genbankcommon.i
icarus/db/genbankwgsmaster.i
icarus/db/iprmatches.i
2017/01/11: fasta Fix for some more parsing problems with GGSEARCH
icarus/db/fasta.is
2017/01/11: entrezgene Removed Plasmid/Organelle from the default EntrezGene downloads as they contain duplicates from the taxon specific data files
icarus/db/entrezgene.it
2017/01/09: fasta system Fixes for some configuration errors for GGSEARCH (the global/global similarity search program in the FASTA package)
icarus/db/fasta.is
icarus/db/fastacommon.i
icarus/db/loader.i
2017/01/05: ensembl_mysql Fix for a problem with the orthologues table in the view for Ensembl genes
icarus/db/ensembl_compara_schema.i
icarus/db/ensemblcommon.i
icarus/db/ensemblgenemodel.i
web/WEB-INF/jsp/views/ensemblgeneentry/orths.jsp
2016/12/20: medline system Updates for the 2017 release of Medline. See README.Medline2017 for full details
icarus/db/medline-ris.il
icarus/db/medline.i
icarus/db/medlinecommon.i
icarus/db/medlinedeleted.i
icarus/db/medlinenew.i
icarus/db/medlinenewfiles.i
icarus/db/medlinenewfiles.it
icarus/db/medlinerelease.i
icarus/db/medlinerelease.it
icarus/db/medlineupdates.i
icarus/db/pubmedarticlesxml.il
icarus/db/xml.il
2016/12/09: ensembl_mysql Update for some schema changes in Ensembl 87
icarus/db/ensemblRDB.i
icarus/db/ensembl_compara_schema.i
icarus/db/ensembl_funcgen_schema.i
icarus/db/ensemblcore_schema.i
2016/11/24: entrezgene Change of the Prisma configuration for EntregGene. The single entrezgene file has become to big of SRS to handle, so we now download EntrezGene by taxononomic division - please see comments in the file on different configuration options
icarus/db/entrezgene.it
2016/11/15: uniref Fix for problems building links betwen the UniRef datasets, caused by the increasing size of these databases. After applying these updates please re-index UniRef50, UniRef90 and UniRef100
icarus/db/uniref50.i
icarus/db/uniref90.i
icarus/db/unirefcommon.i
2016/11/14: chembl Fix for missing DF_PValue field definition
icarus/db/chembl.i
2016/11/07: system Added support for the new PhosphoSitePlus, DisGeNet and OpenTargets references in UniProt
icarus/db/dbxref.i
icarus/db/href.i
2016/11/07: medline Changed the download source for MedLine as the data has moved to a different location
icarus/db/medline.it
icarus/db/medlinedeleted.it
icarus/db/medlinenew.it
icarus/db/medlinenewfiles.it
icarus/db/medlinerelease.it
icarus/db/medlineupdates.it
2016/11/02: chembl Update for Chembl release 22
icarus/db/chembl.i
icarus/db/chembl_mysql_schema.i
icarus/db/chembl_oracle_schema.i
icarus/db/chemblcompound.i
icarus/db/chemblcompound_dm.i
icarus/db/chembltarget.i
2016/10/20: ncbi-nr Changes needed as nr and nt no longer include GI numbers in the fasta description lines.
icarus/db/nr.i
icarus/db/nr.is
icarus/db/nt.i
web/WEB-INF/jsp/views/nrentry/nrentry.jsp
2016/10/11: go_xml Fix for some name and directory structure changes on the go ftp site
icarus/db/go.i
icarus/db/go.it
2016/10/10: kegg Added support for the new reaction pair field in the Kegg reaction database
icarus/db/lreaction.i
icarus/db/lreaction.is
web/WEB-INF/jsp/views/lreactionentry/lreactgeneral.jsp
2016/09/30: embl Updated the data update location information for the EMBLWGSMASTER database
icarus/db/emblwgsmaster.i
2016/09/14: kegg Another fix for problems caused by non-standard characters in the Kegg disease data - now for entry display
icarus/db/lcommon.is
2016/09/14: embl Removed sorting by date from the abridged emblwgs databases, as the sort sets become too large to build - it is better done by sorting the emblwgs master files
icarus/db/emblwgscommon.i
2016/09/13: kegg Fix for a problem caused by some control characters which have slipped in the Brite field of the latest version of the Kegg Disease database
icarus/db/lcommon.is
2016/08/26: system kegg Added support for the Brite classification in the Kegg Glycan library
icarus/db/href.i
icarus/db/lglycan.i
icarus/db/lglycan.is
web/WEB-INF/jsp/views/lglycanentry/lglycangeneral.jsp
2016/07/29: genecards Workaround for a bug giving indexing problems when processing the bA subdirectory
icarus/db/genecardstar.it
2016/07/26: ensembl_mysql update for for Ensembl release 85
icarus/db/ensemblRDB.i
icarus/db/ensembl_compara_schema.i
icarus/db/ensembl_funcgen_schema.i
icarus/db/ensemblcore_schema.i
2016/07/05: kegg Added support for the new CLass field in the Kegg Drugg database (LDRUG)
icarus/db/ldrug.i
icarus/db/ldrug.is
web/WEB-INF/jsp/views/ldrugentry/ldrugentry.jsp
2016/07/04: kegg Added support for the new DBLINKS line in the Kegg Genome database
icarus/db/genKeggSpecies.i
icarus/db/kegg_species.i
icarus/db/kegggenome.i
icarus/db/kegggenome.is
web/WEB-INF/jsp/views/kegggenomeentry/kegggenomeentry.jsp
2016/06/15: blast Fix for a problem recognizing the hit list section of the blast output, which could result in only 3 hits being reported
icarus/db/blast.is
2016/06/15: medline Fix for a problem where some medline IDs would be assigned to a wrong datafile, resulting in them being excluded from medlinenew
icarus/db/medlinenewfiles.i
2016/06/02: pubchem Fixes for some parsing errors caused by data errors in the PubChem files
icarus/db/pubchem.is
2016/05/13: system Added support if the new SIGNOR link in UniProtKB
icarus/db/dbxref.i
icarus/db/href.i
2016/05/09: genpept Fix for a problem with building the links between the GenPeptNew and Taxonomy databases
icarus/db/genpeptnew.i
2016/04/22: prosite Change to allow for a new line format in the comments field of prosite
icarus/db/prosite.is
2016/04/22: pdb Fix for some parsing errors generated during indexing of PDB
icarus/db/pdb.is
2016/04/15: hmdb Update for release 3.6 of HMDB, incuding a change in the download location
icarus/db/hmdb.i
icarus/db/hmdbprotein.i
icarus/db/hmdbprotein.is
icarus/db/hmdbsdf.i
2016/04/14: prisma Improved date checking when comparing file date stamps with those on a remote location in cases where datafiles are not unpacked
icarus/lion/prisma/dbSync.i
2016/04/14: reactome Update for Reactome release 56
icarus/db/reactome.i
icarus/db/reactome_schema.i
2016/04/13: ensembl_mysql Update for some minor schema changes in Ensembl release 84
icarus/db/ensemblRDB.i
icarus/db/ensembl_compara_schema.i
icarus/db/ensembl_funcgen_schema.i
icarus/db/ensemblcore_schema.i
2016/04/12: embl genbank refseq ddbj system A major - but optional - reconfiguration of the WGS sections of GenBank and EMBL. This addresses indexing performace issues with these databases. See README.wgs for full datails.
icarus/db/embl.is
icarus/db/emblwgsenv.i
icarus/db/emblwgsenvfiles.i
icarus/db/emblwgsfun.i
icarus/db/emblwgsfunfiles.i
icarus/db/emblwgshum.i
icarus/db/emblwgshumfiles.i
icarus/db/emblwgsinv.i
icarus/db/emblwgsinvfiles.i
icarus/db/emblwgsmam.i
icarus/db/emblwgsmamfiles.i
icarus/db/emblwgsmus.i
icarus/db/emblwgsmusfiles.i
icarus/db/emblwgsnew.i
icarus/db/emblwgsnewfiles.i
icarus/db/emblwgspln.i
icarus/db/emblwgsplnfiles.i
icarus/db/emblwgspro.i
icarus/db/emblwgsprofiles.i
icarus/db/emblwgsrelease.i
icarus/db/emblwgsrod.i
icarus/db/emblwgsrodfiles.i
icarus/db/emblwgsunc.i
icarus/db/emblwgsuncfiles.i
icarus/db/emblwgsvrl.i
icarus/db/emblwgsvrlfiles.i
icarus/db/emblwgsvrt.i
icarus/db/emblwgsvrtfiles.i
icarus/db/gbemblcommon.i
icarus/db/genbank.is
icarus/db/genbankcommon.i
icarus/db/srsdb.i
icarus/db/emblwgs.is
icarus/db/emblwgscommon.i
icarus/db/emblwgsfiles.i
icarus/db/emblwgsmaster.i
icarus/db/genbankwgs.is
icarus/db/genbankwgsfiles.i
icarus/db/genbankwgsmaster.i
icarus/db/wgsunpack.pl
2016/03/23: system uniprot ipi Added support for the new Top Down Proteomics and Encyclopedia of Proteome Dynamics links in UniProtKB
icarus/db/dbxref.i
icarus/db/href.i
icarus/db/swissprot.is
2016/03/23: chembl Update for ChEMBL release 21, whith support for the new drug indication data
icarus/db/chembl_mysql_schema.i
icarus/db/chembl_oracle_schema.i
icarus/db/chemblcompound.i
icarus/db/chemblcompound_dm.i
web/WEB-INF/jsp/views/chemblentry/chemblcompoundentry.jsp
2016/03/18: kegg Change in the creation of the Kegg Species mapping file so it also maps the non species abbreviations AG (Addendum), PG (Plasmid) and VG (Virusses)
icarus/db/genKeggSpecies.i
icarus/db/kegg_species.i
2016/03/03: system Added support for the new SwissPalm links in UniProtKB
icarus/db/dbxref.i
icarus/db/href.i
2016/02/26: medline Fix for a problem where SRS would not parse the publication year for some medline entries
icarus/db/medline.is
icarus/db/medlinecommon.i
2016/02/11: ncbi-nr Change to make sure the link between GIMAP and UNIPROT_TREMBL is build -in parts
icarus/db/gimap.i
2016/02/11: ncbi-nr Change to make sure the link between NR and UNIPROT_TREMBL is build -in parts
icarus/db/nr.i
2016/02/11: refseq Increased the number of parts in which the number of links between REFSEQRELEASE and REFSEQPRELEASE is build, to prevent memory problems on low-spec machines
icarus/db/refseqrelease.i
2016/02/10: kegg Fix for some problems for kegggenes links caused by experimental code which was accidentally included in the previous updates for the Kegg Genes databases. After applying this update please re-index kegggenes_na and kegggenes_aa (runPrisma -l "kegggenes_na kegggenes_aa" -local -force or srscheck -l "kegggenes_na kegggenes_aa" -force; srsdo) and after that rebuild the readlinks for lenzyme (srsbuild -l lenzyme) and keggorthology (srsbuild -l keggorthology)
icarus/db/kegggenes.is
icarus/db/kegggenes_aa.i
icarus/db/kegggenes_na.i
2016/01/29: system Added support for the new CollecTF and iPTMnet links in UniProtKB
icarus/db/dbxref.i
icarus/db/href.i
2016/01/22: kegg Change needed as the Kegg Genes databases have recently grown to more than 1.67 million entries, which requires a different ID structure in SRS. After applying this update you will have to re-index KEGGGENES_NA and KEGGGENES_AA (use the -force flag of srscheck of runPrisma)
icarus/db/kegggenes_aa.i
icarus/db/kegggenes_na.i
2016/01/18: blast Implemented a more robust way of jumping to the right location in the blast output to find the Query line
icarus/db/blast.is
2016/01/13: patent_prt Correction for the download location for the PATENT_PRT Patent Protein database
icarus/db/patent_prt.i
2016/01/13: pfam Fix for a problem with PfamC caused by recent optimizations for PfamA
icarus/db/pfamc.i
icarus/db/pfamc.is
2015/12/23: srscheck prisma Fixed some issues with chunk and chunksize parallelization
icarus/workflows/buildPhase.i
icarus/workflows/linkPhase.i
2015/12/17: system Added support for the new SwissLipids and MalaCard references in UniProtKB
icarus/db/dbxref.i
icarus/db/href.i
2015/12/15: genpept Fixed a misconfigation of indexing parallelization in GENPEPTRELEASE
icarus/db/genpeptrelease.i
2015/12/15: uniref Fixed a misconfigation of indexing parallelization in UNIREF90
icarus/db/uniref90.i
2015/12/08: pfam Fix for some parsing errors in pfamhmm
icarus/db/pfamhmm.is
2015/12/07: embl Fix for some parsing errors during indxing of IMGTLIGM
icarus/db/embl.is
2015/11/27: ensembl_mysql Update for some minor schema changes in Ensembl 82
icarus/db/ensemblRDB.i
icarus/db/ensembl_compara_schema.i
icarus/db/ensembl_funcgen_schema.i
icarus/db/ensemblcore_schema.i
2015/11/26: uniprot ipi Fix so evidence codes are not included in the protein name when it is displayed
icarus/db/swissprot.is
2015/10/29: genbank refseq ddbj Fix for the problem where multi-species entries in RefSeqP cause problems when creating sortsets for sorting by organism name
icarus/db/genbank.is
2015/10/27: system Added support for the new WBParaSite link in UniProtKB
icarus/db/dbxref.i
icarus/db/href.i
2015/10/27: prisma Improved stability of the code for drawing the Prisma CPU slot usage image
icarus/lion/prisma/cpuslots.il
2015/10/23: genpept Change so SRS Prisma can download GenPept datafiles from a new location - the old location no longer works after a departmental name change
icarus/db/genpeptnew.it
icarus/db/genpeptrelease.it
2015/10/22: uniref Changed the link from the uniref databases to taxonomy so it is indexed in parts, requiring less memory
icarus/db/uniref100.i
icarus/db/uniref50.i
icarus/db/uniref90.i
2015/10/22: drugbank reverted some SRS8.4 specific changes back to SRS8.3
icarus/db/drugbank.i
2015/10/19: go_xml Change so GO is build in more parts
icarus/db/go.i
2015/10/19: uniprot ipi Change so we have separate indices fo GO and InterPro Ids in UniProtKB - this will alleviate memory problems when building link indices between GO/InterPro and the UniProtKB databases
icarus/db/swisscommon.i
icarus/db/swissprot.is
icarus/db/uniprot_swissprot.i
icarus/db/uniprot_trembl.i
2015/10/16: drugbank system Fixes for a few parsing problems with the latest release of DrugBank. Please note that the new standard.is file needs to be installed in SRSSITE
icarus/db/drugbank.i
icarus/db/drugbanksdf.i
icarus/db/standard.is
2015/10/06: hmmer Removed PfamB as a search option from HMMScan, as it has been discontinued
icarus/db/hmmscan.i
2015/10/06: pfam Update for release 28 of Pfam - which include the change from the Sanger Centre for data distribution to the EBI, and a fix to stop indexing crashes for PfamA entries which contain alignments of 100000s of sequences. A fix for the display of entries like this will be provided later. Note that PfamB is now discontnued and should be disabled. If you use HMMer software for HMM searches, then it is recommended to upgrade to the latest version
icarus/db/pfam.is
icarus/db/pfama.it
icarus/db/pfamb.i
icarus/db/pfamb.it
icarus/db/pfamc.it
icarus/db/pfamhmm.it
icarus/db/pfamseed.it
icarus/db/swisspfam.i
icarus/db/swisspfam.it
2015/09/23: embl Fix for a parsing error with some unusual ID lines in IMGTLIGM
icarus/db/embl.is
2015/09/23: uniprot Increased the number of parts in which the link from UniProttrembl to GO and INTERPRO are build, to avoid memory problems
icarus/db/uniprot_trembl.i
2015/09/14: pubchem Fix to handle very long lines in resent PubChem assaey results data
icarus/db/pubchemassayresult.i
2015/08/24: genpept uniprot ipi Change link definitions for GenPept and UniProt so exisiting indices will be used for building links instead of re-reading/parsing GenPept or UniProt data again. This should speed up the inexing of links during data updates.
icarus/db/genpeptnew.i
icarus/db/genpeptrelease.i
icarus/db/swisscommon.i
icarus/db/swissprot.is
icarus/db/uniprot_swissprot.i
icarus/db/uniprot_trembl.i
2015/08/24: refseq Increased the number of parts used to build the link between RefSeq and RefSeqP (full release) to alleviate memory consuption during indexing
icarus/db/refseqrelease.i
2015/08/13: drugbank Removed some SRS8.4 specific code which had crept in with the last update of this file
icarus/db/drugbank.i
2015/08/13: prisma fix for a problem with creating blast indices from file which is already in fasta format
icarus/lion/prisma/reformatPhase.i
2015/08/07: drugbank Update for some small changes in DrugBank 4.3
icarus/db/drugbank.i
icarus/db/drugbank.is
web/WEB-INF/jsp/views/drugbankentry/drugbankentry.jsp
2015/07/27: merops Update for some schema changes in Merops 9.13
icarus/db/merops_schema.i
2015/07/27: reactome Updates for Reactome release 53
icarus/db/reactome.i
icarus/db/reactome.is
icarus/db/reactome_schema.i
2015/07/24: ensembl_mysql Update for some small schema changes in Ensembl version 81
icarus/db/ensemblRDB.i
icarus/db/ensembl_compara_schema.i
icarus/db/ensembl_funcgen_schema.i
icarus/db/ensemblcore_schema.i
2015/07/22: biogrid dip intact mint Fix needed in the PSI_MI XML processing script for a small change in the BioGrid data, and to eliminate a harmless error message when indexing IntAct data
icarus/db/intactProcessData.pl
2015/07/21: embl Fix for indexing problems with some deleted EMBL records which have incomplete molecule and division iformation
icarus/db/embl.is
2015/07/13: system Fix so the indexing of links for uniprot does not throw error messages about the new genevisible link
icarus/db/dbxref.i
2015/07/13: embl updated the remote file specification for EMBLWGSNEW for the new ena structure on the ebi ftp site
icarus/db/emblwgsnew.it
icarus/db/emblwgsnewfiles.it
2015/07/09: system uniprot ipi Added support for the new ESTHER and Genevisible links in UniProt
icarus/db/dbxref.i
icarus/db/href.i
icarus/db/swissprot.is
2015/06/19: kegg Changed the link definitions from the Kegg Orthology database to Pathway and Enzyme, as changes in the data have resulted in empty link indices fore these links. After applying this update re-index keggorthology, rebuild the links to enzyme and pathway (srsbuild keggorthology; srsbuild -i keggorthology enzyme; srsbuild keggorthology pathway)
icarus/db/keggorthology.i
2015/06/16: hmdb Added support for several new fields in the chemical taxonomy section of HMDB
icarus/db/hmdb.i
icarus/db/hmdb.is
web/WEB-INF/jsp/views/hmdbentry/hmdbentry.jsp
2015/06/09: system Added support for the new BioMuta references in UniProtKB
icarus/db/dbxref.i
icarus/db/href.i
2015/06/09: medline Fix for a parsing problem with compound substance names when exporting medline data in medline format
icarus/db/medline.is
2015/05/15: system Changes to the srssection command to make it easier to keep your SRS installation up-to-date. Please see README.srssection for full details. Also moved the distributed version of quickSearch.i from SRSICA to SRSDB
etc/srssection
icarus/util/srssection.i
icarus/db/quickSearch.i
2015/05/12: iprmatches Removed some SRS8.4 specific code
icarus/db/iprmatches.i
2015/05/07: pdb Change so IE9 and later use the javascript version of jmol - needed for jmol version 14
icarus/db/pdb.is
2015/04/29: uniprot ipi Fix for a parsing problem for the UniProt Protein ID field when it is displayed in the web interface
icarus/db/swissprot.is
2015/04/24: iprmatches Added a bew Signature field to IPRMATCHES
icarus/db/iprmatches.i
icarus/db/iprmatches.is
2015/04/24: refseq Added parallization for building the link between REFSEQRELEASe and REFSEQPNEW
icarus/db/refseqrelease.i
2015/04/24: drugbank Fix for a porblem caused by very long lines in Drgbank SDF files
icarus/db/drugbanksdf.i
2015/04/24: go_xml taxonomy Improved internal links in taxonomy and go by splitting them in separate links for each direction
icarus/db/go.i
icarus/db/taxonomy.i
2015/04/24: ncbi-nr Improved stability for parsing the nr/nt databases - fix for problems caused by > characters in the descriptions
icarus/db/nr.is
2015/04/24: intact Increased the number of parts in which intactinteractions is build
icarus/db/intactinteraction.i
2015/04/24: chemicalsearch Replaced the chemical sctructure display in Chemical search results by SVG images, fixed some problems with the description of the hits, and added several views specific for databases againts searches are being made (Kegg, CEmbl, ChEBI)
icarus/db/chemicalsearch.i
icarus/db/chemicalsearch.is
2015/04/24: chemicalsearch chembl hmdb drugbank kegg Some improvements in the way searchable indices for chemical structure searches are made for Keggm HMDB and ChEMBL
icarus/db/getChemblSmiles.i
icarus/db/getHMDBSmiles.i
icarus/db/getKeggSmiles.i
2015/04/24: kegg Update Kegg species mapping file. Note that if you use SRS Prisma for your data updates, this file will be regenerated automatically with each data update
icarus/db/kegg_species.i
2015/04/22: embl genbank refseq ddbj Speedup and fix for a memory problem when trying to retrieve contig information from large genomic records
icarus/db/embl.is
icarus/db/genbank.is
2015/04/20: drugbank Small change to prevent some parsing warnings in DrugBank 4.2
icarus/db/drugbankpartner.is
2015/04/16: drugbank Removed some SRS8.4 specific code which made it into the drugbank.i file with the last update
icarus/db/drugbank.i
2015/04/09: system kegg Added support for the new Brite classification data in the KEGG disease database
icarus/db/href.i
icarus/db/keggdisease.i
icarus/db/keggdisease.is
web/WEB-INF/jsp/views/keggdiseaseentry/keggdiseaseentry.jsp
2015/04/09: ncbi-nr Change to allow for more that 17 million entries in NT
icarus/db/nt.i
2015/04/08: drugbank Added support for the new product data in DrugBank 4.2
icarus/db/drugbank.i
icarus/db/drugbank.is
web/WEB-INF/jsp/views/drugbankentry/drugbankentry.jsp
2015/04/08: ensembl_mysql Update for some minor schema changes in EnsEMBL 79
icarus/db/ensemblRDB.i
icarus/db/ensembl_compara_schema.i
icarus/db/ensembl_funcgen_schema.i
icarus/db/ensemblcore_schema.i
2015/04/07: refseq Fix for parsing warning messages thrown by the product feature qualifier in refseq variations
icarus/db/refseqvariations.is
2015/04/02: dssp Fix for some parsing arrers caused by malformed data lines in some dssp entries
icarus/db/dssp.is
2015/04/02: hssp Fix for some parsing errors in some hssp entries
icarus/db/hssp.is
2015/04/02: pfam Removed sorting for the accession number field of swisspfam, as we now index the accession number with and without the version number
icarus/db/swisspfam.i
2015/04/02: domo Removed sorting for the keyword field of DOMO
icarus/db/domo.i
2015/03/26: prosite Fix for a problem parsing a journal reference with non-standard page references in the latest version of Prosite
icarus/db/prositedoc.is
2015/03/25: system Added missing hypertext definition needed to navigate Brite hierarchies in KEGG data
icarus/db/href.i
2015/03/25: srscheck prisma Fix for errors thrown during the removal of partial link indices
icarus/workflows/linkPhase.i
2015/03/04: dbsnp system Added an accession number field to dbsnp, which allows to search against dbsnp with the rs prepended to the id - like rs123456, and added a field for HGVS genomic sequence identifiers
icarus/db/dbsnp.i
icarus/db/dbsnp.is
icarus/db/href.i
2015/02/27: embl Change in .it files for EMBLRELEASE and EMBLNEWFILES to account for recent reorganization of the EMBL/ENA ftp site. If you have made changes to the previous files then you may need to merge this update with your previous changes.
icarus/db/emblnewfiles.it
icarus/db/emblrelease.it
2015/02/10: chembl Update for ChEMBL release 20
icarus/db/chembl_mysql_schema.i
icarus/db/chembl_oracle_schema.i
2015/01/23: prisma srscheck Fix for a problem induced by the new virtual library defintions for the 2015 release of Medline
icarus/lion/prisma/analyseLibs.i
icarus/lion/prisma/prismaCheckClasses.i
icarus/workflows/buildPhase.i
icarus/workflows/coreCheckClasses.i
icarus/workflows/getSystemLibs.i
icarus/workflows/linkPhase.i
2015/01/21: system Change to allow for the new moonprot and depod references in UniProtKB. Please note that the new dbxref.i and href.i files need to be merged with your copy of these files in SRSSITE.
icarus/db/dbxref.i
icarus/db/href.i
2015/01/19: system Change to allow for the new proteomes reference in UniProtKB. Please note that the new dbxref.i and href.i file need to be merged with your copy of these files in SRSSITE
icarus/db/dbxref.i
icarus/db/href.i
2014/12/19: medline Update for the 2015 release of MedLine. Note that the full release now contains duplicate IDs, as older versions of the records are now included in the data. These are filtered out in the construction of the MedLine virtual database
icarus/db/medline.i
icarus/db/medline.is
icarus/db/medlinecommon.i
icarus/db/medlinenew.i
icarus/db/medlinerelease.i
2014/12/17: dbsnp Added script needed for preprocessing the Human DBSNP vcf file prior to indexing
icarus/db/process_human_dbsnp_vcf.pl
2014/12/08: prisma srscheck Update for SRS Prisma and srscheck which includes
  • A new -p option which allows you to include parent/dependent libraries on the command line without having to specify all of them, like "runPrisma -l embl" to update all libraries involved in the EMBL virtual library
  • A significant speedup during the check phase for very large libraries, like the WGS sections of EMBL/GenBank/DDBJ
  • Improved statbility in cases where the exit status of Sun Grid Engine qrsh does not reliably reflect a failure
  • Fix for an issue with the removal of partial .mergeinf files during the merge phase
  • A few other minor bug fixes
etc/runPrisma
icarus/lion/prisma/analyseLibs.i
icarus/lion/prisma/prismaCheckClasses.i
icarus/lion/prisma/prismaCheckMain.i
icarus/workflows/buildPhase.i
icarus/workflows/getSystemLibs.i
icarus/workflows/linkPhase.i
icarus/workflows/srsCheckClasses.i
icarus/workflows/srsCheckMain.i
2014/12/01: kegg system Update for the KEGG databases. This includes support for the new Carcinogen and Pathogen fields in KeggDisease, a Module field in lcompound lreaction and lglycan, a OtherMap field in ldrug, a History field in lenzyme and fields to support the Brite Categorizations in KeggOrtology, KeggGenes, lcompound and ldrug. For these categorizations it is possible to navigate to other entries within the same categories from within the entryview for these databases. Note that the new version of srsgen.i needs to be merged with your copy of these files in SRSSITE. Also note that the updates for the Kegg databases are only available to customers who are paying the additional subscription fee which is needed to access them
icarus/db/kegg_species.i
icarus/db/keggdisease.i
icarus/db/keggdisease.is
icarus/db/kegggenes.i
icarus/db/kegggenes.is
icarus/db/kegggenes_aa.i
icarus/db/kegggenes_na.i
icarus/db/kegggenes_na.it
icarus/db/keggorthology.i
icarus/db/keggorthology.is
icarus/db/lcommon.is
icarus/db/lcompound.i
icarus/db/lcompound.is
icarus/db/lcompound.it
icarus/db/ldrug.i
icarus/db/ldrug.is
icarus/db/ldrug.it
icarus/db/lenzyme.i
icarus/db/lenzyme.is
icarus/db/lenzyme.it
icarus/db/lglycan.i
icarus/db/lglycan.is
icarus/db/lglycan.it
icarus/db/lreaction.i
icarus/db/lreaction.is
icarus/db/lreaction.it
icarus/db/pathway.it
icarus/db/srsgen.i
web/WEB-INF/jsp/views/keggdiseaseentry/keggdiseaseentry.jsp
web/WEB-INF/jsp/views/kegggenesentry/kegggenesentry.jsp
web/WEB-INF/jsp/views/lcompoundentry/lcompgeneral.jsp
web/WEB-INF/jsp/views/lcompoundentry/lcompoundlinks.jsp
web/WEB-INF/jsp/views/ldrugentry/ldrugentry.jsp
web/WEB-INF/jsp/views/lenzymeentry/lenzymeentry.jsp
web/WEB-INF/jsp/views/lglycanentry/lglycanlinks.jsp
web/WEB-INF/jsp/views/lreactionentry/lreactgeneral.jsp
2014/11/28: blast Update for BlastPlus release 2.2.30, allowing for a new Fast task/algorithm for BlastP, BlastX and TBlastN, and iterating until convergence for PsiBlast. When applying this update also update you blast software !
icarus/db/blastp.i
icarus/db/blastx.i
icarus/db/contpsiblast.i
icarus/db/psiblast.i
icarus/db/tblastn.i
2014/11/25: system Correction for an error in the specification of the newly added EMBLEWGS sections in the SRS exporters configuration
web/WEB-INF/config/srs/srs-export.xml
2014/11/25: embl Correction for some misspelled names for EMBLWGSMUS subentry libraries
icarus/db/emblwgsmus.i
2014/11/25: system Removed some SRS8.4 specific references for external indices for the recently added EMBLWGS subsections. Note that the changes in this file need to be merged with your copy of this file in SRSSITE
icarus/db/srsdb.i
2014/11/24: system dbsnp Added export of DBSNP records in VCF format. Please read the comments in dbsnpvcf.i for full details. Note that the new version of srsdb.i needs to be meregd with your copy of that file in SRSSITE
icarus/db/srsdb.i
icarus/db/dbsnpvcf.i
icarus/db/dbsnpvcf.il
icarus/db/dbsnpvcf.is
2014/11/24: system Update for the SRS exporter configuration file for the new VCF exporter for DBSNP, and the new divisions for EMBLWGS. When updating this file make a backup of your old file, and merge back in any changes you made to enable/disable exporters
web/WEB-INF/config/srs/srs-export.xml
2014/11/18: system Added support for the new expressionAtlas link in UniProtKB. Please note that the new versions of href.i and dbxref.i need to be merged with your files in SRSSITE
icarus/db/dbxref.i
icarus/db/href.i
2014/11/17: embl system We have changed the way EMBLWGS is structured: we have divided the databases in separate databases for each taxonomic section. This should improve indexing/querying performance, and also makes it easy to exclude sections which you do not need from your setup. Please read the comments in emblwgs.i for full details. Also note that we removed EMBLWGS from the EMBL virtual library
icarus/db/embl.i
icarus/db/embl.is
icarus/db/emblwgs.i
icarus/db/emblwgsnew.i
icarus/db/emblwgsnewfiles.i
icarus/db/emblwgsrelease.i
icarus/db/srsdb.i
icarus/db/emblwgsenv.i
icarus/db/emblwgsenvfiles.i
icarus/db/emblwgsfun.i
icarus/db/emblwgsfunfiles.i
icarus/db/emblwgshum.i
icarus/db/emblwgshuman.i
icarus/db/emblwgshuman.i.i
icarus/db/emblwgshumanfiles.i
icarus/db/emblwgshumfiles.i
icarus/db/emblwgsinv.i
icarus/db/emblwgsinvfiles.i
icarus/db/emblwgsmam.i
icarus/db/emblwgsmamfiles.i
icarus/db/emblwgsmus.i
icarus/db/emblwgsmusfiles.i
icarus/db/emblwgspln.i
icarus/db/emblwgsplnfiles.i
icarus/db/emblwgspro.i
icarus/db/emblwgsprofiles.i
icarus/db/emblwgsrod.i
icarus/db/emblwgsrodfiles.i
icarus/db/emblwgsunc.i
icarus/db/emblwgsuncfiles.i
icarus/db/emblwgsvrl.i
icarus/db/emblwgsvrlfiles.i
icarus/db/emblwgsvrt.i
icarus/db/emblwgsvrtfiles.i
2014/11/10: entrezgene Change so SRS can deal with the fact that EntrezGene has now more than 17 million entries. After applying this update you will have to re-index EntrezGene
icarus/db/entrezgene.i
2014/10/24: medline Fixed a problem with the links between medline entries (via citations) and increased the number of parts in which some medline link indices are build
icarus/db/medline.i
icarus/db/medlinenew.i
icarus/db/medlinerelease.i
2014/10/22: chembl Update for some very minor schema changes in ChEMBL release 19
icarus/db/chembl_mysql_schema.i
icarus/db/chembl_oracle_schema.i
2014/09/30: genecards Update for GeneCards release 3.12, adding display of ApexBio compounds, cell location information from Jensen Biolabs and protein glycosylation/ubiquination information from nextProt
icarus/db/genecards.i
icarus/db/genecards.is
web/WEB-INF/jsp/views/genecardsentry/genecardsentry.jsp
web/WEB-INF/jsp/views/genecardsentry/genecardsexpression.jsp
web/WEB-INF/jsp/views/genecardsentry/genecardsproteins.jsp
2014/09/18: uniprot Increased the partSizeKb setting for the index splittiong for UniProt_Trembl so it is build in less parts. This is needed as we are reaching filehandle limits for the merging of partial link indices on some systems
icarus/db/uniprot_trembl.i
2014/09/18: ensembl_mysql Update for Ensembl release 76
icarus/db/ensemblRDB.i
icarus/db/ensembl_compara_schema.i
icarus/db/ensembl_funcgen_schema.i
icarus/db/ensemblcommon.i
icarus/db/ensemblcore_schema.i
2014/09/15: hmdb Correction for the unzip commands for HMDB
icarus/db/hmdb.i
icarus/db/hmdbprotein.i
2014/09/15: system fix for an error in the new genereviews link in UniProt. Please note that the updated dbxref.i file needs to be merged with your copy of that file in SRSSITE
icarus/db/dbxref.i
2014/09/12: pdb Small change to handle chain identifiers consisting of 2 characters - which have appeared in entries like 4TSZ
icarus/db/pdb.is
2014/09/10: system Corrected some wrong examples of dividers in blast/fasta database listings
icarus/db/localApplicationOptions.i
2014/09/10: genpept Fix for a Genpept data download problem with SRS Prisma
icarus/db/genpeptnew.it
icarus/db/genpeptrelease.it
2014/09/09: cosmic Changes for release 70 of COSMIC (Catalogue of somatic mutations in cancer). AFter applying this update, download the new data, process it manually following the instructions at the top of cosmicgene.i, and index the cosmicgene, cosmictumour and cosmicseq databases
icarus/db/cosmicgene.i
icarus/db/cosmicgene.is
icarus/db/cosmicseq.i
icarus/db/cosmictumour.i
icarus/db/cosmictumour.is
web/WEB-INF/jsp/views/cosmicentry/cosmicgeneentry.jsp
web/WEB-INF/jsp/views/cosmicentry/cosmictumourentry.jsp
2014/09/04: system Added support for the new GeneReviews links in UniProtKB. Please note that the new versions of href and dbxref.i need to be merged with your copies in SRSSITE
icarus/db/dbxref.i
icarus/db/href.i
2014/08/20: embl Fix for parsing errors caused by deleted WGS entries which are missing various fields in the ID line
icarus/db/embl.is
2014/08/11: pubchem Increased the maximum length for a PubChem Assay Result entry. After applying this update please re-index PUBCHEMASSAYRESULT
icarus/db/pubchemassayresult.i
2014/08/08: system Fix for a problem with SDF exports for PubChem. Please note that the new version of loader.i needs to be merged with your verion of that file in SRSSITE
icarus/db/loader.i
2014/08/04: dbsnp Change so SRS Prisma will only download SNPs for version 38 of the human genome and ignore version 37
icarus/db/dbsnp.is
icarus/db/dbsnp.it
icarus/db/dbsnplocation.is
icarus/db/dbsnplocation.it
2014/08/04: prisma Update for SRS Prisma to handle https connections correctly. Note that differing versions of the shared ssl libaries may mean that you will have to compile the wgetPrisma binaries yourself (the source code is provided in SRSROOT/gnu_src)
icarus/lion/prisma/remoteConnection.i
2014/08/04: genpept Update to allow SRS Prisma to download the genpept data - this is needed as the download site changed to the use of https instead of http. Note that you will also have to update SRSLION/prisma/remoteConnection.i and possibly compile the wgetPrisma binary
icarus/db/genpeptnew.it
icarus/db/genpeptrelease.it
2014/07/25: hmdb Fix for a problem with the hmdb distribution files - they currently contain both version 3.5 and 3.6 of the data
icarus/db/hmdb.i
icarus/db/hmdbprotein.i
2014/07/24: irefindex Changed the indexing parallization setting from IREFINDEX, as the old setting could result in duplicate ID assignments to different entries
icarus/db/irefindex.i
2014/07/24: merops Updated for some small schema changes in Merops release 9.11
icarus/db/merops_schema.i
2014/07/23: reactome Changes for release 49 of Reactome. Please note that the name of the sql file to be loaded into mysql has changed to gk_current.sql.gz
icarus/db/reactome.i
icarus/db/reactome.it
icarus/db/reactome_datamodel.i
icarus/db/reactome_schema.i
2014/07/17: embl Change to prevent Prisma from downloading multiple copies of the same file, caused by duplication of data on the EBI ftp site
icarus/db/emblwgsrelease.it
2014/07/15: drugbank system Fix for an xml parsing problem in DrugBank. Note that the new copy of standard.is needs to be installed in SRSSITE
icarus/db/drugbank.is
icarus/db/standard.is
2014/07/10: prisma srscheck Improved stability of data processing by SRS Prisma by catching situations where a batch queue returns a exit status of 0 despite failing to execute a command. This has been seen with SGE
icarus/lion/prisma/downloadPhase.i
icarus/lion/prisma/pretransPhase.i
icarus/lion/prisma/reformatPhase.i
icarus/workflows/buildPhase.i
icarus/workflows/linkPhase.i
2014/07/10: drugbank system Update for DrugBank release 4. Note that the data has changed significantly, and that the updated files are incompatible with the old data. The new versions of srsgen.i and href.i will need to be merged with your copies of these files in SRSSITE, and be aware that the update for srs-export.xml mat overwrite changes you may have made to that file to configure data exports
icarus/db/drugbank.i
icarus/db/drugbank.is
icarus/db/drugbankpartner.i
icarus/db/drugbankpartner.is
icarus/db/drugbankxml.il
icarus/db/href.i
icarus/db/srsgen.i
icarus/db/xml.il
web/WEB-INF/config/srs/srs-export.xml
web/WEB-INF/jsp/views/drugbankentry/drugbankentry.jsp
web/WEB-INF/jsp/views/drugbankentry/drugbankpartnerentry.jsp
2014/06/24: prositesearch Change so indexing of PROSITESEARCH results does not hang on results which have a long description line for the input sequence
icarus/db/prositesearch.i
2014/06/24: system Fixes so the PATMATDB Emboss tool no longer shows up as a tool appropriate for Protein Seqeunce database entries, and a fix for a problem with the extraction of multiline prosite patterns as input for PATMATDB. Please note that the new version of srsgen.i needs to be merged with your copy in SRSSITE
icarus/db/srsgen.i
icarus/lion/emboss/getpat.pl
2014/06/20: system Fix for a problem where on submission of a job to a batch queue system, the Tools result page might try to reload a non-existing srs84/true page
web/javascript/srs_ajax.js
2014/06/12: cosmic After a change in the cosmic website, it is no longer possible for SRS Prisma to download the COSMIC data. Data updates of COSMIC by SRS Prisma have now been disabled. Please see the comments in cosmicgene.i for instructions on how to update COSMIC
icarus/db/cosmicgene.i
icarus/db/cosmicseq.i
icarus/db/cosmictumour.i
2014/06/02: system Added support for the new MaxQB links in UniProtKB. Please note that the new versions of href and dbxref.i need to be merged with your copies in SRSSITE
icarus/db/dbxref.i
icarus/db/href.i
2014/05/08: genpept Change needed to handle genpept comments (cc) indices, which are now larger than 4GB. After applying this update, remove the genpeptrelease and genpeptnew cc indices, and re-index these databases.
icarus/db/genpeptcommon.i
2014/05/08: ncbi-nr Change needed to handle gimap accession number (acc) indices, which are now larger than 4GB. After applying this update, remove the gimap acc indices, and re-index these databases.
icarus/db/gimap.i
2014/05/06: refseq Fix for a problem with the construction of variant sequences from contig specifications
icarus/db/refseqvariations.is
2014/04/29: chembl Changes for ChEMBL release 18. Please note that ChEMBL now no longer includes ChEBI ids for compounds, and is no longer linked to other compound databases
icarus/db/chembl.i
icarus/db/chembl_dm.i
icarus/db/chembl_mysql_schema.i
icarus/db/chembl_oracle_schema.i
icarus/db/chemblcompound.i
icarus/db/chemblcompound_dm.i
web/WEB-INF/jsp/views/chemblentry/chemblcompoundentry.jsp
web/WEB-INF/jsp/views/chemblentry/chemblentry.jsp
2014/04/16: pfam Fix for a problem with the indxing of accession numbers in swisspfam, which would result in no links to UniProtKB
icarus/db/swisspfam.is
2014/04/14: srscheck prisma Fix for a problem with the localcopy command for processing of non-SRS data by SRS Prisma
icarus/workflows/buildPhase.i
2014/03/31: ddbj embl genbank With the latest release (119), the EMBLRELEASE database contains identifiers of 16 characters, exceeding the maxNameLen setting for this databases, resulting in failures during indexing. We have now increased this setting to 16. After applying this update, EMBLRELEASE (but not the other EMBL formatted databases) will need re-indexing, as the primary id field for this database will become unreadable. We have made the same change for GENBANKRELEASE and DDBJRELEASE, which will also require re-indexing, but applying this update is less urgent, as these databases do not contain IDs of 16 characaters yet.
icarus/db/ddbjrelease.i
icarus/db/emblrelease.i
icarus/db/genbankrelease.i
2014/03/28: genecards Added support for the display of the new IUPHAR and HUMSAVAR (human disease mutaions) in GeneCards 3.11
icarus/db/genecards.i
icarus/db/genecards.is
web/WEB-INF/jsp/views/genecardsentry/genecardsentry.jsp
2014/03/21: drugbank Fix for a spelling error in the link definition for the link between the drugbankpartner and taxonomy databases
icarus/db/drugbankpartner.i
2014/03/20: srscheck prisma Fix for a problem in srscheck with database dependencies if only link indices are build
icarus/workflows/moveIndicesPhase.i
2014/03/18: system Added a mechanism which allows a user to add SRS search Engines to the browser, derived from the concepts in the quick search toolbar, or using specific databases via the SRS query form
web/WEB-INF/jsp/queryform/main.jsp
web/WEB-INF/jsp/shared/quickSearchBar.jsp
web/queryengine.jsp
2014/03/18: srscheck prisma Change so srscheck and SRS Prisma will be able to recognize link indices which have become unreadable after an index structure change and then remove and rebuild them.
icarus/workflows/linkPhase.i
2014/03/18: blast Fix for a problem with linking blast results to other databases if more than 1 blast database has been used, caused by a small change in the blast output
icarus/db/blast.is
2014/03/17: intact prisma Fix for a problem caused by an = sign in the datafiles for the intact databases. The = sign has a special meaning the the makefiles SRS Prisma generates, and its presence in a file name would break the processing of the makfile, resulting in complete failures of SRS Prisma runs
icarus/db/intactdata.it
icarus/lion/prisma/downloadPhase.i
2014/03/17: ncbi-nr Fix for some parsing errors with the latest release of nr/nt
icarus/db/nr.is
2014/03/14: genbank embl refseq ddbj imgt Additional fix to improve the layout in the EntryView for the main DNA sequence databases if the location strings in the features table are very long
icarus/db/gbemblcommon.is
2014/03/13: genbank embl refseq ddbj imgt Some changes to improve the layout in the EntryView for the main DNA sequence databases if the location strings in the features table are very long
icarus/db/gbemblcommon.i
icarus/db/gbemblcommon.is
2014/03/11: drugbank Change so Prisma will continue to download DrugBank in the version 3.0 structure. version 4.0 is in beta, with its structure still changing. Once Drugbank 4.0 is stable, we will upgrade our implementation to support it
icarus/db/drugbank.i
2014/03/11: uniprot Fix for a problem with unzipping if Prisma decides only to download the release text file
icarus/db/uniprot_swissprot.it
icarus/db/uniprot_trembl.it
2014/03/10: ensembl_mysql Update for some minor schema chanegs in EnsEMBL 75
icarus/db/ensemblRDB.i
icarus/db/ensembl_compara_schema.i
icarus/db/ensembl_funcgen_schema.i
icarus/db/ensemblcore_schema.i
2014/03/10: chebi Update for some small schema changes in ChEBI
icarus/db/chebi_schema.i
icarus/db/chebi_schema_mysql.i
2014/03/05: chebi Fix for a problem with ChEBI links to Kegg Compound if the latter is not installed locally
icarus/db/chebidatamodel.i
2014/03/04: ncbi-nr Fixed some display problems and a tool type association problem
icarus/db/nr.i
icarus/db/nt.i
icarus/db/nt.is
2014/03/03: system Added support for the new TreeFam and BioGrid links in UniProtKB. Please note that the new versions of href and dbxref.i need to be merged with your copies in SRSSITE
icarus/db/dbxref.i
icarus/db/href.i
2014/02/28: refseq embl genbank Improved the layout of the DNA databases entry view, so the feature table section does not get extremely wide
web/WEB-INF/jsp/views/dnadbentry/dnadbentry.jsp
2014/02/28: pubchem Improvement of the query results view for the pubchem databases if the marvin structure viewer is installed - the applet now no longer triggers an browser/applet/java permission request for each entry
icarus/db/pubchem.is
2014/02/28: uniref Increased the number of parts in which uniref link indices are build to cope with increased database sizes
icarus/db/uniref100.i
icarus/db/uniref50.i
icarus/db/uniref90.i
2014/02/28: genpept Removed some SRS8.4 specific code which has made its way into the SRS8.3 version of this file
icarus/db/genpeptcommon.i
2014/02/24: ncbi-nr system Added support for the NR and NT fasta sequence databases from the NCBI, and a databases derived from these two, called GIMAP, which allows for mapping of GI numbers to accession numbers. Note that the new version of srsdb.i needs to be merged with your copy of this file in SRSSITE
icarus/db/gimap.i
icarus/db/gimap.is
icarus/db/nr.i
icarus/db/nr.is
icarus/db/nt.i
icarus/db/nt.is
icarus/db/srsdb.i
web/WEB-INF/jsp/views/nrentry/nrentry.jsp
2014/02/19: system Fix for a problem with annotation creation/editing in IE9 and IE10 (non compatability modes)
web/WEB-INF/jsp/annotationgenerate/edit.jsp
2014/02/13: kegg Fix for a problem where Prisma would erroneously rename a subdirectory name which matches the .gz (extansion) pattern which results in an indexing failure when it tries to index a non-existting file
icarus/db/kegggenes_na.it
2014/02/11: quicktree emboss Change needed to support the Archaeopteryx phylogenetic tree viewer applet, which is the successor of ATV
icarus/db/quicktree.i
icarus/db/quicktree.is
icarus/lion/emboss/ephyliptree.is
icarus/lion/emboss/fdnacomp.i
icarus/lion/emboss/fdnaml.i
icarus/lion/emboss/fdnamlk.i
icarus/lion/emboss/fdnapars.i
icarus/lion/emboss/fdnapenny.i
icarus/lion/emboss/ffitch.i
icarus/lion/emboss/fkitsch.i
icarus/lion/emboss/fneighbor.i
icarus/lion/emboss/fproml.i
icarus/lion/emboss/fpromlk.i
icarus/lion/emboss/fprotpars.i
web/WEB-INF/jsp/views/atvview/atvview.jsp
web/WEB-INF/jsp/views/emboss/embossTreeView.jsp
2014/02/10: embl Correction for the command use by SRS Prisma to derive the release unmber for the EMBLCDS databases
icarus/db/emblcdsnew.i
icarus/db/emblcdsrelease.i
2014/02/03: refseq Change for the REFSEQVARIATONS database to handle a slight change in file name patterns used by RefSeq
icarus/db/refseqvariations.i
2014/01/28: srscheck prisma Change so the -t (touch) option for srscheck will also touch link indices and cache and sortset files
icarus/workflows/buildPhase.i
2014/01/28: prisma Change soe SRS Prisma can determine time stamps from file listings which contain a space in the group name, and a fix for a problem with recursive updates using the file (copy) protocol
icarus/lion/prisma/remoteConnection.i
2014/01/28: prisma Change the way the number of download/index chains is calculated, which should allow for a more efficient usage of download and index cpu slots during updates
icarus/lion/prisma/downloadPhase.i
2014/01/28: prisma Fix for a file installation problem if a file is both an indexed SRS database and a FASTA searchable database
icarus/lion/prisma/reformatPhase.i
2014/01/28: prisma Fix for a potential problems with the setting for the maximum number of simultaneous downloads allowed by SRS Prisma
icarus/lion/prisma/dbSync.i
2014/01/21: system Change to ensure that the protein ID and GID are included in AllID queries. Please note that the new version of srsgen.i needs to be merged with your copy of that file in SRSSITE
icarus/db/srsgen.i
2014/01/20: chemicalsearch Fix for a problem with launching Chemical Structure searches if no structure drawing applet (like Marvin) is installed
icarus/db/chemicalsearch.i
2014/01/13: prisma Fix for a problems with the Prisma test databases if blast is not enabled
icarus/lion/prisma/PrismaToolsTestDb/testdb.i
2014/01/10: system Fix for a problem with the display of database names on the link page
web/WEB-INF/jsp/shared/databankselect.jsp
web/javascript/linkuniverse.js
2014/01/09: system Added support for the new GuidetoPHARMACOLOGY reference in UniProt. Please note that the new versions of dbxref.i and href.i need to be merged with your copies of these files in SRSSITE
icarus/db/dbxref.i
icarus/db/href.i
2014/01/09: ensembl_mysql Changes needed for Ensembl release 74
icarus/db/ensemblRDB.i
icarus/db/ensembl_compara_schema.i
icarus/db/ensembl_funcgen_schema.i
icarus/db/ensemblcore_schema.i
2014/01/09: nrpat Fix for stability problems with sequence display in the nr patent databases 9NRPL1 NRPL2 NRNL1 NRNL2)
icarus/db/nrpat.i
icarus/db/nrpl1.i
icarus/db/nrpl2.i
web/WEB-INF/jsp/views/nrpatentry/nrpatpentry.jsp
2014/01/08: prisma Change so restartPrisma cannot be used if the Prisma job has entered the move phase (at which point it is too late for a restart), and a change so restartPrisma will pick up the original runPrisma command line parameters
etc/restartPrisma
etc/runPrisma
2014/01/08: prisma Improved output for resource and tool tests
icarus/lion/prisma/PrismaToolsTestDb/prismaToolTest
icarus/lion/prisma/PrismaToolsTestDb/prismaToolTest1.i
icarus/lion/prisma/PrismaToolsTestDb/testdb.i
icarus/lion/prisma/getappls.i
icarus/lion/prisma/qualityReport/resourceObjectCheck.i
icarus/lion/prisma/qualityReport/toolTests.i
icarus/lion/prisma/toolsTestSets.i
2014/01/07: dbsnp Change needed as several indices for DBSNP and DBSNPLOCATION are approaching the 4GB limit, which requires a different index structure. After applying this update, remove the ssha, ssbi, sscl, ssmt and ssmc indices for DBSNP and the org and chrl indices for DBSNPLOCATION and reindex both databases
icarus/db/dbsnp.i
icarus/db/dbsnplocation.i
2014/01/07: embl Change needed as several indices for EMBL are approaching the 4GB limit, which requires a different index structure. After applying this update, remove the id, acc, rp, cti and ctn indices for EMBLRELEASE, EMBLNEW, EMBLWGSRELEASE, EMBLWGSNEW and any other DNA databases which you have in EMBL format and reindex these databases
icarus/db/emblcommon.i
2014/01/07: genbank refseq ddbj Change needed as several indices for GENBANK and REFSEQ(P) are approaching the 4GB limit, which requires a different index structure. After applying this update, remove the id, acc amd ftran indices for GENBANKRELEASE, GENBANKNEW, GENBANKWGS, REFSEQRELEASE, REFSEQNEW (and any other DNA databases which you have in GenBank format) and the ftq indices for REFSEQPRELEASE and REFSEQNEW (and any other protein database you have in GenBank format) and reindex these databases
icarus/db/genbankcommon.i
2014/01/07: uniprot Change needed as several indices for UNIPROT are approaching the 4GB limit, which requires a different index structure. After applying this update, remove the tit and dbn indices for UNIPROT_SWISSPROT, UNIPROT_TREMBL and any other protein database which you have in UniProt format and reindex these databases
icarus/db/swisscommon.i
2014/01/07: irefindex Corrected the index parallellization type of irefindex
icarus/db/irefindex.i
2013/12/24: pubchem chemicalsearch Change needed for a format change in PubChem assay results. After applying this change it is recommended to do a fresh download of all PubChem assay results file. Also fixed a problem with the logic used by Prisma to build the chemical searches set of PubChem compounds for which an assay is available (pubchemassayed)
icarus/db/getPubChemAssayedSmiles.i
icarus/db/pubchemassayresult.is
icarus/db/pubchemchemsearch.i
2013/12/24: embl system Change to allow for the new distribution model of EMBLCDS, which now consists of a full release, and a set of update files. (Until recently the full database was generated daily, which made it impossible to have a complete dataset, as it took longer than a day to download the database. Note that the changes in srsdb.i will have to be merged with your copy of that file in SRSSITE, and that you will have to enable the new EMBLCDSRELASE and EMBLCDSNEW databases
icarus/db/emblcds.i
icarus/db/emblcds.is
icarus/db/emblcdsnew.i
icarus/db/emblcdsrelease.i
icarus/db/emblcommon.i
icarus/db/srsdb.i
2013/12/23: system Change to improve stability of tool launches to batchqueue systems which may have a latency in the job status command
icarus/util/appl.i
2013/12/23: system Fix for a problems with saving some types of parameters to parameter sets
web/WEB-INF/jsp/toollaunch/main.jsp
2013/12/23: system Some changes to improve stability for batch jobs listed on the tools results page
web/WEB-INF/jsp/queryhistory/main.jsp
web/WEB-INF/jsp/toollaunch/formElements.jsp
web/WEB-INF/jsp/toollaunch/main.jsp
web/javascript/srs_ajax.js
web/javascript/toollaunch.js
web/javascript/tools/tool_standard.js
2013/12/09: chembl Fix for a code error in the latest update of chembl_mysql_schema.i
icarus/db/chembl_mysql_schema.i
2013/12/06: prisma Added a new errorLimit option to our fasta sequence conversion tool, which allows you to set a maximum number of errors allowed before exiting with a fail
icarus/lion/prisma/getFastaSequence.i
2013/12/06: chembl Changes needed for schema changes in ChEMBL release 17
icarus/db/chembl.i
icarus/db/chembl_mysql_schema.i
icarus/db/chembl_oracle_schema.i
icarus/db/chemblcompound.i
2013/12/06: pfam Fix for a problem with the sort sets for swisspfam. After applying this update you will have to re-index swisspfam
icarus/db/swisspfam.i
2013/12/05: chebi Fix for a problem where we would sometimes use the wrong structure data string for display in Marvin if multiple types of structure strings are available for an entry
icarus/db/chebidatamodel.i
2013/12/04: ccds embl genbank refseq ddbj geneseq nrpat Fix for a potential memory leak in the mechanism we use for determining sequence types when exporting large amounts of sequences
icarus/db/ccds.is
icarus/db/embl.is
icarus/db/genbank.is
icarus/db/geneseq.is
icarus/db/geneseqsupp.is
icarus/db/nrpat.is
2013/12/02: dbgss Fix for a problem with the sortsets for DBGSS. After applying this update it would be recommended to re-index DBGSS
icarus/db/dbgss.i
2013/12/02: genpept Fix for a problem with the sortsets for GenPept (full release), and better handling for a corrupt entry in the current GenPept datafile. After applying this update it would be recommended to re-index both GENPEPTNEW and GENPEPTRELEASE
icarus/db/genpept.is
icarus/db/genpeptcommon.i
2013/12/02: embl genbank refseq ddbj Fix for a stability problem with the display of protein sequences ithe the Entry view usually used for EMBL/GenBank/RefSeq
icarus/db/embl.is
icarus/db/gbemblcommon.i
icarus/db/genbank.is
web/WEB-INF/jsp/views/dnadbentry/sequence.jsp
2013/11/29: prisma Change so getFastaSequence.i will print out the entry name in the error output if it cannot retrieve a sequence
icarus/lion/prisma/getFastaSequence.i
2013/11/28: refseq Change to make sure that the RefSeq variations libraries use the same file set as the main RefSeq full release database
icarus/db/refseqvariations.i
2013/11/28: irefindex Correction for the construction of links from IREFINDEX to other Protein-Protein interaction databases
icarus/db/irefindex.i
icarus/db/irefindex.is
2013/11/28: prosite Fix to allow for days in the data update date field
icarus/db/prosite.is
2013/11/27: pubchem Fix for an indexing problem with the Target Species in PUBCHEMASSAY
icarus/db/pubchemassay.i
2013/11/26: system Added support for the new PRO (protein ontology) link in UniProt. Please note that the new href.i and dbxref.i files need to be merged with your copies of these files in SRSSITE
icarus/db/dbxref.i
icarus/db/href.i
2013/11/26: pubchem Change needed for data preprocessing by SRS Prisma after a changes in the way PubChem assay descrptions (PUBCHEMASSAY database) are delivered. If you have any 275 byte files in your pubchemassay data directory, please remove them so SRS Prisma will replace them.
icarus/db/createpubchemassaydata.pl
2013/11/26: prosite Fix for a parsing problems with one of the literature refrences
icarus/db/prositedoc.is
2013/11/26: uniref Fix for a wrong definition of the link between cluster members and the main UniRef entry, which could result in erroneaus entries being returned when searching with organism names. After applying this update you will have to re-index the UniRef databases
icarus/db/unirefcommon.i
2013/11/26: blocks fix for a problem with hypertext links to UniProt in BLOCKS entries
icarus/db/blocks.is
2013/11/25: genbank refseq ddbj Fix for a display problem with the contig specification for GenBank and RefSeq entries
icarus/db/genbank.is
2013/11/25: dbgss Fix for a problem with the link to GenBank in DBGSS entry display
icarus/db/dbgss.is
2013/11/25: genbank embl refseq ddbj Fix for a sequence display problem with RefSeqP entries
icarus/db/gbemblcommon.i
2013/11/25: go_xml go_mysql go Improved the display speed of GO entries by caching more information on disk during indexing (you will have to re-index go to take davantage of this). We now also list regulatory connections between entities
icarus/db/go.i
icarus/db/go.is
icarus/db/go_datamodel.i
web/WEB-INF/jsp/views/goentry/gorelatives.jsp
web/images/shared/go_r.gif
2013/11/19: system Fix for a problem when selectting databases in a major section of the Querybuild (Classic)
web/javascript/querybuilder.js
2013/11/14: blast Change so PsiBlast Continuations uses clustalw2 to make the starting alignment for the continuation. Note that clustalw2 must be in the unix command path
icarus/db/contpsiblast.i
2013/11/14: omim Changed the omim download site from the archived version on the NCBI site to ftp.omim.org, and fixed a parsing problems with some non-standard formatted references
icarus/db/omim.is
icarus/db/omim.it
2013/11/14: quicktree Fix for an input sequence reformatting problem with QuickTree
icarus/db/quicktree.i
2013/11/12: clustalw system Fix for a parsing problem with alignments in Stockholm format, and removed some debug print statements. Note that the new version of srsgen.i needs to be merged with your copy of that file in SRSSITE
icarus/db/clustalw.is
icarus/db/readseq.i
icarus/db/srsgen.i
2013/11/05: clustalw Change so the output generated by clustal and muscle is displayed in Stockholm format. This allows us to include more sequence annotation information in the results. Note that you will also need the recent updates for readseq.i and srsgen.i for Stockholm format support
icarus/db/clustalo.i
icarus/db/clustalw.i
icarus/db/clustalw.is
icarus/db/clustalwcommon.i
icarus/db/nclustalw.i
icarus/db/nmuscle.i
icarus/db/pmuscle.i
2013/11/04: kegg Fix for a problem with hypertext links in pathway images to Kegg Genes if species abbreviations do not have a standard Kegg three-letter abbreviation
icarus/db/pathway.is
2013/11/04: reactome Update for release 46 of Reactome. We have also added display of pathway diagram images - see the comments in reactome.i for information on how to set this up
icarus/db/reactome.i
icarus/db/reactome.is
icarus/db/reactome_datamodel.i
icarus/db/reactome_schema.i
web/WEB-INF/jsp/views/reactomeentry/event.jsp
2013/11/01: system Added support for Stockholm alignment format to our sequence conversion tools. Please note that the new version of srsgen.i needs to be merged with your copy of that file in SRSSITE
icarus/db/readseq.i
icarus/db/srsgen.i
2013/11/01: blast Change to catch the situation that a user has not selected any database to do a blast or fasta search againts
web/javascript/tools/blast.js
web/javascript/tools/fasta.js
2013/11/01: system Fixed a problem for sequences from blast and fasta results with the recently added Seq views. Note that the new versions of SRSDB/loader.i and SRSDB/views.i need to be merged with your copies of these files in SRSSITE
icarus/db/loader.i
icarus/db/views.i
2013/11/01: system Improved autorefresh and messaging if batch jobs are running
web/WEB-INF/jsp/queryhistory/main.jsp
web/javascript/srs_ajax.js
2013/11/01: blast fasta system Improved the annotation in sequences which are retrieved from blast and fasta results. This now includes the description (if available), range of the match, Evalue and hit ID. There is also noew a configurable parameter in localApplicationOptions.i which can be used to change the primary identifier in these sequences from the blast/fasta ID to the ID of the sequence found. Note that the new version of localApplicationOptions.i needs to be merged with your version of this file in SRSSITE
icarus/db/blast.is
icarus/db/fasta.is
icarus/db/localApplicationOptions.i
2013/10/24: cosmic Change needd to handle a change in the name of the downloadable file for COSMIQSEQ
icarus/db/cosmicseq.i
2013/10/24: prisma Fix for a problem with Prisma reports for file downloads if files are in subdirectories on the remote site
icarus/lion/prisma/printDownloadPages.i
icarus/lion/prisma/prismaCheckClasses.i
icarus/lion/prisma/setReportPhase.i
2013/10/23: uniprot ipi Made a change in the way the link between UniProtKB and RefSeqP is build to fix an index stability problem
icarus/db/swissprot.is
icarus/db/uniprot_swissprot.i
icarus/db/uniprot_trembl.i
2013/10/18: uniprot ipi Change so we include the UniProt ID in the sequence name when we generate sequence data
icarus/db/swissprot.is
2013/10/18: kegg pathway If a pathway map image is missing (Kegg does not seem to provide images for all pathways), we now display a message that the image is unavailable instead of a broken image link
icarus/db/pathway.i
icarus/db/pathway.is
web/WEB-INF/jsp/views/pathwayentry/pathwayentry.jsp
2013/10/17: system Fix for a problem with the positioning of the selection popup in the Related Information Browser with recent versions of FireFox
web/javascript/queryresults.js
2013/10/11: system Fix for an IE8 specific problem with recently added in-page searchboxes. We have added this update to interface_updates_Oct_2013.srs83.tar.gz
interface_updates_Oct_2013.srs83.tar.gz
2013/10/04: system Improved the recently added "Seq" view so it works better in the web interface, and added a similra view (Ali) for alignments. Please note that the new views.i file needs to be merged with your copy of that file in SRSSITE
icarus/db/views.i
2013/10/03: system A number of web interface improvements, including in-page search boxes and the setting of tool launch parameters via a url. Please see README.interface_updates_Oct_2013 for full details. For your convenience we supply this update as a single tar archive: interface_updates_Oct_2013.srs83.tar.gz. Note that you also should update SRSDB/localApplicationOptions.i - which is not included in the tar archive
interface_updates_Oct_2013.srs83.tar.gz
2013/10/03: system Added a new view (called Seq) for quick and dirty fasta sequence retrieval. This view can be used when fancier views, like fastaSeq, are not applicable. Note that the new versions of views.i and loader.i need to be merged with your copies of those files in SRSSITE
icarus/db/loader.i
icarus/db/views.i
2013/10/03: kegg Change needed after a change in the pathway kgml files to ensure that the pathway images are displayed by SRS
icarus/db/pathway.is
2013/10/03: system Change so the SRS sequence format converter can also take srs query strings as input.
icarus/db/readseq.i
2013/10/03: system Updated the comments in localApplicationOptions.i to explain how to add a searchbox and an extra level of nesting in the blast/fasta database selection area for blast/fasta tool launch pages. For this you will also need the interface update of October 2013
icarus/db/localApplicationOptions.i
2013/09/30: geneseq Minor change to allow patent DBs to show up in quickSearch pull-down.
icarus/db/aageneseq.i
icarus/db/nageneseq.i
2013/09/30: emboss minor update to allow prisma tool tests to run.
icarus/lion/emboss/patmatdb.it
2013/09/19: uniprot Removed the now obsolete Medline field from UniProt. It has now been fully replaced by PubMed
icarus/db/swisscommon.i
2013/09/18: pubchem Added support for the CAS number in the PubChem Substance database
icarus/db/pubchem.i
icarus/db/pubchem.is
web/WEB-INF/jsp/views/pubchementry/pubchemsubstanceentry.jsp
2013/09/18: ensembl_mysql Changes for Ensembl release 73
icarus/db/ensemblRDB.i
icarus/db/ensembl_compara_schema.i
icarus/db/ensembl_funcgen_schema.i
icarus/db/ensemblcore_schema.i
2013/09/13: blast Fix for a problem with saving the psiblast parameters needed for a restart
icarus/db/alipsiblast.i
icarus/db/contpsiblast.i
icarus/db/psiblast.i
2013/09/13: blast Fix for a problem with the "default" matrix option, introduced by the update of September 2
icarus/db/blastcommon.i
2013/09/11: system Fixes for page number calculations in query results pages for very large datasets or when viewed with browsers which are not set to english as the local prefered language
web/WEB-INF/jsp/queryresults/displayoptions.jsp
web/WEB-INF/jsp/queryresults/paging.jsp
2013/09/06: system Fix for a page numbering problem caused by browser locale settings influencing the way numbers are processed
web/WEB-INF/jsp/queryresults/displayoptions.jsp
web/WEB-INF/jsp/queryresults/paging.jsp
2013/09/05: prisma Fix for a problem where prisma would hang on building the prismatimelinks database on some platforms, and removed an unnecessary error message generated by archive checking
icarus/lion/prisma/prismaArchive.i
icarus/lion/prisma/prismatime.is
2013/09/04: pdb Fix for a problem where query term highlighting could cause the PDB structure not to be displayed in jmol
icarus/db/pdb.is
2013/09/03: pdb Added some refinements for the latest version of JMol - we now use the new HTML5 rendering engine, unless the browser does not support it, or is Internet Explorer (where rendering is really slow)
icarus/db/pdb.i
icarus/db/pdb.is
2013/09/03: nrpat Fixed a problem with the inclusion of accession numbers in Excel exports for the NR patent databases
icarus/db/nrpat.is
2013/09/02: blast fasta hmmer tacg Changes to improve consistency in the way dropdown menus for tool options have Display names, logical names and values which are passed on to the tool. There are no functional changes
icarus/db/alipsiblast.i
icarus/db/bl2seq.i
icarus/db/blastcommon.i
icarus/db/blastn.i
icarus/db/contpsiblast.i
icarus/db/fastacommon.i
icarus/db/fastsmf.i
icarus/db/hmmscan.i
icarus/db/hmmsearch.i
icarus/db/nfastsm.i
icarus/db/psiblast.i
icarus/db/restrictionmap.i
icarus/db/tfastsmf.i
2013/09/02: system Fixed a page number calculation problem casued by rounding errors
web/WEB-INF/jsp/queryresults/displayoptions.jsp
web/WEB-INF/jsp/queryresults/paging.jsp
2013/09/02: pdb Updated JMol support for displaying PDB entries for JMol 13.2 - please see the remarks in pdb.i for updated instructions for the installation of JMol
icarus/db/pdb.i
icarus/db/pdb.is
web/WEB-INF/jsp/views/pdbentry/pdbentry.jsp
2013/08/27: pubchem Fix for a problem when indexing PubChem assay results (PUBCHEMASSAYRESULT) if no online copy of the PubChem assay (PUBCHEMASSAY) database is available
icarus/db/pubchemassayresult.is
2013/08/22: system Fix for a problem in calculating the number of results pages if more than 300.000.000 entries are found
web/WEB-INF/jsp/queryresults/displayoptions.jsp
web/WEB-INF/jsp/queryresults/paging.jsp
2013/08/22: embl Fix for a problem with the construction of contig sequences
icarus/db/embl.is
2013/08/16: uniprot Increased the partSizeKb setting for the index splittiong for UniProt_Trembl so it is build in less parts. This is needed as we are reaching filehandle limits for the merging of partial link indices on some systems
icarus/db/uniprot_trembl.i
2013/08/14: resid Change in concept assigments in the links for ResID, so UniProt is no longer described as a litarature database
icarus/db/resid.i
2013/08/14: biogrid dip intact mint Fix for a problem with exporting Protein-Protein interaction data in mitab format
icarus/db/mitab.il
icarus/db/mitabstrict.il
2013/08/14: embl genbank refseq ddbj uniprot imgt ipi hmdb drugbank Fixed a problem with the export of references in RIS format
icarus/db/embl.is
icarus/db/genbank.is
icarus/db/seqreferences.il
2013/08/14: kegg Simplified the unpack commands for Kegg Orthology to make them more robust in various compting environments
icarus/db/keggorthology.it
2013/08/13: prisma Fixed a problem with database dependencies, which was giving problems for several Kegg databases
icarus/lion/prisma/localcopyPhase.i
2013/08/12: kegg Fix for an unpackCommand used for removing obsolete files
icarus/db/pathwaytar.it
2013/08/12: medline Removed a debug print statement which resulted in a some error messeages when indexing the whole of Medline
icarus/db/medline.is
2013/08/09: pdbfinder Fix for an indexing error in pdbfinder
icarus/db/pdbfinder.is
2013/08/05: kegg Fix for a problem in the code used by SRS prisma to remove obsolete image files from the pathway data directories - you will also need to update SRSLION/prisma/pretransPhase.i
icarus/db/pathwaytar.it
2013/08/05: prisma Fix for problems caused by different levels of escaping needed by batchqueues and plain shelld when backticks are used in unPackCommands
icarus/lion/prisma/pretransPhase.i
2013/08/03: system *** empty log message ***
icarus/db/href.i
2013/08/03: system Changes to support new links in Uniprot. Please remember to merge href.i and dbxref.i into your copy in SRSSITE.
icarus/db/dbxref.i
icarus/db/href.i
2013/08/01: genecards Changes needed to ensure that the GeneCards gene and protein expression images are displayed
icarus/db/genecards.i
icarus/db/genecards.is
web/WEB-INF/jsp/views/genecardsentry/genecardsentry.jsp
web/WEB-INF/jsp/views/genecardsentry/genecardsexpression.jsp
2013/07/31: embl system genbank refseq ddbj Change needed so we can construct sequences for RefSeqP entries which no longer contain an actual sequence, but just a specification how to construct it from RefSeqP WD_ entries. Also a correction for sequence display in complete text entry display for the major DNA sequence databases
icarus/db/embl.is
icarus/db/ftseq.is
icarus/db/genbank.is
2013/07/31: hmdb Change to make the unpackCommand for hmdb more stable
icarus/db/hmdb.i
2013/07/31: genecards Fix for a change in the naming conventions for Chromosome location images
icarus/db/genecards.is
2013/07/30: genecards system Update for release 3.10 of Genecards, with support for the new Pathway Cluster and NCBI BioSys data. Note that GeneCards is now distributed by LifeMap Sciences and that the download location has changed. Also note that the new copy of href.i needs to be merged with your copy in SRSSITE
icarus/db/genecards.i
icarus/db/genecards.is
icarus/db/genecardstar.it
icarus/db/href.i
web/WEB-INF/jsp/views/genecardsentry/genecardsentry.jsp
2013/07/25: hmdb system Some changes to improve display performance for HMDB proteins, and some updates for some minor data changes in HMDB. Please note that the new version of srsgen.i needs to be merged with your copy of that file in SRSSITE
icarus/db/hmdb.is
icarus/db/hmdbprotein.i
icarus/db/hmdbprotein.is
icarus/db/hmdbprotein_datamodel.i
icarus/db/srsgen.i
2013/07/24: srscheck prisma Improved the touch option of srscheck (invoked by "srscheck -t") so it will now also touch link indices and the various caches and sortset files which srs uses
icarus/workflows/linkPhase.i
icarus/workflows/moveIndicesPhase.i
2013/07/17: emboss Upgraded emboss support to emboss 6.6.0 For your convenience we make this upgrade available as a separate tarball: EMBOSS6.6.0.tar.gz. If you upgrade from emboss 6.4 or 6.5, simply untar this file in SRSROOT, and run srssection.
EMBOSS6.6.0.tar.gz
2013/07/16: ccds Fixed a problem with the code SRS Prisma uses to extract the version number of CCDS (Protein)
icarus/db/ccdsprot.it
2013/07/16: hmdb removed a duplicate Alltext field definition
icarus/db/hmdb.i
2013/07/15: genpept Change to make the termination of srssection more obvious when the no longer needed gpnewfiles library is still enabled
icarus/db/gpnewfiles.i
2013/07/09: reactome update for some schema changes in Reactome 45
icarus/db/reactome_schema.i
2013/07/08: ensembl_mysql Update for some minor schema changes in ensembl 72
icarus/db/ensemblRDB.i
icarus/db/ensembl_compara_schema.i
icarus/db/ensembl_funcgen_schema.i
icarus/db/ensemblcore_schema.i
2013/07/02: system Fixed a problem with external hypertext links to PDB
icarus/db/href.i
2013/06/27: drugbank Changes needed for the latest (June 2013) release of drugbank
icarus/db/drugbank.i
icarus/db/drugbank.is
icarus/db/drugbanksdf.i
2013/06/25: enzyme Correction for the hypertext links in enzyme to prosite
icarus/db/enzyme.is
2013/06/20: medline Change to facilitate the display of multipart abstracts (as found in MEDLINE:21710270)
icarus/db/medline-endnote.il
icarus/db/medline.is
icarus/db/medlinecommon.i
icarus/db/medlineformat.il
2013/06/10: system Update for SignaLink links in Uniprot DBs
icarus/db/dbxref.i
icarus/db/href.i
2013/05/29: chembl update for some schema changes in ChEMBL release 16
icarus/db/chembl_mysql_schema.i
icarus/db/chembl_oracle_schema.i
icarus/db/chembltarget.i
2013/05/28: biogrid dip intact mint change to ensure IDs in the inteactinteartions database are unique
icarus/db/psimi.is
icarus/db/psimi_interaction.i
2013/05/22: medline Several improvements for medline: Fixed a problem with the MeshHeading subentries, changed the way keywords are indexed so keywords consisting of two words separated by a / are also searchable by those undividual words, and changed the results view for medline so it includes the first lines of the abstract, expandable to the full abstract by a + button
icarus/db/medline.i
icarus/db/medline.is
icarus/db/medlinecommon.i
web/WEB-INF/jsp/views/medlineentry/medlineresults.jsp
2013/05/17: prisma Added a --cache=off option to prisma download commands to prevent problems caused by proxies persisiting in caching old versions of a file
icarus/lion/prisma/remoteConnection.i
2013/05/17: hmdb Change needed to allow different filenames in the hmdb distribution zip archive
icarus/db/hmdb.i
2013/05/17: hmdb Changed the indexing of hmdbprotein so it is done in 8 parts - this is needed to reduce the indexing time, which has been increasing due to some entries now referring to a very large number of metabolites
icarus/db/hmdbprotein.i
2013/05/01: chembl Update for release 15 of ChEMBL. Note that there have been significant schema changes with ChEMBL15, and that these updated icarus files are incompatible with earlier releases of ChEMBL
icarus/db/chembl_oracle_schema.i
2013/04/26: blast fasta Fixed a problem in the graphical homolgy view for blast and fasta results with the display of reversed hits in the hit sequence graph, and a problem with the display of anchors indicating a match between the beginning or end of both query and match sequences
icarus/db/blastgraphicdatamodel.i
2013/04/25: ipi updated the location of IPI data for downloads by SRS Prisma. Note that the last release of IPI was in November 2011, and that the data has been incorporated into UniProt
icarus/db/ipi.it
2013/04/16: ensembl_mysql Update for some minor schema changes in EnsEMBL 71
icarus/db/ensemblRDB.i
icarus/db/ensembl_compara_schema.i
icarus/db/ensembl_funcgen_schema.i
icarus/db/ensemblcore_schema.i
2013/04/12: homologene Change to prevent failures for Homologene indexing if the taxonomy database indices are missing
icarus/db/homologene.is
2013/04/12: system improved stability of the mechanism used to build contig sequences
icarus/db/ftseq.is
2013/04/11: irefindex Change to allow for a change in the download directory name for irefindex
icarus/db/irefindex.i
2013/04/09: pdb Fix for a problems with the PDB download link in the PDB entry view
icarus/db/pdb.i
web/WEB-INF/jsp/views/pdbentry/pdbentry.jsp
2013/03/21: ccds improved stability of the unzip commands for ccdsnuc
icarus/db/ccdsnuc.it
2013/03/19: system correction to dbxref.i to support the chitars database link
icarus/db/dbxref.i
2013/03/13: system uniprot ipi Added support for the new ChiTaRS and SABIO-RK links in UniProtKb. Please note that the new href.i and dbxref.i files need to be merged with your copies of these files in SRSSITE.
icarus/db/dbxref.i
icarus/db/href.i
icarus/db/swissprot.is
2013/03/07: hmdb Update for some recent changes in hmdb
icarus/db/hmdb.i
icarus/db/hmdb.is
icarus/db/hmdb_datamodel.i
icarus/db/hmdbprotein.i
icarus/db/hmdbprotein.is
icarus/db/hmdbprotein_datamodel.i
icarus/db/hmdbsdf.i
web/WEB-INF/jsp/views/hmdbentry/hmdbentry.jsp
web/WEB-INF/jsp/views/hmdbentry/hmdbproteinentry.jsp
2013/03/06: rebase Change to allow for a larger entry name in ReBase
icarus/db/rebase.i
2013/03/06: blast moved some defintions around to prevent problems with running srssection if not all blast tools are enabled
icarus/db/blastcommon.i
icarus/db/contpsiblast.i
icarus/db/psiblast.i
2013/03/04: dbsnp Added a new field giving access to the validation source for a SNP
icarus/db/dbsnp.i
icarus/db/dbsnp.is
web/WEB-INF/jsp/views/dbsnpentry/dbsnpentry.jsp
2013/03/04: system Fix for a problem with the selection of fields in the query builder for some browsers
web/javascript/queryform.js
2013/03/01: blast Enabled several views for the new CONTPSIBLAST tool
icarus/db/blastcommon.i
2013/03/01: prisma Fix a problem in prisma remote connection testing
icarus/lion/prisma/testRemoteConnection.i
2013/03/01: blast fasta Fix for an alignment problem of the selection checkboxes with the hits in the blast graphical view
web/WEB-INF/jsp/views/blastentry/blastgraphic.jsp
2013/03/01: chembl Update for release 15 of ChEMBL. Note that there have been significant schema changes with ChEMBL15, and that these updated icarus files are incompatible with earlier releases of ChEMBL
icarus/db/chembl.i
icarus/db/chembl_dm.i
icarus/db/chembl_mysql_schema.i
icarus/db/chembl_oracle_schema.i
icarus/db/chemblcompound.i
icarus/db/chembltarget.i
2013/02/27: pdb Change so we no longer use a separate url to load the PDB structure into jmol, but use a string embedded in the applet call instead
icarus/db/pdb.i
icarus/db/pdb.is
web/WEB-INF/jsp/views/pdbentry/pdbentry.jsp
2013/02/27: prisma Fix for a problem where filenames used for downloads could get corrupted during retries, and improvevents to the lock file mechanism which is used to limit the number of simutaneous downloads, with better lock file names and more debug info
icarus/lion/prisma/checkRemoteFiles.i
icarus/lion/prisma/dbSync.i
icarus/lion/prisma/remoteConnection.i
2013/02/27: blast fasta system Several improvements on the implementation of the BLAST programs in SRS: The blast graphical view now also includes match-on-hit projections, so you can see where an hsp is located on the hit. We added a new tool CONTPSIBLAST (or "PsiBlast Continuation") which allows the user to continue a PsiBlast search which has not converged. The user can use two methods for this: he can either continue with the PSSM file from the previous job, or he can make his own selection of HSPs, which will then be aligned using ClustalW, and the resulting alignment will be used to start PsiBlast. We extended the scope of the export of blast results in gff format to include BLASTX, and gff exports can now be used where the query sequence is the long genomic sequence. This allows for the display of hits along the genomic sequence in popular gene viewers like IGV. Note that the new versions of loader.i and srsdb.i need to be merged with your copies of that file in SRSSITE (and you need enable the new CONTPSIBLAST_DB in srsdb.i). There is also a new SRSROOT/web/WEB-INF/config/srs/srs-export.xml file. Please take care when updating this file in order not to loose any edits you may have made to that file.
icarus/db/alipsiblast.i
icarus/db/bl2seq.i
icarus/db/blast.is
icarus/db/blastcommon.i
icarus/db/blastgff.il
icarus/db/blastgraphicdatamodel.i
icarus/db/blastx.i
icarus/db/fasta.is
icarus/db/loader.i
icarus/db/psiblast.i
icarus/db/psiblast.is
icarus/db/psiblast.it
icarus/db/readseq.i
icarus/db/srsdb.i
icarus/db/tblastx.i
web/WEB-INF/config/srs/srs-export.xml
icarus/db/contpsiblast.i
2013/02/20: prisma Change so remaining download lock files are removed between update retries
etc/runPrisma
2013/02/18: fasta system pdb pdbfinder Change so the nice fastaseqs view can be used with pdb and pdbfinder data. Note that the new version of loader.i needs to be merged with your copy of that file in SRSSITE
icarus/db/fasta.il
icarus/db/loader.i
icarus/db/pdb.i
icarus/db/pdbfinder.i
2013/02/18: prisma Change to improve robustness to errors during the unpack/pretranslation phase
icarus/lion/prisma/pretransPhase.i
2013/02/18: prisma srscheck Fixed a problem with the reporting in Prisma on the moving of indices and data online
icarus/lion/prisma/movePrismaData.i
icarus/lion/prisma/setReportPhase.i
icarus/workflows/moveIndicesPhase.i
2013/02/13: system Added support for the new mycoClAP link in UniProtKb. Please note that the new href.i and dbxref.i files need to be merged with your copies of these files in SRSSITE
icarus/db/dbxref.i
icarus/db/href.i
2013/02/12: pubchem Change so the PubChem ID indices take less space. This update does not require re-indexing
icarus/db/pubchem.i
icarus/db/pubchem.is
icarus/db/pubchemassayresult.i
2013/02/12: uniprot Change so the cc (comment) index for UniProtKB can be larger than 4GB. We expect this to be necessary for UNIPROT_TREMBL within a few release cycles. After applying this update you should remove the existing cc indices (uniprot*_cc.i*) and re-index. This also applies to any other database which you have in UniProt like format.
icarus/db/swisscommon.i
2013/02/12: genbank refseq ddbj Change so the gid indices for databases in GenBank format (GenBank, RefSeq, DDBJ) can be larger than 4GB. We expect this to be needed with the next full release of GenBank. After applying this change, remove all gid indices for databases in GenBank format (genbank*_gid.i* refseq[rn]*_gid.i* ddbj*_gid.i*) and if you have the GeneSeq databases, also remove the link indices between nageneseq and the genbank/refseq family: nageneseq_genban* genbank*_nageneseq.i* refseq*_nageneseq.i* nageneseq_refseq*. Then re-index.
icarus/db/genbankcommon.i
2013/02/12: geneseq Change so the pat (Patent Title) index of NAGENESEQ can be larger than 4GB (it has recently started to exceed this linit). After applying this update remove the nageneseq_pat.i* indices and re-index
icarus/db/nageneseq.i
2013/02/12: dbsnp Change to allow for the fact that the rsid indices for dbsnp and dbsnplocation, and the exsid index for dbsnp now need more than 4GB of disk space. After applying this update, remove the dbsnp_rsid.i* dbsnp_exsid.i* dbsnplocation_rsid.i* indexfiles, as well as the link indices between dbsnp and dbsnplocation (dbsnp_dbsnplocation.i* and dbsnplocation_dbsnp.i*), and re-index
icarus/db/dbsnp.i
icarus/db/dbsnplocation.i
icarus/db/dbsnplocation.is
icarus/db/dbsnplocation.it
2013/01/25: ensembl_mysql Update for Ensembl release 70
icarus/db/ensemblRDB.i
icarus/db/ensembl_compara_schema.i
icarus/db/ensembl_funcgen_schema.i
icarus/db/ensemblcore_schema.i
2013/01/21: srscheck prisma Fix for a problem with cached file listings if prismacheck is used as a standalone program
icarus/workflows/coreCheckClasses.i
2013/01/10: genpept Change needed so SRS Prisma can update GENPEPTNEW after another change on the GenPept download site
icarus/db/genpeptnew.it
2013/01/10: system Fix for a problems displaying the new HMDB xml format in a web browser
icarus/db/xml.il
2013/01/10: system Replaced various hypertext links which were pointing to the EBI srs server by links to the orginal data sources. Please note that the new href.i file needs to be merged with your copy of that file in SRSSITE
icarus/db/href.i
2013/01/09: prisma Fix for a crash in usage reporting if no files are downloaded during a prisma run
icarus/lion/prisma/printUsageReport.i
2013/01/08: refseq Split indexing for some REFSEQNEW links in parts to avoid memory problems
icarus/db/refseqnew.i
2013/01/07: prisma Fix for a problem in the Prisma reports calender if the current month does not have any reports
icarus/lion/prisma/generateCalendar.i
2013/01/07: emboss Improvements for the SRS integration of EMBOSS programs. We have added options for limited editing of input sequences, setting of titles for graphs and added a lot more information about the tool in the toolInfo page. Please use the EMBOSS6.5.0.tar.gz file to apply all the updates.
EMBOSS6.5.0.tar.gz
2013/01/04: prisma Fixes for some prisma tool tests
icarus/lion/prisma/PrismaToolsTestDb/prismaToolTest1.i
icarus/lion/prisma/PrismaToolsTestDb/prismaToolTest2.i
2013/01/04: hmmer New hmm data so the prisma test suite works for hmmscan
icarus/db/hmmbuild.i
icarus/db/hmmscan.i
icarus/lion/prisma/PrismaToolsTestDb/testdb/hmm.testdata
icarus/lion/prisma/PrismaToolsTestDb/testdb/hmm.testdata.h3f
icarus/lion/prisma/PrismaToolsTestDb/testdb/hmm.testdata.h3i
icarus/lion/prisma/PrismaToolsTestDb/testdb/hmm.testdata.h3m
icarus/lion/prisma/PrismaToolsTestDb/testdb/hmm.testdata.h3p
2013/01/02: genecards system Changes to allow for some new data lines in GeneCards 3.09. Note that the new version of href.i needs to be merged with your copy of this file in SRSSITE
icarus/db/genecards.i
icarus/db/genecards.is
icarus/db/href.i
web/WEB-INF/jsp/views/genecardsentry/genecardsentry.jsp
web/WEB-INF/jsp/views/genecardsentry/genecardsexpression.jsp
2012/12/19: system Added a missing group needed for the emboss programs sigcleave and tmap. Note that this file needs to be merged with your copy in SRSSITE
icarus/db/applGroups.i
2012/12/18: embl go_xml geneseq iprmatches Changes to build indices in more parts, needed to avoid memory problems caused by the growing size of the databases
icarus/db/emblcds.i
icarus/db/go.i
icarus/db/gswpi.i
icarus/db/iprmatches.i
icarus/db/pdbml.i
2012/12/17: prisma Fix for a problem where the prisma installer would hang
icarus/lion/prisma/generateCalendar.i
2012/12/17: srscheck prisma Fix for crashes in srscheck caused by recent code changes for SRS Prisma
icarus/workflows/coreCheckClasses.i
2012/12/17: prisma Implementented a more accurate estimate for actual download times in the usage report - taking parallel downloads in account
icarus/lion/prisma/printUsageReport.i
2012/12/14: genpept Update needed if you use SRS Prisma to mantain GenPept - the distrubuted file has changed to a compressed file
icarus/db/genpeptnew.it
icarus/db/genpeptrelease.it
2012/12/10: prisma A large number of improvements and some fixes for SRS Prisma. See README.PRISMA.201212 for full details. Please use the prisma.latest_update.tar.gz archive to install the updates
prisma.latest_update.tar.gz
2012/12/10: medline Added Author affiliation and page numbers to the RIS export for medline
icarus/db/medline-ris.il
icarus/db/medlinecommon.i
2012/12/10: system Added LibLocs for the new COSMICGENE, COSMICTUMOUR, COSMICSEQ, BIOGRIDDATA and HMDBPROTEIN databases, removed LibLocs for GPNEWFILES, HMDBENZYME and HMDBSPECTRA. Replaced LibLocs for REFSEQVARIATIONSRELEASE1-2 and REFSEQVARIATIONSNEW1-2 with REFSEQVARIATIONS1-4. You will have to merge the new version of srsdb,i with your copy of this file in SRSSITE
icarus/db/srsdb.i
2012/12/10: system Added some additional field information definitions. Note that the new version of this file needs to be merged with your copy in this file in SRSSITE
icarus/db/general.it
2012/12/10: cosmic Added support for the COSMIC database (Catalogue of Somatic Mutations in Cancer)
icarus/db/cosmicgene.i
icarus/db/cosmicgene.is
icarus/db/cosmicseq.i
icarus/db/cosmicseq.is
icarus/db/cosmictumour.i
icarus/db/cosmictumour.is
web/WEB-INF/jsp/views/cosmicentry/cosmicgeneentry.jsp
web/WEB-INF/jsp/views/cosmicentry/cosmictumourentry.jsp
2012/12/10: system Added various hypertext link definitions needed for the new Cosmic database and the new HMDB XML format. Please note that the new version of this file needs to be merged with your copy in SRSSITE
icarus/db/href.i
2012/12/10: dbsnp Change parallization parameters and links to address indexing performance problems with dbsnp
icarus/db/dbsnp.i
icarus/db/dbsnplocation.i
2012/12/10: genbank refseq ddbj Change to allow the SeqVersion (sv) field of GenBank to be larger than 4GB. After applying this change, the sv field needs to be indexed for all databases in GenBank Format - all GenBank, RefSeq and DDBJ databases, and any custom databases you may have which is also in GenBank format. Prior to indexing you should remove all sv indices for these databases
icarus/db/genbankcommon.i
2012/12/10: nrpat Change to build links for the patentequivalenst database in parts to prevent memory problems
icarus/db/patentequivalents.i
2012/12/10: system Changed the way the newly compiled srs.om file is saved, so it less likely to cause problems if you run srssection while the system is in use, Added a mechnism to pull literature information from a local copy of Medline to be displayed on the library information page
icarus/util/srssection.i
icarus/db/medlinedbinfo.il
2012/12/10: genpept Changes needed to allow downloads from the newly restructured Genpept download site. Note that you will also need the latest updates of SRS Prisma in order to maintain GenPept, and that there is no longer a need to use the GPFILES helper library to remove duplicatew from the updates
icarus/db/genpeptnew.i
icarus/db/genpeptnew.it
icarus/db/genpeptrelease.i
icarus/db/genpeptrelease.it
icarus/db/gpnewfiles.i
2012/12/10: chemicalsearch hmdb drugbank system Changes to allow for the the new XML structure of HMDB. The HMDBENZYME database has been replaced by HMDBPROTEIN, and we no longer use the HMDBSPECTRA database for compound spectra information. Note that you will need to install the latest prisma updates to be able to maintain HMDB with SRS Prisma
icarus/db/getHMDBSmiles.i
icarus/db/hmdb.i
icarus/db/hmdb.is
icarus/db/hmdb_datamodel.i
icarus/db/hmdbenzyme.i
icarus/db/hmdbsdf.i
icarus/db/hmdbsdf.is
icarus/db/hmdbspectra.i
web/WEB-INF/config/srs/srs-export.xml
web/WEB-INF/jsp/views/hmdbentry/hmdbentry.jsp
icarus/db/hmdbprotein.i
icarus/db/hmdbprotein.is
icarus/db/hmdbprotein_datamodel.i
web/WEB-INF/jsp/views/hmdbentry/hmdbproteinentry.jsp
2012/12/10: uniprot ipi Fix for a problem with the query string used for linking to some RESID entries
icarus/db/swissprot.is
2012/12/10: drugbank genecards pubchem system Moved some field defintions from library specific icarus files to srsgen.i, as tehy are now also used by HMDB. Please note that you will need to merge the new version of srsgen.i with your copy in SRSSITE
icarus/db/drugbank.i
icarus/db/genecards.i
icarus/db/pubchem.i
icarus/db/srsgen.i
2012/12/10: refseq Reorganised the refseqvariation database to address indexing performace prolems - it now consists of 4 partial databases, and no longer includes data from RefSeqnew
icarus/db/refseqvariations.i
icarus/db/refseqvariations.is
2012/12/10: merops Update for a schema change in merops
icarus/db/merops_schema.i
2012/12/10: biogrid We are now able to use SRS Prisma to maintain BioGrid data. The dat download is handled by the new BIOGRID data database. Note that you will need to install the latest SRS Prisma updates for this
icarus/db/biogridexperiment.i
icarus/db/biogridinteraction.i
icarus/db/biogridinteractor.i
icarus/db/biogridmitab.i
icarus/db/biogriddata.i
2012/12/04: system Changes to allow for new links in UniProtKB, and updates for links to DNA and protein sequences at the NCBI so we use the latest url syntax for that. Update for hypertext links to LigandBox. Please note that these files need to be merged with your copies of these files in SRSSITE
icarus/db/dbxref.i
icarus/db/href.i
2012/12/04: bind Updated the library information for BIND to reflect that it is no longer available for download by ftp
icarus/db/bindcomplex.it
icarus/db/bindinteraction.it
icarus/db/bindpathway.it
2012/12/04: chembl change so we can use the CHEMBL Id for targets, rather than the (unstable) internal databases identifier
icarus/db/chembl.i
icarus/db/chemblcompound.i
icarus/db/chembltarget.i
2012/11/30: pdbfinder FIx for a problem with displaying pdb sequences in the pdbfinder entry view
icarus/db/pdbfinder.i
2012/11/28: kegg added a --wildcard command line option to the tar command for unpacking the kegg image files - needed as the latest version of tar no longer have --wildcard as default setting
icarus/db/pathwaytar.it
2012/11/27: enzyme Update for change in the structure of the download location for the enzyme database. Also refreshed the annotation section
icarus/db/enzyme.it
2012/11/21: biogrid dip intact mint Update to allow for a change in the biogrid psimi xml data, and also improved performance of the pre-processing of the data by the intactProcessData.pl script
icarus/db/intactProcessData.pl
icarus/db/mitab.is
icarus/db/psimi.is
2012/11/21: prosite Update to deal with the new structure of the prosite download site. Also updated the annotation of prosite
icarus/db/prosite.it
icarus/db/prositedoc.it
2012/11/12: unigene uniprot Updatet some database display names for UniProtKB, and reorganised links to UniGene
icarus/db/unigene.i
icarus/db/uniprot.i
icarus/db/uniprot_swissprot.i
icarus/db/uniprot_trembl.i
icarus/db/uniprotvarsplic.i
2012/10/30: pubchem chemicalsearch refseq uniprot uniref Increased the number of parts in which some links are build to avoid memory problems
icarus/db/pubchem.i
icarus/db/pubchemassayresult.i
icarus/db/pubchemchemsearch.i
icarus/db/refseqvariations.i
icarus/db/uniprotxml.i
icarus/db/uniref90.i
2012/10/30: ensembl_mysql update for some minor schema changes in ensembl 69
icarus/db/ensemblRDB.i
icarus/db/ensembl_compara_schema.i
icarus/db/ensembl_funcgen_schema.i
2012/10/17: resid Fix for a coding error which would result in RESID being updated with every prisam run
icarus/db/resid.i
2012/10/16: blast fix for a problems where SRS sometimes would populate the database name column in the blast view with sequence IDs
icarus/db/blast.is
2012/10/03: merops Update for some small schema changes in merops version 9.7
icarus/db/merops_schema.i
2012/10/02: reactome Update for some small schema changes in Reactome release 42
icarus/db/reactome_schema.i
2012/09/28: blast Fix for a problem when matching hits from the results summary to the actual hits with certain fasta headers
icarus/db/blast.is
2012/09/28: chemicalsearch disabled the ChemicalSearchResults view for dataabses with chemical compounds, as it was not really useful, and could give errors if there are no Chemical search results available
icarus/db/chemicalsearch.i
2012/09/28: biogrid dip intact mint fix for a array problem when doing exports in strict (15 cols) mitab format
icarus/db/mitab.is
2012/09/28: genbank embl refseq ddbj fixed a problem with the gff export view which occurs if the optional SRSSITE/gffconfig.i file is not found
icarus/db/gff.il
2012/09/21: blast Fix for a problem in a recent change in the part of the blast parser which tries to extract the database name
icarus/db/blast.is
2012/09/21: genbank embl refseq ddbj system With version 2.1 of IGV, IGV is no longer able to read fasta sequences embedded in gff files. So we have added a new view and exporter for the export of sequences in fasta format, suitable for import in IGV, with IDs matching those used in our GFF exporter/view - please take care when updating srs-export.xml to avoid loosing edits you may have made to that file
icarus/db/gbemblcommon.i
icarus/db/gff.il
web/WEB-INF/config/srs/srs-export.xml
icarus/db/igvgenome.il
2012/09/14: ensembl_mysql Fix for a display problem which occurs for some hypertexct links to databases which are not installed locally
icarus/db/ensembldatamodel.i
icarus/db/ensemblgenemodel.i
icarus/db/ensemblproteinmodel.i
icarus/db/exondatamodel.i
2012/09/13: blast Fix which allows the blast parser to capture the database name from the blast summary if additional information (indexing date) is included in the database description
icarus/db/blast.is
2012/09/11: system Added support for the new GenomeRNAi and UniPathway links in UniProt. Note that the new versions of these files need to be merged with your copies in SRSSITE
icarus/db/dbxref.i
icarus/db/href.i
2012/09/11: hmdb Fix to prevent some parsing errors caused by badly formatted syhthesis reference lines in the latest version of HMDB
icarus/db/hmdb.i
icarus/db/hmdb.is
2012/09/06: medline Added partN=16 for building links between MEDLINERELEASE_CITEDBY and MEDLINERELEASE_CITES
icarus/db/medlinerelease.i
2012/09/06: resid Removed debug printing statement from parser
icarus/db/resid.is
2012/09/06: resid Updated resource info for changes to the ftp site information.
icarus/db/resid.i
2012/09/06: nrpat add in code to make sure gbcheck is defined so that indexing can occur
icarus/db/nrpat.is
2012/08/15: embl genbank ddbj refseq Fix for a problem where certain entries with lattitide/longitude would not be displayed on the map in the GeoMapView
icarus/db/geomap.il
2012/08/14: system embl genbank ddbj uniprot Change so we can display multiple comments for literature references. The new version of loader.i needs to be merged with your copy of that file in SRSSITE
icarus/db/loader.i
web/WEB-INF/tags/referencetable.tag
2012/08/14: system Fix for a problem where srssection would crash if none of the major sequence databases is enabled. Note that the new version of quickSearchOptions .i needs to be merged with your copy of this file in SRSSITE
icarus/db/quickSearchOptions.i
2012/08/14: system uniprot ipi Fixed a problem with the hypertext links from UniProtKB to RESID. The new version of href.i needs to be merged with your copy of that file in SRSSITE
icarus/db/href.i
icarus/db/swissprot.is
2012/08/14: resid Improved linking and fixed some display issues for resid
icarus/db/resid.i
icarus/db/resid.is
2012/08/13: system embl genbank ddbj refseq Added a Predefined query and a result view which use Google Maps to query/display by geographical location. Note that this requires a licence key for the Google Maps Javascript API - see comments in quickSearchOptions.i for details. Note that the new copy of quickSearchOptions.i needs editing and merging with your copy of that file in SRSSITE
icarus/db/quickSearchOptions.i
web/javascript/predefinedqueries/mapsearch.js
icarus/db/geomap.il
icarus/db/mapsearch.i
web/css/biowisdom/queryresults.css
web/css/biowisdom/quicksearches.css
2012/08/13: embl genbank refseq ddbj imgt system Added support for sample origin (country,region,locality), longitude and lattitude as searchable fields to facilitate search by geographical location in the main DNA sequence databases. Also added a small Google map in the entry view which displays the location (if available). Note that the new versions of general.it, href.i and srsgen.i need to be merged with your copies of these files in SRSSITE
icarus/db/embl.is
icarus/db/emblcds.i
icarus/db/emblcommon.i
icarus/db/gbemblcommon.is
icarus/db/genbank.is
icarus/db/genbankcommon.i
icarus/db/href.i
icarus/db/srsgen.i
2012/08/13: hssp Added support for the new dbref lines in hssp
icarus/db/hssp.i
icarus/db/hssp.is
web/WEB-INF/jsp/views/hsspentry/hsspentry.jsp
2012/08/10: nrpat Added Alltext and AllIDs fields to the patentequivalents database
icarus/db/patentequivalents.i
2012/08/10: blast fasta fastasequence Fix for a database name assignment problem if multiple database names are associated with an identifier in localApplicationOptions.i
icarus/db/blast.is
icarus/db/fasta.is
icarus/db/fastaseq.is
2012/08/09: system Removed a debug print statement which would show up during indexing of xml files. Plases note that the new version of standard.is needs to be merged with your copy of this file in SRSSITE
icarus/db/standard.is
2012/08/03: genecards system Update for new data lines in GeneCards 3.08 - note that there are three new fields to index (frnadb, reacd and genego). The new version of href.i needs to be merged with your copy of that file in SRSSITE
icarus/db/genecards.i
icarus/db/genecards.is
icarus/db/href.i
web/WEB-INF/jsp/views/genecardsentry/genecardsentry.jsp
2012/08/03: ensembl_mysql Update for some Ensembl release 68
icarus/db/ensemblRDB.i
icarus/db/ensembl_compara_schema.i
icarus/db/ensembl_funcgen_schema.i
icarus/db/ensemblcore_schema.i
2012/07/31: nrpat Added a mechanism to filter out duplicate entries during indexing for the patent equivalents database
icarus/db/patentequivalents.is
2012/07/26: nrpat Fix for a problem in calculationg the SeqCrcDigest field for the new NRNL1 and NRNL2 databases. After applying this update this field (scd) will have to be re-indexed
icarus/db/nrpat.is
2012/07/26: geneseq nrpat patent_prt Fixes for various inconsistencies in concepts used for the various patent databases, which affected the places where these databases show up in the query builder
icarus/db/aageneseq.i
icarus/db/aageneseqsupp.i
icarus/db/gswpi.i
icarus/db/nageneseq.i
icarus/db/nageneseqsupp.i
icarus/db/nrnl1.i
icarus/db/nrnl2.i
icarus/db/nrpl1.i
icarus/db/nrpl2.i
icarus/db/patent_prt.i
icarus/db/patentequivalents.i
2012/07/25: biogrid dip Fixed some wrong link annotations which caused EntrezGene to show up as a Protein Sequence database in the query builder
icarus/db/biogridinteractor.i
icarus/db/dipinteractor.i
2012/07/17: system nrpat Added support for a number of non-redundant patent sequence databases available from the ebi (see http://www.ebi.ac.uk/patentdata/nr/. Note that the new versions of srsdb.i general.it and href.i need to be merged with your copies of these files in SRSSITE
icarus/db/general.it
icarus/db/href.i
icarus/db/nrnl1.i
icarus/db/nrnl2.i
icarus/db/nrpl1.i
icarus/db/nrpl2.i
icarus/db/patentequivalents.is
icarus/db/srsdb.i
icarus/db/nrpat.i
icarus/db/nrpat.is
icarus/db/patentequivalents.i
web/WEB-INF/jsp/views/nrpatentry/nrpatentry.jsp
web/WEB-INF/jsp/views/nrpatentry/patentequivalents.jsp
2012/07/17: resid system Fix for a problem where the icarus based xml parser would not see attributes in a empty tag without a separate closing tag. Note that the new version of stardard.is needs to be merged with your copy of that file in SRSSITE
icarus/db/resid.is
icarus/db/standard.is
2012/07/17: dbsts Improved the display of citations in dbsts entries
web/WEB-INF/jsp/views/dbstsentry/references.jsp
2012/07/17: ddbj Removed link from DDBJ to IMGT, as it is also defined in imgt.i
icarus/db/ddbj.i
2012/07/17: kegg Update for kegg species mapping file. Note that it you have prisma, this file will be regenrated automatically when the kegggome database is updated
icarus/db/kegg_species.i
2012/07/17: emboss Upgraded emboss support to emboss 6.5.0. For your convenience we make this upgrade available as a separate tarball: EMBOSS6.5.0.tar.gz. If you upgrade from emboss 6.4, simply untar this file in SRSROOT, and run srssection. If you upgrade from an eearlier version of emboss, please have a look at the various Emboss README files
EMBOSS6.5.0.tar.gz
2012/07/17: geneseq added a link between the PatenNumber (Derwent Patent Index) and PATENT_PRT databases
icarus/db/gswpi.i
2012/07/16: refseq Added a command so SRS Prisma will set the release number of RefSeq(P). Note that applying this update will trigger a re-indeing if RefSeq(P), so it is best done if there is a real data update available
icarus/db/refseqprelease.it
icarus/db/refseqrelease.it
2012/07/16: uniref Increased the number of parts in which the uniref - uniprot_trembl links are build to prevent memory problems during indexing
icarus/db/uniref100.i
icarus/db/uniref50.i
icarus/db/uniref90.i
2012/07/04: pfam Fix for a wrong link definition between PfamA and UniProtSwissprot. After applying this update you will have to build the indices for this link: srsbuild -l pfama -xl uniprot_swissprot
icarus/db/pfama.i
2012/07/02: reactome Updates for release 41 of Reactome
icarus/db/reactome.i
icarus/db/reactome_schema.i
web/WEB-INF/jsp/views/reactomeentry/notevent.jsp
2012/06/26: kegg Made date unpack commands for Pathway and Kegg Genome more robust
icarus/db/kegggenome.it
icarus/db/pathway.it
2012/06/25: embl Added a command so SRS Prisma can set the release number for EMBLWGSRELEASE, and modified the search path so SRS will index EMBLWGSRELEASE from subdirectories (this is the way the data is now organised on the EBI ftp server)
icarus/db/emblwgsrelease.i
icarus/db/emblwgsrelease.it
2012/06/22: chemicalsearch resid Added code so prisma can set the release number for resid, and added a link from resid to Chemical structure search results
icarus/db/chemicalsearch.i
icarus/db/resid.i
2012/06/22: ccds Change to allow for some name changes for CCDS on the ncbi ftp server
icarus/db/ccdsnuc.it
2012/06/21: pubchem Increase of the number of parts in which the link between pubchemassayresult and taxonomy is build to prevent memory problems
icarus/db/pubchemassayresult.i
2012/06/20: hssp Fix to prevent problems caused by garbage in some of the compressed hssp data files
icarus/db/hssp.is
2012/06/19: drugbank Addded support for the the Organism field in the Drugbank Partner data
icarus/db/drugbank.i
icarus/db/drugbankpartner.i
icarus/db/drugbankpartner.is
web/WEB-INF/jsp/views/drugbankentry/drugbankpartnerentry.jsp
2012/06/18: kegg Change needed for the Kegg Genes database after a change in the ftp structure on the Kegg downloads site
icarus/db/kegggenes_na.it
2012/06/18: geneseq Changes so we index the patent number in GeneSeq with and without the kind (-A, -A1 etc) extension
icarus/db/aageneseq.i
icarus/db/geneseq.is
icarus/db/nageneseq.i
2012/06/18: pdb Fix for a problem wich occurs if one wants to display the pdb.is file in the web interface
icarus/db/pdb.is
2012/06/18: chemicalsearch hmdb drugbank Small change needed for the generation of Smiles files for drugbank used for chemical structure searches with OpenBabel
icarus/db/getHMDBSmiles.i
2012/06/15: kegg Correction for the link defintion between the Kegg Genes databases and Taxonomy - we now use the more precice Taxon (scientific name) field in taxonomy
icarus/db/kegggenes_aa.i
icarus/db/kegggenes_na.i
2012/06/12: blast Fix for a problems where SRS might skip the second entry in a blast result during indexing
icarus/db/blast.is
2012/06/07: kegg updated citation information for some Kegg ligand database, replacing medline Ids for PubMed IDs
icarus/db/lcompound.it
icarus/db/lenzyme.it
icarus/db/lglycan.it
icarus/db/lreaction.it
2012/06/07: pdb updated web and citation information for PDB
icarus/db/pdb.it
2012/05/30: embl Change so Prisma will be able to download emblwgs with the next full update of EMBL, when the directory structure for the WGS files will change. Note that untill that data Prisma will throw errors when it is chacking for the EMBL WGS section, but these errors are harmless if your current EMBLWGS data is up-to-date. If not, you should apply this update with the next full release of EMBL (expected in June).
icarus/db/emblwgsrelease.it
2012/05/28: pubchem Change needed to allow for the fact that index for the Comments (cc) field of pubchemsubstance is now larger than 4GB. This change requires re-indexing of the cc field and users will not be able to query the cc field until this has been done.
icarus/db/pubchem.i
2012/05/28: dbsnp Change needed to allow for the fact that index for the ID field of dbsnp is now larger than 4GB. This change requires re-indexing of the id fields for dbsnp and since the ID field is required for any access to dbsnp, users will not be able to query dbsnp until this has been done.
icarus/db/dbsnp.i
2012/05/28: pubchem Change needed to allow for the fact that index for the ID field of pubchemassayresult is now larger than 4GB. This change requires re-indexing of the id field for pubchemassayresult and since the ID field is required for any access to pubchemassayresults, users will not be able to query dbsnp until this has been done.
icarus/db/pubchemassayresult.i
2012/05/28: embl Change needed to allow for the fact the the EMBL Sequence version (sv) field soon will be larger than 4GB. This change requires re-indexing of the sv field for all databases in EMBL Format and users will not be able to query this field until this has been done. It is probbaly a good idea to apply this change with the next full release of EMBL (expected in June)
icarus/db/emblcommon.i
2012/05/28: entrezgene Change needed to allow for the fact the the EntrezGene All text field is now larger than 4GB. This change requires re-indexing of the Alltext field and users will not be able to query this field until this has been done
icarus/db/entrezgene.i
2012/05/28: genbank refseq ddbj Change needed to allow for the facts that index for the GenBank Sequence version (sv) field soon will be larger than 4GB, and that the indices for the CountedItam (cti) and CountedN (ctn) are already larger than 4GB. This change requires re-indexing of the sv,cti and ctn fields for all databases in GENBANK Format (GenBank, RefSeq, DDBJ) and users will not be able to query these fields until this has been done.
icarus/db/genbankcommon.i
2012/05/28: geneseq Change needed to allow for the facts that index for the Keyword (key) field soon will be larger than 4GB, and that the indices for the Patent Title (pat) are already larger than 4GB. This change requires re-indexing of the key and pat fields for NAGENESEQ and users will not be able to query these fields until this has been done.
icarus/db/nageneseq.i
2012/05/28: iprmatches Change of IdType for iprmatches so we can accomodate the 2.2 million entries of this database. This Change requries re-indexinf of iprmatches. Note that srscheck/prisma will not notice that re-indexing is neede, so you need to use a -force flag (or delete the iprematches_id index files)
icarus/db/iprmatches.i
2012/05/28: uniprot Change to allow for the fact that the indices for the Author (aut) and DBXref (dr) fields in UNIPROT_TREMBL will soon be larger than 4GB in size. This change requires re-indexing of the aut and dr fields for all databases in UNiProt/Swissprot format, and users will not be able to query these fields until this has been done
icarus/db/swisscommon.i
2012/05/28: fasta Changes needed to parse the output of the GLSEARCH and GGSEARCH programs from the Fasta Suite
icarus/db/fasta.is
2012/05/28: fasta Changes to allow for a changes in command line options for fastx, fasty, tfastx and tfasty in fasta 3.6.5 - Do not install these updates if you are using fasta 3.6.4 or older
icarus/db/fastacommon.i
icarus/db/fastx.i
icarus/db/fasty.i
icarus/db/tfastx.i
icarus/db/tfasty.i
2012/05/28: fasta Fixes for some errors reported by Prisma when it tests the fasta tools
icarus/db/fastsmf.i
icarus/db/nfastsm.i
icarus/db/tfastsmf.i
2012/05/21: drugbank system Added suport for the new salt and IUPHAR data in drugbank, and fixed some issues with hypertext links. Please note that the new version of href.i needs to be merged with your copy of that file in SRSSITE
icarus/db/drugbank.i
icarus/db/drugbank.is
icarus/db/href.i
web/WEB-INF/jsp/views/drugbankentry/drugbankentry.jsp
2012/05/21: pubchem Added support for the new patent number field in PubChem Substances
icarus/db/pubchem.i
icarus/db/pubchem.is
web/WEB-INF/jsp/views/pubchementry/pubchemsubstanceentry.jsp
2012/05/16: prisma Change to prevent prisma from hanging on gibberish in the command timing records
icarus/lion/prisma/prismatime.i
2012/05/16: irefindex fix for a harmless indexing error in irefindex
icarus/db/irefindex.is
2012/05/14: ensembl_mysql Updates for Ensembl 67. There have been some significant from release 66, and you should apply these updates at the same time as you bring the new data on-line. We also fixed some performance problems for sequence display/export views
icarus/db/ExonsandIntrons.il
icarus/db/OutputExons.il
icarus/db/OutputTranscripts.il
icarus/db/UTRandCDS.il
icarus/db/ensemblRDB.i
icarus/db/ensembl_compara_schema.i
icarus/db/ensembl_funcgen_schema.i
icarus/db/ensemblcommon.i
icarus/db/ensemblcore_schema.i
icarus/db/ensemblproteinmodel.i
icarus/db/exondatamodel.i
web/WEB-INF/jsp/views/ensemblgeneentry/geneentry.jsp
web/WEB-INF/jsp/views/ensemblproteinentry/proteinentry.jsp
web/WEB-INF/jsp/views/transcriptentry/transcriptentry.jsp
2012/05/10: chebi Updated comments about the loading of chebi in mysql and oracle. No functional changes
icarus/db/chebi.i
icarus/db/chebi_schema_mysql.i
2012/05/10: medline removed the from medline to pdb, as that link is now defined from pdb in pdb.i
icarus/db/medline.i
icarus/db/medlinenew.i
icarus/db/medlinerelease.i
icarus/db/medlineupdates.i
2012/05/08: mint Change so SRS Prisma can handle the changed structure of the mint download site
icarus/db/mintdata.i
2012/05/08: kegg Change so that the three letter organism part of the entry identifier in KEGGGENES is obtained from the organism field, and no longer from the file name
icarus/db/kegggenes.is
2012/05/04: chembl Updates for schema changes in ChEMBL release 13
icarus/db/chembl.i
icarus/db/chembl_dm.i
icarus/db/chembl_mysql_schema.i
icarus/db/chembl_oracle_schema.i
web/WEB-INF/jsp/views/chemblentry/chemblentry.jsp
2012/05/02: genecards Fix for a table display problem with diseases, genes and compounds from BioAlma lines in genecards
icarus/db/genecards.i
icarus/db/genecards.is
2012/05/01: system Added support for the new EvolutionaryTrace link in uniprot. Note that dbxref.i and href.i need to be merged with your copies of these files in SRSSITE
icarus/db/dbxref.i
icarus/db/href.i
2012/04/30: embl system Change so that for EMBL records the link to a genome project points to the EBI, and not to the NCBI. Note that the updated href.i file needs to be merged with your copy of this file in SRSSITE
icarus/db/embl.is
icarus/db/href.i
2012/04/30: embl imgt Change so we coorectly index the release number for imgt, and added a command so SRS Prisma will be able to set the imgt release number after installing new data
icarus/db/embl.is
icarus/db/imgt.it
2012/04/30: uniref Change to the ID type used for the UniRef databases, needed to accomodate the increased number of entries in UniRef100 (more than 256^3 - which no longer fits in the standard 3 byte ID type in SRS). After applying this update you will have to re-index the UniRef databases
icarus/db/unirefcommon.i
2012/04/30: prisma Fixed some usage/options display issues for the -help option
etc/runPrisma
2012/04/13: imgt Update to allow for some changes on the imgt download site
icarus/db/imgt.it
2012/04/11: kegg Removed unnecessary content from the kegg species mapping file (no longer needed due to changes in kegg databases)
icarus/db/genKeggSpecies.i
icarus/db/kegg_species.i
2012/03/29: omim Added information for use with OMIM data at omim.org. File needs to be edited to activate omim.org information.
icarus/db/omim.it
2012/03/29: system Added support for dnasu link in Uniprot
icarus/db/dbxref.i
icarus/db/href.i
2012/03/19: kegg Change to allow for the new ORGANISM line in the Kegg Genes database
icarus/db/kegggenes.is
icarus/db/kegggenes_aa.i
icarus/db/kegggenes_na.i
icarus/db/kegggenes_na.it
2012/03/13: ensembl_mysql Changes for ensembl version 66
icarus/db/ensemblRDB.i
icarus/db/ensembl_compara_schema.i
icarus/db/ensembl_funcgen_schema.i
icarus/db/ensemblcore_schema.i
icarus/db/ensemblgenemodel.i
2012/03/08: patent_prt Changed the field used for linking PATENT_PRT to AAGENESEQ from Patentnumber to Sequence CRC Digest, as the link becomes meaningless for patents with hundreds of thousends of sequences (and also becomes nearly impossible to build).
icarus/db/patent_prt.i
2012/03/08: system removed link to PDB from hypertext link for the Sequence CRC Digest field, as a bug in SRS results in a broken query for that
icarus/db/href.i
2012/03/06: system Change to ensure that the system reads emblcommon.i when EMBLCDS or PATENT_PRT is enabled. Note that this file needs to be merged with your copy of this file in SRSSITE
icarus/db/srsdb.i
2012/03/05: patent_prt Fix so prisma will not download the EMBL DNA data for PATENT_PRT
icarus/db/patent_prt.i
2012/03/02: geneseq system Change in the way prisma handles GeneSeq data - it will no longer keep copies of the downloaded tar archivs in the offline data directory. The AAGENESEQTAR and NAGENESEQTAR helper databases (used for downloading the data) are now obsolete and have been removed from srsdb.i
icarus/db/aageneseq.it
icarus/db/nageneseq.it
icarus/db/srsdb.i
2012/03/02: geneseq Fix for the handling of the entry creation and revision dates in GeneSeq
icarus/db/aageneseq.i
icarus/db/geneseq.is
icarus/db/nageneseq.i
web/WEB-INF/jsp/views/aageneseqentry/aageneseq.jsp
web/WEB-INF/jsp/views/nageneseqentry/nageneseq.jsp
2012/03/01: pdb Added a pubmed id field to PDB, and links to medline, and display of DOI literature links in the entry display
icarus/db/pdb.i
icarus/db/pdb.is
2012/03/01: embl genbank refseq ddbj retired Medline ID as in indexed field in EMBL/Genbank/Refseq/DDBJ, as it is empty in EMBL and the few entries in GenBank and RefSeq which have a MedlineID also have a PubMed ID
icarus/db/emblcommon.i
icarus/db/genbankcommon.i
2012/02/29: system Added LibLocs for the new EMBLCDA and PATENT_PRT datasets, and removed the LibLoc for the now obsolete PDBMODEL database, as we now include that data with the main PDB database. Note that the changes in this file need to be merged with your copy of this file in SRSSITE
icarus/db/srsdb.i
2012/02/29: embl Added support for EMBLCDS - a database derived from EMBL which gives easy access to CDS features in an EMBL like format
icarus/db/emblcds.i
icarus/db/emblcds.is
2012/02/29: patent_prt Added support for PATENT_PRT, which is a set of patent protein sequences, obtained from patent submissions to the US, European, Japanese and Korean patent offices. This data is available from the EBI and is provided in an EMBL like format
icarus/db/patent_prt.i
2012/02/29: dbsnp Change in the dbsnp download specification needed for a change in the way SRS Prisma traverses remote directories during recursive downloads
icarus/db/dbsnp.it
icarus/db/dbsnplocation.it
2012/02/29: prisma Change so SRS Prisma will not descend into all subdirectories during recursive downloads if it is clear from the wanted filename patterns that a path can never match those patterns. When applying this update also update the dbsnp.it and dbsnplocation.it files, otherwise prisma will not be able to download dbsnp data
icarus/lion/prisma/remoteConnection.i
2012/02/29: genpept Correction for the retrieval of the GenPept accession number field
icarus/db/genpeptcommon.i
2012/02/29: prisma srscheck Fix for a problem where Prisma would try to re-index dependent databases without first having linked the online data to the offline directories
icarus/lion/prisma/localcopyPhase.i
icarus/lion/prisma/pretransPhase.i
icarus/workflows/buildPhase.i
2012/02/29: srscheck prisma Fix for a problem where prisma would not index data files in the correct order if only a few fields need re-indexing
icarus/workflows/checkLocalFiles.i
icarus/workflows/coreCheckClasses.i
2012/02/29: srscheck prisma Fixes for various problems where SRS would build unneccesary virtual link sets, or would not move them online
icarus/workflows/getSystemLibs.i
icarus/workflows/linkPhase.i
2012/02/29: uniprot Increased the partsize paramter for parallel indexing of uniprot_trembl, as we are now hitting the common 1024 filehandles limit when merging link indices for this database
icarus/db/uniprot_trembl.i
2012/02/29: genbank embl refseq ddbj Small correction for data exports in gff format
icarus/db/gff.il
2012/02/29: system pdb Various changes for pdb: We have added fields (NCBI taxon ID, Genbank accession, sequence CRC digest, obsolete date), we added links to the taxonomy database and the major DNA sequence databases. We also changed the way SRS Prisma updates the PDB data, so it will include obsolete and model records (this can be controlled by editing pdb.it). With this change the separate PDBMODEL database is now no longer necessary. This change also requires that SRS Prisma needs to traverse recursively through the ftp direcories on the PDB download site and to stop Prisma from taking too much time going through irrelevant subdirectories, we have also an update for SRS Prisma (remoteConnection.i) which will limit the subdirectories SRS Prisma is traversing. After applying this update PDB will have to be re-indexed. Note that the new href.i file needs to be merged with your copy in SRSSITE
icarus/db/href.i
icarus/db/pdb.i
icarus/db/pdb.is
icarus/db/pdb.it
web/WEB-INF/jsp/views/pdbentry/pdbdescription.jsp
web/WEB-INF/jsp/views/pdbentry/pdbsequence.jsp
2012/02/29: embl genbank refseq ddbj We moved the NCBI taxon ID field (which is available in the "source" feature) from the feature subentry database to the main part of the data for EMBL/Genbank/DDBJ/RefSeq/Refseqp. This will allow for easier querying by taxon ID. This update requires re-indexing of the taxon id (txi) field. After applying this update the old txi indices will return errors, and srscheck or prisma will not be able to detect that the indices need rebuilding. Therefore the best way of handling this update is to renove all _txi.i* for all embl/genbank/ddbj/refseq/refseqp datasets you have and than use srscheck of prisma to build the new indices. You may also have to look at other code you have (for instance to build blast datasets) which use taxon ids in queries
icarus/db/embl.is
icarus/db/emblcommon.i
icarus/db/gbemblcommon.i
icarus/db/genbank.is
icarus/db/genbankcommon.i
web/WEB-INF/jsp/views/dnadbentry/dnadbentry.jsp
2012/02/29: kegg updated species mapping file for Kegg. Note that if you use prisma, this file will be generated by prisma and there is no need to update this file
icarus/db/kegg_species.i
2012/02/28: system Change to allow of the new pomBase references in uniprot (they replace the GeneDB_Spombe references)). Please note that the new dbxref.i and href.i files need to be merged with your copies in SRSSITE
icarus/db/dbxref.i
icarus/db/href.i
2012/02/28: kegg Changes to allow for the new MODULE line in the Kegg Genes database. Also some changes to improve robustness for downloads of the Kegg Genes data by Prisma
icarus/db/kegggenes.i
icarus/db/kegggenes.is
icarus/db/kegggenes_aa.i
icarus/db/kegggenes_na.i
icarus/db/kegggenes_na.it
icarus/db/lcommon.is
web/WEB-INF/jsp/views/kegggenesentry/kegggenesentry.jsp
2012/02/28: genecards system Update to allow for the new BIOTIME (cell lines) in GeneCards. Note that the new href.i file needs to be merged with your copy of that file in SRSSITE
icarus/db/genecards.i
icarus/db/genecards.is
icarus/db/href.i
web/WEB-INF/jsp/views/genecardsentry/genecardsentry.jsp
2012/02/27: chembl update for some minor schema changes in CHEMBL release 12
icarus/db/chembl.i
icarus/db/chemblcompound.i
icarus/db/chembltarget.i
2012/02/20: kegg fix for a parsing error during indexing of the Kegg Glycan database, caused by a malformed authors line in a single entry
icarus/db/lcommon.is
2012/02/17: drugbank Change needed as in the latest release of DrugBank the biotransformation and pharmacology fields have been replaced by metabolism and pharmacodynamics fields
icarus/db/drugbank.i
icarus/db/drugbank.is
web/WEB-INF/jsp/views/drugbankentry/drugbankentry.jsp
2012/02/17: irefindex Change so info messages from the unzip command used by SRS Prisma are suppressed and do not end up in the data
icarus/db/irefindex.i
2012/02/17: dbsnp Change to allow for several extra columns in the dbsnp location data - for the moment they contain no information.
icarus/db/dbsnplocation.is
2012/02/15: reactome Update for some minor schema changes in REACTOME release 29
icarus/db/reactome_schema.i
2012/02/15: chembl update for some minor schema changes in CHEMBL release 12
icarus/db/chembl_mysql_schema.i
icarus/db/chembl_oracle_schema.i
2012/02/09: blast system Added a view which allows for the export of BLASTN, TBLASTN and TBLASTX results in GFF format. This allows the user to align the results of a blast job against a genome with that genome in a genome browser (The standard views in SRS are not particularly usefull for thes type of blast jobs). Take care when you update the srs-export.xml file, to avoid loosing edits you have made to that file
icarus/db/blast.is
icarus/db/blastcommon.i
web/WEB-INF/config/srs/srs-export.xml
icarus/db/blastgff.il
2012/02/09: genbank embl refseq ddbj Made some changes so features which have been added as annotations to entries in SRS are also included in exports in GFF format
icarus/db/gbemblcommon.i
icarus/db/gff.il
2012/01/31: uniprot Fix for a display problem with features in uniprot text entries, introduced with the recently added FtResidKey field
icarus/db/swisscommon.i
2012/01/30: imgt Changed the name of the IMGT database to IMGTLIGM to avoid confusion with the other IMGT databases. Please note that fater applying this update you need to rename the imgt indices to imgtligm (or reindex imgtligm)
icarus/db/imgt.i
icarus/db/imgt.it
2012/01/25: pubchem Change needed to handle the increased line length (now more than 20000 chars for some records) in Pubchem Assay results data
icarus/db/pubchemassayresult.i
2012/01/20: system Added export functionality for sequence features in GFF format and resid XML. Be careful when you update this file as your own version may contain edits to enable/disable certain exporters
web/WEB-INF/config/srs/srs-export.xml
2012/01/20: fasta system Changed the fastaseqs view (for the export of sequences in fasta format) so the output is more in line with the format used by the NCBI. The header line now includes a gi number (when available) and an accession number which includes the version number (when available). We also extended the database name/abbrviation mappings we use, which you may want to modify to reflect your local setup. Please note that the new version of loader.i needs to be merged with your copy in SRSSITE
icarus/db/fasta.il
icarus/db/loader.i
2012/01/20: system Fix to make sure that the proper xml headers are wrapped around resid entries during xml exports
icarus/db/xml.il
2012/01/20: genbank embl refseq ddbj imgt Some fixes for the insertion of hypertext links in EMBL/GenBank/RefSeq/DDBJ feature tables
icarus/db/gbemblcommon.is
2012/01/20: embl genbank refseq ddbj We have added a new view (gff_export) which allows for the export of EMBL/GenBank/RefSeq/DDBJ feature tables in gff (3) format, suitable for import in genomw viewers like IGV. There are some customizations configurable for this - please see the notes in gff.il
icarus/db/embl.is
icarus/db/gbemblcommon.i
icarus/db/genbank.is
icarus/db/gff.il
2012/01/04: ccds Added support for the CRC sequences digest field to the ccds databases
icarus/db/ccds.i
icarus/db/ccds.is
web/WEB-INF/jsp/views/ccdsentry/ccdsentry.jsp
2012/01/04: geneseq Added support for the CRC sequences digest field to the geneseq databases, and modified geneseq views to display all patentnumbers for a entry, taken from the patentnumbers (geneseq world patent index) database - but only if you have this database enabled
icarus/db/aageneseq.i
icarus/db/geneseq.is
icarus/db/geneseqsupp.is
icarus/db/geneseqsuppcommon.i
icarus/db/gswpi.i
icarus/db/nageneseq.i
web/WEB-INF/jsp/views/aageneseqentry/aageneseq.jsp
web/WEB-INF/jsp/views/nageneseqentry/nageneseq.jsp
2012/01/04: resid Added support for the RESID database of Amino Acid residu modifications. Please see notes in resid.i for information on the display of resid chemical structures. Note that the new version of srsdb.i file needs to be mered with your copy of this file in SRSSITE
web/WEB-INF/jsp/views/residentry/residentry.jsp
2012/01/04: system resid Added support for the RESID database of Amino Acid residu modifications. Please see notes in resid.i for information on the display of resid chemical structures. Note that the new version of srsdb.i file needs to be merged with your copy of this file in SRSSITE
icarus/db/srsdb.i
icarus/db/resid.Makefile
icarus/db/resid.i
icarus/db/resid.is
icarus/db/residchemsearch.i
2012/01/04: system Added the DDBJ, CCDS and GeneSeq databases to the hypertext link used to find identical sequences using the CRC sequence digest field. Please note that the new href.i file needs to be merged with your copy of this file in SRSSITE
icarus/db/href.i
2011/12/20: hssp Fix to allow for a change in the format of the date line in hssp
icarus/db/hssp.is
2011/12/20: system support added for PATRIC and DMDM links in UniProt libraries
icarus/db/dbxref.i
icarus/db/href.i
2011/12/19: ensembl_mysql Updates for Ensembl release 65
icarus/db/ExonsandIntrons.il
icarus/db/OutputExons.il
icarus/db/OutputPeptides.il
icarus/db/OutputTranscripts.il
icarus/db/UTRandCDS.il
icarus/db/ensemblRDB.i
icarus/db/ensembl_compara_schema.i
icarus/db/ensembl_funcgen_schema.i
icarus/db/ensemblcommon.i
icarus/db/ensemblcore_schema.i
icarus/db/ensembldatamodel.i
icarus/db/ensemblgenemodel.i
icarus/db/ensemblproteinmodel.i
icarus/db/exondatamodel.i
2011/12/16: blast fasta Change so we have sequence selection checkboxes with the graph in the blast/fasta graphical results view. Please only apply this update if you have the SRS8.3.0.6 patch release installed. If for some reason you have installed this update without having installed the 8.3.0.6 pathc release, then the old version of this file is available as blastgraphic.jsp.8.3.0.5
web/WEB-INF/jsp/views/blastentry/blastgraphic.jsp
2011/12/16: embl genbank refseq ddbj imgt Correction for the Sequence CRC Digest hypertext link for protein sequences
icarus/db/emblcommon.i
icarus/db/gbemblcommon.is
icarus/db/genbankcommon.i
2011/12/16: genpept Fix for a display problem in GenPept
web/WEB-INF/jsp/views/genpeptentry/genpeptentry.jsp
2011/12/16: srscheck prisma Fix for a problem where partial link databases for uniprot_trembl where not removed during indexing due too a removal command which was too long for the shell (resulting in an "Argument list too long" error
icarus/workflows/linkPhase.i
2011/12/14: system ipi Added support for the new Sequence CRC Digest field to IPI. Please merge the new version of href.i with your copy in SRSSITE
icarus/db/href.i
icarus/db/ipi.i
2011/12/14: uniprot ipi Additional changes needed to link to RESID
icarus/db/swissprot.is
web/WEB-INF/jsp/views/swissentry/swissentry.jsp
2011/12/13: genpept kegg Added a new Sequence CRC digest field, which allows the user to quickly identify identical sequences
icarus/db/genpept.is
icarus/db/genpeptcommon.i
icarus/db/kegggenes.i
icarus/db/kegggenes.is
icarus/db/kegggenes_aa.i
icarus/db/kegggenes_na.i
web/WEB-INF/jsp/views/genpeptentry/genpeptentry.jsp
web/WEB-INF/jsp/views/kegggenesentry/kegggenesentry.jsp
2011/12/13: uniprot ipi system embl genbank ddbj Added a new Sequence CRC digest field, which allows the user to quickly identify identical sequences and added links to RESID, UniRef100, UniParc (only if UniParc or UniRef is installed locally) and a link to the UniProt version archive (UniSave).
icarus/db/swisscommon.i
icarus/db/swissprot.is
icarus/db/uniprotvarsplic.i
icarus/db/uniprotvarsplic.is
web/WEB-INF/jsp/views/swissentry/swissentry.jsp
web/WEB-INF/tags/featuretable.tag
web/WEB-INF/tags/referencetable.tag
2011/12/13: embl genbank refseq ddbj imgt Added a new Sequence CRC digest field, which allows the user to quickly identify identical sequences, and added links to the EMBL or NCBI version archives for EMBL, GenBank and RefSeq entries
icarus/db/embl.is
icarus/db/emblcommon.i
icarus/db/gbemblcommon.i
icarus/db/gbemblcommon.is
icarus/db/genbank.is
icarus/db/genbankcommon.i
web/WEB-INF/jsp/views/dnadbentry/dnadbentry.jsp
web/WEB-INF/jsp/views/dnadbentry/sequence.jsp
2011/12/13: system Changes needed for the new Sequence CRC Digest field - please note that these files need to be merged with your copies of these files in SRSSITE
icarus/db/general.it
icarus/db/href.i
icarus/db/srsgen.i
2011/12/09: unigene Change so building links from UniGene to EMBL/GenBank is done in more parts, so less memory is used
icarus/db/unigene.i
2011/12/03: pfam Correction to fix broken pfamhmm entry view.
icarus/db/pfamhmm.i
web/WEB-INF/jsp/views/pfamhmmentry/pfamhmmentry.jsp
2011/12/03: emboss Fix to correct output error that breaks viewing of plot.
icarus/lion/emboss/polydotp.i
2011/12/01: embl genbank refseq ddbj Change to allow for non-numerical characters in Genomic project identifiers
icarus/db/embl.is
icarus/db/genbank.is
2011/12/01: system Change to allow for the new ko (Kegg Orthology) link in UniProt records. Please note that the updated dbxref.i file needs to be merged with your copie of this file in SRSSITE
icarus/db/dbxref.i
2011/12/01: unigene Fix for a parsing error in some unigene entries for Danio Rerio
icarus/db/unigene.is
2011/12/01: biogrid dip intact mint Fix in the conversion script which converts psimi XML into data suitable for SRS indexing to allow for a change in the itact database. If your intactexperiment and intacinteractor databases contain no entries, please run this script in the the directory with your intact datafiles, and then re-index intactexperiment and intacinteractor
icarus/db/intactProcessData.pl
2011/12/01: biogrid dip intact mint Fixes for some issues with export of DIP data in mitab format
icarus/db/mitab.i
icarus/db/mitab.il
icarus/db/mitab.is
icarus/db/mitabstrict.il
2011/12/01: omim Updated omim.it so SRS Prisma will download the frozen (Frebrary 2011) version available from the NCBI. If you have access to the up-to-date omim data, then you will have to modify omim.it so Prisma will download the correct data. As we have not been able to get access to that, we cannot guarantee that our implementation of omim in SRS will continue to work with the latest omim data
icarus/db/omim.it
2011/12/01: hssp Updates for HSSP parser files to work with bz2 compression and add new ftp and www info.
icarus/db/hssp.i
icarus/db/hssp.it
2011/11/30: enzyme getReleaseCommand add for ENZYME database.
icarus/db/enzyme.it
2011/11/29: hmmer Note added to remind admin that PFAMHMM is required when enabling HMMSCAN
icarus/db/hmmscan.i
2011/11/29: system added ProteinProperties group that was causing error in a few EMBOSS libraries.
icarus/db/applGroups.i
2011/11/28: hmmer Add missing .is file for hmmscan from the HMMER3 package update
icarus/db/hmmscan.is
2011/11/27: geneticcode Minor change to add in release command for geneticcode
icarus/db/geneticcode.it
2011/11/15: kegg The Kegg Pathway KGML distribution does not include files for the reference pathways (mapXXXXX entries). To ovecome problems with external data linking to these we now create the relevant entries from the "ko" (ortology) entries. The ko entries are indexed twice, once as "ko" and once as "map". Note that this still does not entirely eliminate the dead link problem, as "ko" data is only available for regular metabolic pathways
icarus/db/pathway.is
2011/11/15: system Updated the package information for various tools to reflect the latest versions we support. Please note that this file needs to be merged with your copy of this file in SRSSITE
icarus/db/packages.i
2011/11/15: hmmer system pfam Upgraded the SRS integration of the HMMER package to version 3.0 - Please note that the hhmpfam tool has been replaced by hmmscan. The changes in href.i, srsgen.i, localApplicationOptions.i and srsdb.i need to be merged with your copies of these files in SRSSITE
icarus/db/hmmbuild.i
icarus/db/hmmbuild.it
icarus/db/hmmpfam.i
icarus/db/hmmpfam.it
icarus/db/hmmsearch.is
icarus/db/hmmsearch.it
icarus/db/href.i
icarus/db/localApplicationOptions.i
icarus/db/pfamhmm.i
icarus/db/pfamhmm.is
icarus/db/pfamhmm.it
icarus/db/srsdb.i
icarus/db/srsgen.i
icarus/db/hmmscan.i
icarus/db/hmmsearch.i
web/WEB-INF/jsp/views/pfamhmmentry/pfamhmmentry.jsp
2011/11/14: blast system Added a new SRS implementation of PsiBlast: ALIPSIBLAST, which allows you to start a search with a sequence alignments. Our standard PSIBLAST implementation only allows you to start a search with a sequence. Please note that the new version of srsgen.i, srsdb.i and laoder.i need to be merged with your copies of these files in SRSSITE
icarus/db/blastcommon.i
icarus/db/loader.i
icarus/db/psiblast.i
icarus/db/psiblast.it
icarus/db/srsdb.i
icarus/db/srsgen.i
icarus/db/alipsiblast.i
2011/11/14: biogrid dip intact mint system irefindex Added support for the irefindex protein interaction database. Note that the new versions of srsgen.i and srsdb.i need to be merged with your copy of these files in SRSSITE
icarus/db/mitab.i
icarus/db/mitab.il
icarus/db/mitabstrict.il
icarus/db/srsdb.i
icarus/db/srsgen.i
icarus/db/irefindex.i
icarus/db/irefindex.is
web/WEB-INF/jsp/views/irefindexentry/irefindexentry.jsp
2011/11/14: system Change neede for the construction of variant sequences by refseqvariations, and improved stability for mixed online/offline querying situations which might arise during sequence reformatting by SRS Prisma
icarus/db/ftseq.is
2011/11/14: fasta Change needed to handle sequences from the new refseqvariations database with the fastaseqs view - as this database can return multiple sequences for the same entry
icarus/db/fasta.il
2011/11/14: genbank embl refseq ddbj uniprot imgt ipi genpept system Change to the way sequence outpout in INSDSeq and TinYSeq XML is generated - instead of using a parsing step with a .is file we now use a cleaner method with new functionality (8.3.0.4) of the ToXML icarus function. Do not apply this update if you are not using SRS 8.3.0.4 or later. Note that the new version of views.i needs to be merged with your copy of this file in SRSSITE
icarus/db/gbemblcommon.i
icarus/db/insdseqxml.il
icarus/db/tinyseqxml.il
icarus/db/views.i
2011/11/14: system Fix for crashes with readseq.i - the sequence format conversion script available in SRS
icarus/db/readseq.i
2011/11/14: fasta Fix for spelling error in the description of ssearch
icarus/db/ssearch.i
2011/11/14: kegg Latest Kegg species mapping file. Note that if you use SRS prisma this file will be generated by Prisma
icarus/db/kegg_species.i
2011/11/14: system refseq Some time ago we started suppressing sequence variation features in the RefSeq data, as the large number of varitions which are currently available in some RefSeq entries was destroying performance. We now give access to the sequence variation information again, using a separate refseqvariations database, which uses the RefSeq data files. Unlike with the original processing of the RefSeq feature tables, the new refseqvariation database allows for on the fly construction of the variant sequence(s), if the information in the RefSeq feature table is sufficient. Please note that the new copy of srsdb.i needs to be merged with your copy in SRSSITE
icarus/db/srsdb.i
icarus/db/findrefseqacc.is
icarus/db/refseqvariations.i
icarus/db/refseqvariations.is
web/WEB-INF/jsp/views/refseqvariationsentry/refseqvariationsentry.jsp
web/WEB-INF/jsp/views/refseqvariationsentry/sequence.jsp
2011/11/08: system Change to ensure that annotations are not included in the linkpath for multistep links. This will become effective if you enable annotations for a new library by running SRSLION/annotations//addAnnotationLibrary.i -l "libnames"
icarus/lion/annotations/addAnnotationLibrary.i
2011/11/03: prisma srscheck Added a new option (-novirtual), which will exclude virtual libraries from checking. This is useful in combination with the -nolinks option during first time updates
etc/runPrisma
icarus/lion/prisma/prismaCheckClasses.i
icarus/lion/prisma/prismaCheckMain.i
icarus/workflows/getSystemLibs.i
icarus/workflows/srsCheckClasses.i
icarus/workflows/srsCheckMain.i
2011/11/03: srscheck prisma Change to ensure that (memory intensive) sort operations are done sequentially and not simultaneously
icarus/workflows/buildPhase.i
2011/11/03: prisma Change which should result in better parallization if there are multiple unpack commands
icarus/lion/prisma/pretransPhase.i
2011/11/03: srscheck prisma Fix for a problem in srscheck which occurs if the -L option is used in combination with -nolinks
icarus/workflows/moveData.i
2011/11/03: srscheck Fix for a problem with makefile target names when using srscheck with libraries which have dependencies
icarus/workflows/srsCheckMain.i
2011/11/03: srscheck prisma Fix to ensure that all links for relational databases with a staticlinks setting are build
icarus/workflows/getSystemLibs.i
icarus/workflows/linkPhase.i
2011/11/02: kegg Correction for an error in the defintion of the new Structure Map field
icarus/db/ldrug.i
2011/11/01: dbsnp Change to allow for indices larger than 4GB for some fields in dbsnp. After applying this update you will have to re-index dbsnp
icarus/db/dbsnp.i
2011/11/01: ensembl_mysql Fix for a sequence display problem with some Ensembl Pufferfish transcripts
icarus/db/exondatamodel.i
2011/10/27: kegg Added support for the new Molecular weight, Sequence and Structure Map fields in the Kegg Drug database
icarus/db/lcompound.i
icarus/db/ldrug.i
icarus/db/ldrug.is
web/WEB-INF/jsp/views/ldrugentry/ldrugentry.jsp
2011/10/24: system uniprot Another fix for the links subemtries in UniProt (our apologies for these multiple updates). The new version of srsgen.i will need to be merged with your copy of that file in SRSSITE, and you will have to re-index all databases in uniprot format.
icarus/db/srsgen.i
icarus/db/swisscommon.i
2011/10/19: system uniprot Fix for an error in the ID type used for the uniprot link subentry libraries. After applying this update, please re-index all libraries which are in Uniprot format (uniprot_swissprot, uniprot_trembl). Note that the new version of srsgen.i needs to be merged with your copy of that file in SRSSITE
icarus/db/srsgen.i
icarus/db/swisscommon.i
2011/10/14: ipi Added a note to the library information for IPI explaining that IPI is now retired and that the data is available via UniProtKB
icarus/db/ipi.it
2011/10/12: prosite Change to prevent a parsing error on a non-standard date value in a certain prosite entry
icarus/db/prosite.is
2011/10/10: kegg Changes so SRS Prisma can work with the new structure of the Kegg download site. Note that even if you do not use Prisma, there are some changes as we now require the renaming of some data files. See README.KEGG_NEW_STRUCTURE for details
icarus/db/kegg_images.i
icarus/db/keggdisease.i
icarus/db/kegggenes_na.i
icarus/db/kegggenes_na.it
icarus/db/kegggenome.i
icarus/db/kegggenome.it
icarus/db/keggorthology.i
icarus/db/keggorthology.it
icarus/db/lcompound.i
icarus/db/lcompound.is
icarus/db/lcompound.it
icarus/db/ldrug.i
icarus/db/ldrug.is
icarus/db/ldrug.it
icarus/db/lenzyme.i
icarus/db/lenzyme.it
icarus/db/lglycan.i
icarus/db/lglycan.is
icarus/db/lglycan.it
icarus/db/lreaction.i
icarus/db/lreaction.is
icarus/db/lreaction.it
icarus/db/pathway.i
icarus/db/pathway.is
icarus/db/pathway.it
icarus/db/pathwaybiopax.i
icarus/db/pathwaytar.it
2011/10/10: system Removed the now obsolete keggimages and pathwaybiopax databases, and set an offline data directory for pathway. Note that these changes need to be merged with your copy of srsdb.i in the SRSSITE directory
icarus/db/srsdb.i
2011/10/07: srscheck prisma Fix for a problem where srscheck correctly detects offline data files which need indexing, but then fails to use the offline settings in the resulting indexing and data move commands
icarus/workflows/moveData.i
icarus/workflows/srsCheckMain.i
2011/10/05: genecards correction for the link definition between GeneCards and HMDB
icarus/db/genecards.i
2011/10/04: drugbank Fix for a problem with the display of enzymes in the partner section of the DrugBank entry view
icarus/db/drugbank.is
2011/10/03: uniprot Changed the ID type used for databases in uniprot format from using a 3 byte identifier to a 4 byte internal identifier, so SRS can accomodate the more than 16.7 million entries which are available in the current release of uniprot_trembl. After this update you will have to re-index uniprot_tremblxml
icarus/db/uniprotxml.i
2011/09/30: uniprot Changed the ID type used for databases in uniprot format from using a 3 byte identifier to a 4 byte internal identifier, so SRS can accomodate the more than 16.7 million entries which are available in the current release of uniprot_trembl. After this update you will have to re-index uniprot_trembl
icarus/db/swisscommon.i
2011/09/29: imgt Change to allow for the fact the imgt is now provided a .gz file, and no longer as a .Z file
icarus/db/imgt.it
2011/09/28: iprmatches Added code so Prisma wil set the release number for the iprmatches database after a data update
icarus/db/iprmatches.it
2011/09/28: interpro Fix so prisma can correctly extrat the InterPro version number from the datafile
icarus/db/interpro.it
2011/09/28: iprmatches Split the building of links between interpro and iprmatches in parts, as it becomes difficult to build th link in one indexing command
icarus/db/iprmatches.i
2011/09/19: ensembl_mysql Update for some small schema chanegs in Ensembl 64
icarus/db/ensemblRDB.i
icarus/db/ensembl_compara_schema.i
icarus/db/ensembl_funcgen_schema.i
icarus/db/ensemblcore_schema.i
2011/09/08: chembl Change to allow for the way inchi identifiers are provided in chembl release 11
icarus/db/chembl.i
icarus/db/chembl_dm.i
icarus/db/chemblcompound.i
web/WEB-INF/jsp/views/chemblentry/chemblcompoundentry.jsp
web/WEB-INF/jsp/views/chemblentry/chemblentry.jsp
2011/09/07: system Corrections for some examples of fasta/blast database entries - no functional changes
icarus/db/localApplicationOptions.i
2011/09/07: embl Fix for a problem during indexing which could result in SRS not returning sequences for contig entries
icarus/db/embl.is
2011/09/07: intact biogrid dip mint Fix for a problem when displaying entries without a sequence
web/WEB-INF/jsp/views/intactentry/intactinteractor.jsp
2011/08/19: prodom Removed sorting on the keyword field of prodom, as it contains multiple values per entry
icarus/db/prodom.i
2011/08/18: kegg Correction for the handling of the molecular weight fields in Kegg Compound
icarus/db/lcompound.i
2011/08/18: kegg Some updates for the Kegg Drug database. A molecular weight field was added, as well as the display of sequence information for peptides
icarus/db/ldrug.i
icarus/db/ldrug.is
web/WEB-INF/jsp/views/ldrugentry/ldrugentry.jsp
2011/08/16: kegg Update for the kegg species mapping file we use. Note that if you use SRS Prisma, the updated file will be generated for you by Prisma each time the kegg databases are updated
icarus/db/kegg_species.i
2011/08/15: dssp CHange to allow for that fact that DSSP is now provided as .gz files, and no longer as .Z files
icarus/db/dssp.i
2011/08/15: prisma Fix for a problems where prisma would time-out on or misinterpret symbolic links on remote download sites
icarus/lion/prisma/remoteConnection.i
2011/08/15: srscheck prisma Made some changes to the building of links for virtual databases, so a few unnecessay files are no longer build
icarus/workflows/linkPhase.i
2011/08/15: chembl Update for some schema changes in ChEMBL release 11
icarus/db/chembl_mysql_schema.i
icarus/db/chembl_oracle_schema.i
2011/08/12: kegg Changed the command for the removal of obsolete pathway files to allow for different behaviour of find on some systems
icarus/db/pathwaytar.it
2011/08/12: embl genbank refseq ddbj imgt system Reduced memory usage for EMBL/GenBank/Refseq/DDBJ entries with very large feature tables. Also introduced a mechanism to limit the number of sequence variant features which are processed for RefSeq (default limit is 10000 - this can be customized by editing a parameter in SRSSITE/standard.is). Note that the new version of standard.is needs to be merged with your copy in SRSSITE
icarus/db/embl.is
icarus/db/gbemblcommon.i
icarus/db/gbemblcommon.is
icarus/db/genbank.is
icarus/db/genbankcommon.i
icarus/db/standard.is
2011/08/12: srscheck prisma Some changes so srscheck knows abou database depedencies. This means that databases which share data files (like emblnewfiles/emblnew, refseqfiles/refseqnew or uniseq/uniest) can be indexed in the same srsheck/srsdo run
icarus/workflows/moveData.i
icarus/workflows/moveIndicesPhase.i
icarus/workflows/srsCheckMain.i
2011/08/11: system Enabled the PATHWAY KGML to be available by default (since we now use the pathway kgml files), and added exporters for protein-protein interaction data (INTACT, DIP, MINT, BIOGRID) for export in MITAB of PSi-MI XML format, suitable for inport in programs like cytoscape. When you update this file, please take care that you not overwrite existing edits to this file
web/WEB-INF/config/srs/srs-export.xml
2011/08/11: prisma Fixes for some problems in prisma, where it would loose track of index files created, or datafiles to be installed, occuring within database dependencies when prisma is used to re-index databases locally. Also a few other minor corrections
icarus/lion/prisma/checkDependentDbs.i
icarus/lion/prisma/localcopyPhase.i
icarus/lion/prisma/movePrismaData.i
icarus/lion/prisma/pretransPhase.i
icarus/lion/prisma/prismaCheckClasses.i
icarus/lion/prisma/reformatPhase.i
icarus/lion/prisma/remoteConnection.i
2011/08/11: system biogrid dip intact mint Upgraded our support for intact to use the psi-mi 2.5 data, and added support for BioGrid, DIP and MINT protein-protein interaction databases. We also added helper databases for these to allow for exprot in MITAB format. Note that the new version of href.i and srsgen.i will need to be merged with your copies of these files in SRSSITE
icarus/db/href.i
icarus/db/intactProcessData.pl
icarus/db/intactdata.i
icarus/db/intactdata.it
icarus/db/intactexperiment.i
icarus/db/intactinteraction.i
icarus/db/intactinteractor.i
icarus/db/srsdb.i
web/WEB-INF/jsp/views/intactentry/intactexperiment.jsp
web/WEB-INF/jsp/views/intactentry/intactinteraction.jsp
web/WEB-INF/jsp/views/intactentry/intactinteractor.jsp
icarus/db/biogridexperiment.i
icarus/db/biogridinteraction.i
icarus/db/biogridinteractor.i
icarus/db/biogridmitab.i
icarus/db/dipexperiment.i
icarus/db/dipinteraction.i
icarus/db/dipinteractor.i
icarus/db/dipmitab.i
icarus/db/intactmitab.i
icarus/db/mintdata.i
icarus/db/mintexperiment.i
icarus/db/mintinteraction.i
icarus/db/mintinteractor.i
icarus/db/mintmitab.i
icarus/db/mitab.i
icarus/db/mitab.il
icarus/db/mitab.is
icarus/db/mitabstrict.il
icarus/db/psimi.is
icarus/db/psimi_common.i
icarus/db/psimi_experiment.i
icarus/db/psimi_interaction.i
icarus/db/psimi_interactor.i
icarus/db/psimixml.il
2011/08/08: prosite Change so prosite patterns can be used to launch the EMBOSS patmatdb program
icarus/db/prosite.i
2011/08/08: srscheck prisma Fixes for several issues with srscheck (and also prisma), which in some circomstances could result in srscheck not detecting valid on-line data files, warnings for duplicate targets when running srsdo or prisma, and some wrong link dependencies when multiple links exist between libraries
icarus/workflows/buildPhase.i
icarus/workflows/coreCheckClasses.i
icarus/workflows/linkPhase.i
2011/08/08: system LibLoc and data-tool related changes for EMBOSS 6.4, Fasta 3.6 and ClustalW 2.1. Please note that the changes need to be merged with your copies of these files in SRSSITE
icarus/db/loader.i
icarus/db/srsdb.i
icarus/db/srsgen.i
2011/08/08: clustalw Updated our support for ClustalW to version 2.1. We also added support for Clustal Omega (clustalo)
icarus/db/clustalo.i
icarus/db/clustalw.i
icarus/db/clustalw.is
icarus/db/clustalw.it
icarus/db/clustalwcommon.i
icarus/db/nclustalw.i
icarus/db/nclustalw.it
2011/08/08: emboss Upgraded emboss support to emboss 6.4.0. For your convenience we make this upgrade also available as a separate tarball: EMBOSS6.4.0.tar.gz. Before applying this update make sure you read README.EMBOSS6.4.0
EMBOSS6.4.0.tar.gz
2011/08/08: blast fasta Upgraded our support for the Fasta programs to release 3.6. Main change for the user is that the output can now contain additional alignments for a hit (like blast HSPs). We also added support for the GLSearch and GGSearch programs, and for searching with peptides/oligos using FastS/M/F. Note that we still provide an integration for TfastA, although this program no longer automatically is compiled if you install FastaA, and the author recommends to use TFastX
icarus/db/blastgraphicdatamodel.i
icarus/db/fasta.i
icarus/db/fastacommon.i
icarus/db/fastx.i
icarus/db/fasty.i
icarus/db/nfasta.i
icarus/db/ssearch.i
icarus/db/tfasta.i
icarus/db/tfastx.i
icarus/db/tfasty.i
icarus/db/fastsmf.i
icarus/db/fastsmf.pl
icarus/db/ggsearch.i
icarus/db/ggsearch.it
icarus/db/glsearch.i
icarus/db/glsearch.it
icarus/db/nfastsm.i
icarus/db/tfastsmf.i
2011/08/05: genecards Added support for the new DrugBank, HMDB and I2D data in the latest version of GeneCards
icarus/db/genecards.i
icarus/db/genecards.is
web/WEB-INF/jsp/views/genecardsentry/genecardsentry.jsp
2011/08/05: cath Update to allow for some changes on the CATH download site
icarus/db/cath.it
2011/08/04: ccds Some changes to work around some problems when downloading ccds fron the ncbi ftp site
icarus/db/ccds.i
icarus/db/ccds.is
icarus/db/ccdsnuc.it
2011/08/04: reactome Updates for some schema changes in Reactome 36
icarus/db/reactome_schema.i
2011/08/03: kegg Change to prevent parser crashes for the latest version of pathway
icarus/db/pathway.is
2011/08/03: srscheck prisma Fix for a problem where srscheck might not find valid online files
icarus/workflows/coreCheckClasses.i
2011/08/01: chembl Some schema changes fro release 10 of ChEMBL
icarus/db/chembl_mysql_schema.i
icarus/db/chembl_oracle_schema.i
2011/07/19: ensembl_mysql Some minor schema changes for release ensembl release 63
icarus/db/ensemblRDB.i
icarus/db/ensembl_funcgen_schema.i
icarus/db/ensemblcore_schema.i
2011/07/18: blast fasta Fix for an issue when linking to the matched results after refining the original blast result
web/WEB-INF/jsp/views/blastentry/blastgraphic.jsp
2011/07/07: kegg Switch to use the pathway kgml files to provide the KEGG pathway database, as KEGG no longer provides the html files we used for this. See comments in pathway.i for details
icarus/db/pathway.i
icarus/db/pathway.is
icarus/db/pathwaykgml.i
icarus/db/pathwaytar.it
icarus/db/pathwayxml.il
2011/07/07: kegg Updates for several KEGG databases: removed some obsolete fields (structure from lenzyme, compound and binding from lglycan, compound and glycan from lreaction. Added new Mass fields to lcompound, and changed the way these databases are linked to the pathway database
icarus/db/lcommon.is
icarus/db/lcompound.i
icarus/db/lcompound.is
icarus/db/lenzyme.i
icarus/db/lglycan.i
icarus/db/lglycan.is
icarus/db/lreaction.i
icarus/db/lreaction.is
web/WEB-INF/jsp/views/lcompoundentry/lcompgeneral.jsp
web/WEB-INF/jsp/views/lenzymeentry/lenzymeentry.jsp
web/WEB-INF/jsp/views/lglycanentry/lglycangeneral.jsp
web/WEB-INF/jsp/views/lreactionentry/lreactgeneral.jsp
2011/06/08: system Fixes for some memory problems and problems with virtual databases which use a virtualQueryAny
icarus/util/makeVirtualLibSets.i
2011/06/07: Conversion information needed for old usage objects after extending usage recording in prisma
icarus/util/classAttic/Class_PrismaLibResourceUsage_2429876272.i
icarus/util/classAttic/Class_PrismaResourceUsage_1123318200.i
2011/06/01: kegg Change so SRS Prisma wil download the Kegg Disease database from its new location
icarus/db/keggdisease.i
2011/06/01: pfam Change to allow for the new WK (wikipedia) line in Pfam
icarus/db/pfam.i
icarus/db/pfam.is
web/WEB-INF/jsp/views/pfamentry/pfamentry.jsp
2011/06/01: kegg Fix for a parsing error occuring with the latest version of the Kegg Genome database
icarus/db/kegggenome.is
2011/06/01: pubchem Fixes for parsing errors occuring during the indexing of several out of spec PubChemCompound entries
icarus/db/pubchem.is
2011/06/01: transfac Fixes for some parser errors occurring with the latest data
icarus/db/tffactor.is
icarus/db/tffragment.is
2011/06/01: ensembl_mysql Update to allow for some minor scheme changes in EnsEMBL 62
icarus/db/ensemblRDB.i
icarus/db/ensembl_compara_schema.i
icarus/db/ensemblcore_schema.i
2011/05/23: dbsnp Change so we also index the dbnsp class (FxnSet_fxnClass/ fxcl) which will allow you to do queries which exclude irrelevant snps, like upstream/downstream variants. Also modified the downolad settings so the clinical human dbsnp file is no longer included (this file contains duplicates of entries which are also present in the regular files)
icarus/db/dbsnp.i
icarus/db/dbsnp.it
2011/05/19: prisma Change so the main dates on the prisma reports refer to the date a prisma run was started, and no longer to the date the report was generated (but we still mention the generation date)
icarus/lion/prisma/decisionReport.i
icarus/lion/prisma/dumpTarget.i
icarus/lion/prisma/generateLinkReports.i
icarus/lion/prisma/printBuildPages.i
icarus/lion/prisma/printDownloadPages.i
icarus/lion/prisma/printLinkPages.i
icarus/lion/prisma/printMainPage.i
icarus/lion/prisma/printMovePages.i
icarus/lion/prisma/printPretransPages.i
icarus/lion/prisma/printReformatPages.i
2011/05/19: prisma Change to include the display of cpu/walltime and dowload size and time in the prisma usage reports
icarus/lion/prisma/cpuslots.il
icarus/lion/prisma/printUsageReport.i
icarus/lion/prisma/prismaCheckClasses.i
icarus/lion/prisma/prismatime.i
icarus/lion/prisma/setReportPhase.i
2011/05/19: prisma Change to reduce the amount of STDOUT when downloading large files, and a change to allow for a odd behaviour of the ls command on SELinux systems
icarus/lion/prisma/remoteConnection.i
2011/05/19: prisma Fix for a problem with sending reports by Email in some configurations
etc/runPrisma
icarus/lion/prisma/printMainPage.i
icarus/lion/prisma/prismaRunWatcher.i
2011/05/18: chembl Removed code which was trying to display an image - which was obsolete, as chembl no longer includes an image, and which was casuing problems as some of the underlying code had already been removed in a previous update of chembl.i
web/WEB-INF/jsp/views/chemblentry/chemblentry.jsp
2011/05/11: uniprot Fix for a problem with the indexing of the xml version of UniProt. If you have enabled the uniprot xml databases in SRS, and they contain 0 entries, you should re-index uniprot_swissprotxml and uniprot_tremblxml
icarus/db/uniprotxml.is
2011/05/11: transfac Removed sorting for the ElementDomination field in tfsite, as it soes not provide a single value per entry
icarus/db/tfsite.i
2011/04/20: srscheck prisma Fix for a problem where srscheck or prisma might not detect valid online datafiles
icarus/workflows/coreCheckClasses.i
2011/04/11: blast fasta system Improved the blast/fasta graphical view by displaying the alignments on the same page as the image, with selectionboxes to select results for further analysis. Note that the new version of loader.i needs to be merged with your copy of this file in SRSSITE
icarus/db/blastgraphicdatamodel.i
icarus/db/loader.i
web/WEB-INF/jsp/views/blastentry/blastgraphic.jsp
2011/04/08: srscheck prisma Fix for a problem where srscheck and prisma might not find the current datafiles if the indices are missing
icarus/workflows/checkLocalFiles.i
icarus/workflows/coreCheckClasses.i
2011/04/08: prisma Fix for an email problem if reporting is invoked using the reportPrisma command
icarus/lion/prisma/printMainPage.i
2011/04/06: genecards Adjusted codes to get better behaviour when using getz -f for the display of fields. Note that for GeneCards we would recomment to use getz -vf for field retrieval, as for some fields where the data has to be collected from differnt parts of the data the -f option will not work.
icarus/db/genecards.i
2011/04/06: genecards Changed Genecards so IDs are now case-sensitive (this is needed to avoid duplicate ID proplems. After applying this update you will have to re-index the GeneCards ID field
icarus/db/genecards.i
2011/03/30: ensembl_mysql Fix for a problem with the ExonSequence view for Ensembl transcripts
icarus/db/ensemblRDB.i
2011/03/30: omim Removed debug code which was displaying the SRS internal XML reoresentation of the entry within the omim entry view
web/WEB-INF/jsp/views/omimentry/omimentry.jsp
2011/03/29: system Chaneg which allows the use of the FastaSeqs view for ChEMBL target sequences. Please note that the new version of loader.i needs to be merged with your copy of this file in SRSSITE
icarus/db/loader.i
2011/03/29: prisma Fix for a problem where fasta/blast file generation result in duplicates if a fasta file generated by a previous Prisma run is still present in an offline location when a new Prisma run is started
icarus/lion/prisma/reformatPhase.i
2011/03/28: prisma Fix for a problem where fasta data generated during the Prisma Reformat phase could end up in the STDOUT of a command instead of in a datafile
icarus/lion/prisma/reformatPhase.i
2011/03/25: pfam Change to allwo once again for the download of swisspfam (it was not available for a while), and fix for a prsing problem with the latest version of the swisspfam data
icarus/db/swisspfam.is
icarus/db/swisspfam.it
2011/03/25: genbank embl refseq ddbj imgt Fix for some parsing errors in IMGT
icarus/db/gbemblcommon.is
2011/03/25: blast fasta Modified a step which removes version numbers from EMBL/GenBank/RefSeq identifiers to be more specific, so it does not strip numbers from other identifiers
icarus/db/blast.is
icarus/db/fasta.is
2011/03/23: srscheck prisma Change so srscheck and Prisma will keep the file order for multiple files of the original indexing job in cases where only a few fields are (re-)indexed.
icarus/workflows/buildPhase.i
icarus/workflows/coreCheckClasses.i
2011/03/23: rebase Changed the rebase entry view to use a standard way for displaying literature references
web/WEB-INF/jsp/views/rebaseentry/rebaseentry.jsp
2011/03/23: kegg Updated Kegg species mapping file. Note that if you use SRS Prisma you do not need to update this file as Prisma will generate it automatically
icarus/db/kegg_species.i
2011/03/22: medline Added a new field which contains PubMed Ids for references which are cited by an article. We use this to create an internal link within the medline databases, which allows us not only to display in the entry viewthe references wich are cited, but also to display a list of articles which are refering to the article you are viewing. It should be noted that this list will be incomplete, as currently only about 7% of medline entries contain citation information. After applying this update you should fully re-index all medline databases is SRS
icarus/db/medline.i
icarus/db/medline.is
icarus/db/medlinecommon.i
icarus/db/medlinenew.i
icarus/db/medlinerelease.i
web/WEB-INF/jsp/views/medlineentry/medlineentry.jsp
2011/03/22: system kegg Added hypertext links to LigandBox, LipidBank, LipidMap, pdb ligands, 3DMet, NikkaJi (the Japan Chemical Substance Dictionary) and KnapSack to the Kegg Drug and Compound databases. Please note that the new href.i file needs to be merged with your copy of that file in SRSSITE
icarus/db/href.i
icarus/db/lcommon.is
icarus/db/ldrug.is
2011/03/22: kegg Change for the way the keyword field in Kegg Genome is indexed, as the keywords are no longer separated by a ; but by a ,
icarus/db/kegggenome.i
icarus/db/kegggenome.is
2011/03/22: dbsts embl genbank refseq ddbj interpro omim pdb pfam prosite rebase system uniprot ipi Harmonized the way author names and journal abbreviations are indexed for various databases, so they match the way these are indexed for medline - which is without "." between initials and abbreviation terms. Previously we were including "." in this for the major sequence databases. If you anticipate that this change might confuse your users, the new standard.is file (to be merged with your copy in SRSSITE) contains a mechanism to retain the old behaviour, or to have both the old and new way of indexing the author and journal fields
icarus/db/dbsts.is
icarus/db/embl.is
icarus/db/genbank.is
icarus/db/interpro.is
icarus/db/omim.is
icarus/db/pdb.is
icarus/db/pfam.is
icarus/db/prositedoc.is
icarus/db/rebase.is
icarus/db/standard.is
icarus/db/swissprot.is
2011/03/22: dbsts interpro omim pdb pfam prosite rebase system uniprot medline embl genbank ddbj Harmonized the way literature references are displayed for different databases, sticking to a format which resembles the Vancouver style for citations, which is also used by the NLM. See also http://www.nlm.nih.gov/bsd/uniform_requirements.html
icarus/db/dbsts.i
icarus/db/interpro.i
icarus/db/omim.i
icarus/db/pdb.i
icarus/db/pfam.i
icarus/db/prositedoc.i
icarus/db/rebase.i
icarus/db/srsgen.i
icarus/db/swisscommon.i
web/WEB-INF/jsp/views/interproentry/interproentry.jsp
web/WEB-INF/jsp/views/medlineentry/medlineresults.jsp
web/WEB-INF/jsp/views/omimentry/omimentry.jsp
web/WEB-INF/jsp/views/pdbentry/pdbentry.jsp
web/WEB-INF/jsp/views/pfamentry/pfamentry.jsp
web/WEB-INF/jsp/views/prositedocentry/prositedocentry.jsp
web/WEB-INF/tags/referencetable.tag
2011/03/22: refseq Reduced partsize for inedxing to prevent memory problems with some RefSeq datafiles
icarus/db/refseqrelease.i
2011/03/21: prisma Removed a debug print statement
icarus/lion/prisma/prismastatus.is
2011/03/18: uniprot Added a (non-indexed) field which allows for the retrieval of the coordinates of a sequence feature
icarus/db/swisscommon.i
2011/03/17: genecards system Updates for release 3.05 of GeneCards. Note that the name of the download server has changed, so if you do not use prisma you may have to change your own update procedure. As usual, the new href.i will need to be merged with your copy of this file in SRSSITE
icarus/db/genecards.i
icarus/db/genecards.is
icarus/db/genecards_datamodel.i
icarus/db/genecardstar.it
icarus/db/href.i
web/WEB-INF/jsp/views/genecardsentry/genecardsentry.jsp
2011/03/17: merops Updates for release 94 of Merops
icarus/db/merops_schema.i
icarus/db/meropsseq.i
2011/03/16: chebi Fix for a problem with the display of comments in ChEBI
web/WEB-INF/jsp/views/chebientry/chebientry.jsp
2011/03/14: chebi chemicalsearch Change needed as once again the ChEBI sdf files are available as gz archive
icarus/db/chebichemsearch.i
2011/03/14: ccds Fix needed to handle empty fields in CCDS
icarus/db/ccds.is
2011/03/03: ensembl_mysql Fix for a display problem for some Pufferfish ensembl gene entries
icarus/db/ensemblgenemodel.i
2011/03/02: system Added several generic xml parsing routines to the standard parser. They are used the DrugBank parser. Please note that this new version of standard.is will nedd to be merged with your copy of that file in SRSSITE
icarus/db/standard.is
2011/03/02: drugbank chemicalsearch hmdb system Changed our implementation of DrugBank to use the new XML version of DrugBank 3. Note that the drugbanktarget database has been replaced by a drugbankpartner database. There are new versions of srsdb.i and loader.i which will have to be merged with your copy of these files in SRSSITE. We have added XML exporters for DrugBank in srs-export.xml - be carefull when updating this file, as you may have edited your copy of that file to enable certain data exporters. If you use prisma to update your data, you will also need to get the latest prisma updates.
icarus/db/drugbank.i
icarus/db/drugbank.is
icarus/db/drugbanksdf.i
icarus/db/getHMDBSmiles.i
icarus/db/loader.i
icarus/db/srsdb.i
icarus/db/xml.il
web/WEB-INF/config/srs/srs-export.xml
web/WEB-INF/jsp/views/drugbankentry/drugbankentry.jsp
icarus/db/drugbankpartner.i
icarus/db/drugbankpartner.is
icarus/db/drugbankxml.il
web/WEB-INF/jsp/views/drugbankentry/drugbankpartnerentry.jsp
2011/03/01: chebi chemicalsearch Change needed as the chebi sdf files are no longer distributed as a .gz archive, but as plain sdf file
icarus/db/chebichemsearch.i
2011/03/01: prisma Change needed to be able to traverse the website from which drugbank can be downloaded. Note that this also requires the latest version of the wgetPrisma binaries
icarus/lion/prisma/remoteConnection.i
2011/03/01: prisma Change so one cannot activate on obsolete feature image generation feature which we had in provious version of SRS/Prisma
icarus/lion/prisma/configurePrisma.i
2011/03/01: chembl chemicalsearch system Changes for release 9 of chembl. There have been major schema changes, so only apply this update if you have loaded ChEMBL release 9. The main changes visible to the end-user are that CHMBLCOMPOUNDS now contains drug information (if appropriate), and that the default table for CHEMBLCOMPOUNDS no longer includes a image with the chemical structure (that data is no longer included with the data dumps), so we are now using an applet (Marvin or JChemPaint) to display the structure. (See README.applets for information about these applets).
icarus/db/chembl.i
icarus/db/chembl_dm.i
icarus/db/chembl_mysql_schema.i
icarus/db/chembl_oracle_schema.i
icarus/db/chemblcompound.i
icarus/db/chemblcompound_dm.i
icarus/db/chembltarget.i
icarus/db/chembltarget_dm.i
icarus/db/getChemblSmiles.i
icarus/db/href.i
web/WEB-INF/jsp/views/chemblentry/chemblcompoundentry.jsp
web/WEB-INF/jsp/views/chemblentry/chemblentry.jsp
web/WEB-INF/jsp/views/chemblentry/chembltargetentry.jsp
web/WEB-INF/jsp/views/chemblentry/chemblcompoundtable.jsp
2011/03/01: prisma Fix for a potential crash during the generation of the usage report image if all commands timed during a prisma run have take very little time to complete
icarus/lion/prisma/cpuslots.il
2011/03/01: prisma Fix for a problem with sending Emails during reporting and monitoring of a prisma run
icarus/lion/prisma/printMainPage.i
icarus/lion/prisma/prismaRunWatcher.i
2011/03/01: prisma srscheck We added the collection of timing information to the various checking steps in prisma, so the usage report can show how much time is spend in these stages. Added more timestamps in the debug output, which should help troubleshooting. Removed some duplication of tasks which was occuring between update rounds in prisma.
etc/runPrisma
icarus/lion/prisma/dumpTarget.i
icarus/lion/prisma/inspectClasses.i
icarus/lion/prisma/prismaCheckMain.i
icarus/lion/prisma/prismadata.i
icarus/lion/prisma/reformatPhase.i
icarus/workflows/coreCheckClasses.i
2011/03/01: prisma srscheck We implemented a new mechanism for staging the index merge steps for large databases, which should greatly reduce the number of partial index files which accumulates in the offline index directory. This can be controlled via a new -mergeThreads command line option available to both srscheck and runPrisma. For a full explanation see README.mergethreads
icarus/lion/prisma/checkRemoteFiles.i
icarus/workflows/buildPhase.i
icarus/workflows/srsCheckClasses.i
icarus/workflows/srsCheckMain.i
2011/03/01: prisma We made some changes to the prisma status database to prevent duplicate ID errors occuring during a prisma run
icarus/lion/prisma/prismaCheckClasses.i
icarus/lion/prisma/prismaInvalidate.i
icarus/lion/prisma/prismastatus.i
icarus/lion/prisma/prismastatus.is
icarus/lion/prisma/prismaview.i
2011/02/11: system Added support for the new GeneTree and NextProt hypertext links in UniProtKB. Please note that the new href.i and dbxref.i need to be merged with your copies of these files in SRSSITE
icarus/db/dbxref.i
icarus/db/href.i
2011/02/10: reactome Removed a debug print statement
web/WEB-INF/jsp/views/reactomeentry/go.jsp
2011/02/09: ensembl_mysql Modifications to allow for some schema changes in ensembl 61
icarus/db/ensemblRDB.i
icarus/db/ensembl_compara_schema.i
icarus/db/ensembl_funcgen_schema.i
icarus/db/ensemblcore_schema.i
2011/02/07: dbsnp Changes needed to handle datafiles which do not contain any data
icarus/db/dbsnplocation.is
2011/02/03: ipi Change in the way prisma looks for ipi file updates, as the previous method had to follow some symbolic links, which on some platforms could cause the wgetPrisma program to crash
icarus/db/ipi.it
2011/01/28: prisma Improve error handling for contigs/joins when extracting sequences
icarus/lion/prisma/getFastaSequence.i
2011/01/24: blast Fix for a problem with linking to uniseq data
icarus/db/blast.is
2011/01/21: system Added support for the new Allergome link in UniProt. Please note that the new versions of href.i and dbxref.i need to be merged with your copies of those files in SRSSITE
icarus/db/dbxref.i
icarus/db/href.i
2011/01/18: blast Change so blast indexing will not stop at entry IDs which contain characters which have a special meaning in regular expressions
icarus/db/blast.is
2011/01/05: entrezgene removed debug statement that writes output to terminal window
icarus/db/entrezgene_dm.i
2010/12/23: entrezgene Change so the entryview does not crash if there is a failure when trying to retrieve information needed for drawing the genomic context cartoon
icarus/db/entrezgene_dm.i
2010/12/22: kegg Added support for the new drug target field in the kegg gene databases
icarus/db/kegggenes.i
icarus/db/kegggenes.is
icarus/db/kegggenes_aa.i
icarus/db/kegggenes_na.i
web/WEB-INF/jsp/views/kegggenesentry/kegggenesentry.jsp
2010/12/21: blast Change so psiblast uses the the same set of protein sequence databases which is available for the other blast programs
icarus/db/psiblast.i
2010/12/21: reactome Updates for Reactome version 35. Note that there are fairly major schema changes in this release, so you should apply this update at the same time when you load Reactome 35 into mysql.
icarus/db/reactome.i
icarus/db/reactome_schema.i
web/WEB-INF/jsp/views/reactomeentry/go.jsp
2010/12/15: pdb Change so we can export all models in PDB files which contains multiple structures (usually NMR derived)
icarus/db/pdb.is
2010/12/13: kegg Change to deal with stricter session management in SRS 8.3.0.5
icarus/db/pathwayxml.is
2010/12/09: chembl Changes for release 08 of chembl. Note that for chemblcompounds we now use the new chembl_id as primary identifier. If you are using mysql, then you will need to create an index for this in mysql after data import in order to get acceptable performance. See the comments in chembl_mysql_schema.i for details
icarus/db/chembl.i
icarus/db/chembl_dm.i
icarus/db/chembl_mysql_schema.i
icarus/db/chembl_oracle_schema.i
icarus/db/chemblcompound.i
icarus/db/chembltarget.i
2010/12/08: pubchem Change to allow for a new PUBCHEM_HOLD_UNTIL_DATE line in PubChemSubstance
icarus/db/pubchem.is
2010/12/08: entrezgene Fix for a coding error which could couse entrezgene indexing to crash
icarus/db/entrezgene.is
2010/12/08: chemicalsearch kegg Fix for the conversion script which builds data for chemical structure searching for the Kegg databases, needed to deal with session management changes in SRS 8.3.0.5
icarus/db/getKeggSmiles.i
icarus/db/lcommon.is
2010/12/06: entrezgene We have added a genomic context image, showing neighbouring genenes on the chromosome, to the entry display for entrezgene. Note that this update requires two new fields: chrll and chrlr - and that the entrydisplay will fail until these fields have been indexed. If you have a seperate test installation we would recommend that you index these new fields first on that installation, and then apply the update to your production installation with the new indices. If that is not possible, first update the entrezgene.i and entrezgene.is files, then build the new indices, and then apply the updates entrezgene_dm.i and entrezgeneentry.jsp files.
icarus/db/entrezgene.i
icarus/db/entrezgene.is
icarus/db/entrezgene_dm.i
web/WEB-INF/jsp/views/entrezgeneentry/entrezgeneentry.jsp
2010/12/02: kegg Change to ensure that the Kegg Drug data is downloaded and unpacked, as the tar archive containing this data sometime only changes its timestamp, but not its size
icarus/db/kegg_images.i
2010/12/01: fasta Another small fix needed for correct html linking in fasta results
icarus/db/fasta.is
2010/11/29: taxonomy Fix for a problem which would stop prisma from downloading the taxonomy data file due to an issue with a symbolic link in the taxonomy download directory
icarus/db/taxonomy.it
2010/11/29: fasta Some corrections to handle linking from fasta results
icarus/db/fasta.is
2010/11/29: ensembl_mysql Updates for release ensembl release 60. The main change is that the table containing ontology references has been renamed
icarus/db/ensemblRDB.i
icarus/db/ensembl_compara_schema.i
icarus/db/ensembl_funcgen_schema.i
icarus/db/ensemblcommon.i
icarus/db/ensemblcore_schema.i
icarus/db/ensembldatamodel.i
2010/11/26: pubchem Change to allow for a new label for the INCHY and INCHYKEY fields in pubchem
icarus/db/pubchem.is
2010/11/25: fasta Fix for linking when multiple databases have been selected for a fasta search and ensure fasta hits have hypertext links in the graphical results view
icarus/db/fasta.is
2010/11/05: blast Added an option to switch off sequence filtering for bl2seq
icarus/db/bl2seq.i
2010/11/03: pubchem The NCBI have sanitized the way PubChem assay data is distributed, and this has allowed us to change the unpacking and pre-processing of this data to happen on a per-file basis, instead of having to wait until all data has been downloaded. This should speed up downloading/processing/indexing of this data by SRS Prisma
icarus/db/createpubchemassaydata.pl
icarus/db/createpubchemassayresultdata.pl
icarus/db/pubchemassay.i
icarus/db/pubchemassayresult.i
2010/11/01: prisma Extend the method for estimating the uncompressed file size for remote data by using existing local data as a guide to zip archives
icarus/lion/prisma/checkRemoteFiles.i
2010/11/01: prisma Fix so the inspection part of prisma will not crash if a tool is not part of a group
icarus/lion/prisma/inspectReport.i
2010/10/26: prisma Fix for a problem with dependent databases which are updated by mirroring, where SRS/Prisma might try to index the data before the downloading of the data has finished.
icarus/lion/prisma/pretransPhase.i
2010/10/18: chemicalsearch Added some additional information to be displayed to to user if he ends up trying to launch a chemistry search from a regular tool launch page rather than the quick search page
icarus/db/chemicalsearch.i
2010/10/18: system Changed some single quotes in blast database selection examples to double quotes - as they involved variable substition, and added some database mapping values for refseq
icarus/db/localApplicationOptions.i
2010/10/18: genecards Corrected some database names used in linking from GeneCards to RefSeq
icarus/db/genecards.i
2010/10/18: prisma Fix for a crash during the generation of tool quality reports in prisma, caused by the fact that the new chemicalsearch tool is not part of a group
icarus/lion/prisma/inspectReport.i
2010/10/18: homologene Removed PubMed links/fields from HomoloGene, as the data no longer contains PubMed references
icarus/db/homologene.i
icarus/db/homologene_datamodel.i
web/WEB-INF/jsp/views/homologeneentry/homologeneentry.jsp
2010/10/14: drugbank Added missing parser for drugbank sdf exports
icarus/db/drugbanksdf.is
2010/10/13: cath Change to allow for new file names on the cath download site. Since the new filenames still have a date stamp well in the past, you may to do a "runPrisma -force cath -nomove" to force a new download
icarus/db/cath.i
icarus/db/cath.it
2010/10/13: ccds Fix for a display problem for ccds (dna and protein) caused by a loader mismatch
icarus/db/ccds.i
2010/10/13: dbsnp Fix for a indexing failure with the latest version of DBSNP - caused by a new species (Alectoris) which according to the taxonomy databases is not actually a species, but a genus
icarus/db/dbsnp.i
icarus/db/dbsnp.is
2010/10/13: go_xml Fix for a wget stability problem when trying to accecc the go ftp site
icarus/db/go.it
2010/10/11: system uniprot ipi Change so our hypertext links to ensembl can use the new simplified unique ID method of accessing the ensembl website (which is needed as uniprot no longer provides the species name in the ensembl reference line), while retaining the hypertext links to an internal SRS installation of ensembl. Note that the new version of href.i needs to be merged with your copy of that file in SRSSITE
icarus/db/href.i
icarus/db/swissprot.is
2010/10/07: taxonomy Small change in the way the species field is indexed - mainly to prevent virusses ending up with the name of their target as their species name
icarus/db/taxonomy.is
2010/10/07: intact We have split the indexing of the intact interactions library in parts as indixing it in one run was starting to take too much time
icarus/db/intactinteraction.i
2010/10/05: pdb Fix for a parsing error caused by a missing journal name in a PDB entry
icarus/db/pdb.is
2010/10/04: merops Allow for some small schema changes in Merops release 9.2
icarus/db/merops_schema.i
2010/09/28: kegg latest kegg species mapping file. Note that if you use prisma, prisma will generate this file automatically with each kegg update
icarus/db/kegg_species.i
2010/09/27: system chemicalsearch Added a facility for doing chemical structure (identity, similarity, substructure) searches using OpenBabel. Please check the notes in chemicalsearch.i for details. The new version of srsdb.i, and the list of searchable databases in localApplicationOptions.i need to be merged with your copies of these files in SRSSITE
icarus/db/localApplicationOptions.i
icarus/db/srsdb.i
icarus/db/chemicalsearch.i
icarus/db/chemicalsearch.is
2010/09/27: pubchem chemicalsearch chebi drugbank hmdb kegg Added icarus files containing prisma configurations so prisma can build the necessary data files for chemical structures searches for ldrug, lcompound, drugbank, hmdb, chebi and pubchem
icarus/db/pubchemchemsearch.i
icarus/db/chebichemsearch.i
icarus/db/drugbankchemsearch.i
icarus/db/hmdbchemsearch.i
icarus/db/lcompoundchemsearch.i
icarus/db/ldrugchemsearch.i
2010/09/27: chebi chemicalsearch chembl hmdb drugbank kegg pubchem Added scripts which convert data from ldrug, lcompound, chembl, hmdb, drugbank and pubchem for use with chemical structure searches
icarus/db/chebi2smiles.pl
icarus/db/getChemblSmiles.i
icarus/db/getHMDBSmiles.i
icarus/db/getKeggSmiles.i
icarus/db/getPubChemSmiles.i
2010/09/27: pubchem system Added support for pubchem. Please note that the pubchem compound and pubchem substance databases are rather large (together about 420 GB), and that the pubchem assay and assayresult datasets require pre-processing by the provided perl scripts - see the notes in pubchemassay.i. The new versions of srsgen.i and href.i need to be merged with your copies of these files in SRSSITE
icarus/db/createpubchemassaydata.pl
icarus/db/createpubchemassayresultdata.pl
icarus/db/href.i
icarus/db/pubchem.i
icarus/db/pubchem.is
icarus/db/pubchemassay.i
icarus/db/pubchemassay_dm.i
icarus/db/pubchemassayresult.i
icarus/db/pubchemassayresult.is
icarus/db/srsdb.i
web/WEB-INF/jsp/views/pubchementry/pubchemassayentry.jsp
web/WEB-INF/jsp/views/pubchementry/pubchemassayresultentry.jsp
web/WEB-INF/jsp/views/pubchementry/pubchemcompoundentry.jsp
web/WEB-INF/jsp/views/pubchementry/pubchemsubstanceentry.jsp
2010/09/27: genbank refseq ddbj Moved the protein id, taxonomy id and gene name fields from the feature subentry to the main entry of refseqp, as they only occur in the CDS feature, of which there is only in in refseqp. After applying this update you will have to reindex the ge,prd and txi fields for refseqprelease and refseqpnew - and it may be better to remove the existing indices, as otherwise srscheck or prisma will not detect that re-indexing is required
icarus/db/genbankcommon.i
2010/09/23: system Change to the way blast/fasta searchable databases are displayed when "guiType:multi" is set - instead of a html multiselect box, a nested menu with checkboxes is presented to the user. Please have a look at the notes/example in the new localApplicationOptions.i file to see how to configure this
web/WEB-INF/jsp/toollaunch/index.jsp
web/WEB-INF/jsp/toollaunch/main.jsp
2010/09/23: system Update localApplicationOptions.i to include parameters for blastplus and added example databases for remote blast. Added examples and comments on how to provide menu nesting, and changed the default guiType setting for blast/fasta databases from menu (single database selection) to multi (multi database selection)
icarus/db/localApplicationOptions.i
2010/09/23: blast Updated our implementation of blast to use blastplus - the latest revamp of the ncbi blast suite. Please check README.blastplus for some notes and further details
icarus/db/bl2seq.i
icarus/db/bl2seq.is
icarus/db/blast.is
icarus/db/blastcommon.i
icarus/db/blastn.i
icarus/db/blastp.i
icarus/db/blastx.i
icarus/db/psiblast.i
icarus/db/psiblast.is
icarus/db/tblastn.i
icarus/db/tblastx.i
web/javascript/tools/blast.js
2010/09/23: system updated quickSearchOptions.i so the database names provided for blast quicksearches match those in the new localApplicationOptions.i file - note that both quickSearchOptions.i and localApplicationOptions.i are meant to be costomized, with the active copy located in SRSSITE
icarus/db/quickSearchOptions.i
2010/09/22: prisma Change so prisma will print out a warning during the checking phase if a subdirectory cannot be accessed while traversing a directory tree
icarus/lion/prisma/remoteConnection.i
2010/09/21: kegg Change needed as reaction pair field has been removed, and glycan fields is now located in the comments line, and drug references have been added
icarus/db/lcommon.is
icarus/db/lcompound.i
icarus/db/lcompound.is
icarus/db/ldrug.i
web/WEB-INF/jsp/views/lcompoundentry/lcompoundlinks.jsp
2010/09/21: embl Change so we will not automatically include the expanded contigs in emblnew - SRS will then use the contigs from the release, and build the relevant sequences on the fly. If you prefer to have the expanded contigs (this takes significant diskspace), comment in the relevant section in emblnewfiles.it
icarus/db/emblnewfiles.it
2010/09/21: prisma Change to allow for somewhat more flexibility in specifying non-standard fasta and blast converters
icarus/lion/prisma/reformatPhase.i
2010/09/21: kegg Change to suppress a parsing error (caused by a fault in the data) during indexing
icarus/db/pathway.is
2010/09/21: hssp Increased the number of parts used for indexing hssp
icarus/db/hssp.i
2010/09/21: chembl Update for some schema changes in chembl release 06, and corrections for some hypertext links in chembl entry views
icarus/db/chembl_dm.i
icarus/db/chembl_mysql_schema.i
icarus/db/chembl_oracle_schema.i
icarus/db/chemblcompound_dm.i
icarus/db/chembltarget_dm.i
2010/09/20: prisma Change which allows the use of database dependencies for libraries which are updateded by mirroring, so they can be scheduled later in the update cycle
icarus/lion/prisma/checkDependentDbs.i
icarus/lion/prisma/localcopyPhase.i
icarus/lion/prisma/prismaCheckClasses.i
2010/09/10: kegg Support added to KEGGGENOME for KEYWORDS field
icarus/db/kegggenome.i
icarus/db/kegggenome.is
web/WEB-INF/jsp/views/kegggenomeentry/kegggenomeentry.jsp
2010/08/13: system Change to allow for the new ProteinModelPortal link in uniprot. Please note that the new versions of href.i and dbxref.i need to be merged with your copies of these files in SRSSITE
icarus/db/dbxref.i
icarus/db/href.i
2010/08/13: dbest Change to be more tolerant for non-standard characters in est names
icarus/db/dbest.is
2010/08/12: genecards Workaround for a data production problem in genecards 3.03 which left the PDB references in the ENSEMBL lines empty. We now collect the PDB references from the SWISSPROT line in the genecards files
icarus/db/genecards.i
icarus/db/genecards.is
2010/08/11: genecards system Update for genecards release 3.03. Please note that after unpacking the genecards tar archive, the data is now located in a subdirectory called old_website. We have modified the unpackcommand used by prisma to create symlinks to the directories in the old_website subdirectory, but if you are not using prisma, or if prisma has already downloaded and unpacked the file, you may have to create the relevant symlinks manually. Also not that the new copy of href.i needs to be merged with your copy of that file in SRSSITE
icarus/db/genecards.i
icarus/db/genecards.is
icarus/db/genecardstar.it
icarus/db/href.i
web/WEB-INF/jsp/views/genecardsentry/genecardsentry.jsp
2010/08/09: ensembl_mysql Updates for ensembl release 59
icarus/db/ensemblRDB.i
icarus/db/ensembl_compara_schema.i
icarus/db/ensembl_funcgen_schema.i
icarus/db/ensemblcore_schema.i
2010/08/05: imgt Change to allow for longer entrynames, as found in the latest release of imgt
icarus/db/imgt.i
2010/08/04: chebi Update for some minor schema changes in release 71 of ChEBI
icarus/db/chebi.i
icarus/db/chebi_schema.i
icarus/db/chebi_schema_mysql.i
2010/08/03: chembl Allow for some minor schema changes in ChEMBL release 5
icarus/db/chembl_mysql_schema.i
icarus/db/chembl_oracle_schema.i
2010/07/26: chebi Fix for a case-sensitive name assignement problems slipped in with the recent changes we made to make chebi work with mysql
web/WEB-INF/jsp/views/chebientry/chebientry.jsp
2010/07/21: prisma Change to allow for a %d placeholder in an updateCheckCommand
icarus/lion/prisma/checkRemoteFiles.i
2010/07/21: prisma Fix so prisma will not stop an update if a subdirectory is inaccessible during a recursive download
icarus/lion/prisma/remoteConnection.i
2010/07/21: drugbank Fix so we do not display a sequence box if there is no sequence to display
icarus/db/drugbank.is
2010/07/21: hmdb Fix to make sure that prisma will not remove other hmdb files when updating the hmdb sdf file
icarus/db/hmdbsdf.i
2010/07/21: system LibLoc and data-tool relation changes for EMBOSS 6.3. Please note that the changes need to be merged with your copy of these files in SRSSITE
icarus/db/srsdb.i
icarus/db/srsgen.i
2010/07/21: emboss Upgraded emboss support to emboss 6.3.0. For your convenience we make this upgrade also available as a separate tarball: EMBOSS6.3.0.tar.gz. Before applying this update make sure you read README.EMBOSS6.3.0
EMBOSS6.3.0.tar.gz
2010/07/20: chembl Added links between the differen chembl databases
icarus/db/chembl.i
icarus/db/chemblcompound.i
icarus/db/chembltarget.i
2010/07/20: system Fix for a problem when entering single digit date numbers in date fields in the SRS query form
web/javascript/srs_standard.js
2010/07/20: chebi system Modified our implementation of ChEBI so it can also work with mysql in addition to oracle. Please see the comments in chebi.i on how to select the database system. The new chebi.i file also contains some instructions on how to increase speed for entry display. Note that the new versions of srsdb.i and rdbaccess.i need to be merged with your copies of these files in SRSSITE
icarus/db/chebi.i
icarus/db/chebi_schema.i
icarus/db/chebidatamodel.i
icarus/db/rdbaccess.i
icarus/db/srsdb.i
2010/07/19: system Fix for a problem which would prevent the tools/export slider to be visible in Internet Explorer 8
web/javascript/slider.js
2010/07/13: geneseq Fix for a problem where data compression is used with geneseq files
icarus/db/geneseq.is
2010/07/13: reactome update for release 33 of Reactome (Note that without this update the reactome entrview will crash)
icarus/db/reactome.i
icarus/db/reactome_schema.i
2010/06/25: embl Correction for the indexing of the length of sequence features in databases in EMBL format
icarus/db/emblcommon.i
2010/06/24: kegg Fix for a display error for chemical structures in lcompound and ldrug when using the Marvin applet
icarus/db/lcommon.is
2010/06/18: system Added support for several new ensembl hypertext links in uniprot. Please note that the new version of href.i and dbxref.i will need to be merged with your copies of these files in SRSSITE
icarus/db/dbxref.i
icarus/db/href.i
2010/06/18: drugbank Another fix for stability problems when browsing through drugbank entries
icarus/db/drugbank.i
icarus/db/drugbank.is
web/WEB-INF/jsp/views/drugbankentry/drugbankentry.jsp
2010/06/18: chembl Some small schema changes for chembl release 4
icarus/db/chembl_mysql_schema.i
icarus/db/chembl_oracle_schema.i
2010/06/18: merops system updates for merops release 92
icarus/db/merops_schema.i
icarus/db/meropssmi.i
icarus/db/meropssmi_dm.i
icarus/db/srsgen.i
web/WEB-INF/jsp/views/meropssmientry/meropssmientry.jsp
2010/06/08: drugbank system Added a drugbanksdf helper database which allows for the export/display of drugbank chemical structures in sdf or molfile formats. Please note that the new version of srsdb.i needs to be merged with your copy of this file in SRSSITE
icarus/db/drugbank.is
icarus/db/srsdb.i
icarus/db/drugbanksdf.i
2010/06/08: chebi hmdb kegg system Added a view to export chemical structure data in sdf format. To use this view in an exporter please have a look at README.sdfexport. Please note that the new versions of view.i and loader.i need to be merged with your copy of this file in SRSSITE
icarus/db/chebi.i
icarus/db/hmdb.is
icarus/db/hmdbsdf.is
icarus/db/lcommon.is
icarus/db/loader.i
icarus/db/views.i
2010/06/08: system Added sdf exported and extended molfile exporter coverage
web/WEB-INF/config/srs/srs-export.xml
2010/06/04: chembl Workaround for a SRS bug causing a display problem in the chembl target view
icarus/db/chembl.i
icarus/db/chembl_dm.i
2010/06/01: uniref Change so we build the link between uniref50 and uniref90 in parts, in order to reduce memory usage
icarus/db/uniref90.i
2010/06/01: blast Fix for a bug when using external links in blast results
icarus/db/blast.is
2010/06/01: ensembl_mysql Updates for ensembl release 58
icarus/db/ensemblRDB.i
icarus/db/ensembl_compara_schema.i
icarus/db/ensembl_funcgen_schema.i
2010/05/28: chembl system A reorganization of our intergration of ChEMBL. The main chembl database is now renamed and called "chemblbioactivity", giving access to the bioactivity results. We added a chemblcompound and chembltarget database for easy access to the compounds used and targets tested in ChEMBL. Please note that the new version of srsdb.i needs to be merged with your copy of this file in SRSSITE, and that you also need to update concpets.i (also in SRSSITE)
icarus/db/chembl.i
icarus/db/chembl.it
icarus/db/chembl_dm.i
icarus/db/srsdb.i
web/WEB-INF/jsp/views/chemblentry/chemblentry.jsp
icarus/db/chemblcompound.i
icarus/db/chemblcompound_dm.i
icarus/db/chembltarget.i
icarus/db/chembltarget_dm.i
web/WEB-INF/jsp/views/chemblentry/chemblcompoundentry.jsp
web/WEB-INF/jsp/views/chemblentry/chembltargetentry.jsp
2010/05/28: system drugbank entrezgene go_mysql Added some new concepts (Gene, Small Molecule), which should make it easier for your users to find certain databases. Also added new cocepts to some databases. Note that the new concepts.i file should be merged with your copy of this file in SRSSITE.
icarus/db/concepts.i
icarus/db/drugbank.i
icarus/db/entrezgene.i
icarus/db/gogeneproducts.i
2010/05/21: emboss Added colourps for the relevant tools, and moved non-sequence input options to PRIM_OPTS
icarus/lion/emboss/scripts/acd2ica.i
2010/05/21: emboss Change so the mandatory pattern option is more prominently displayed on the launch pages for fuzzpro, fuzznuc and fuzztran
icarus/lion/emboss/fuzznuc.i
icarus/lion/emboss/fuzzpro.i
icarus/lion/emboss/fuzztran.i
2010/05/21: system interpro iprmatches Updated, added and fixed various hypertext links for interpro and iprmatches. Please note that the new version of href.i needs to ne merged with your copy of that file in SRSSITE
icarus/db/href.i
icarus/db/interpro.is
icarus/db/iprmatches.is
2010/05/21: chembl update for some schema changs in release 3 of chembl
icarus/db/chembl_mysql_schema.i
icarus/db/chembl_oracle_schema.i
2010/05/18: blast fasta Added a button in the blast graphical view which allows you to directly retrieve the sequences found by a blast run. Please only apply this update when you are using srs8.3.0.4 or later
web/WEB-INF/jsp/views/blastentry/blastgraphic.jsp
2010/05/18: system Several fixes neede for the SRS8.3.0.4 patch release - note that you need to install these changed files in addtion to the patch release itself
web/WEB-INF/jsp/views/displayoptions_hiddenfields.jsp
web/WEB-INF/jsp/views/displayoptions_reportpanel.jsp
web/WEB-INF/jsp/views/slider.jsp
2010/05/13: genecards system Added support for the new LSDB and EPITOMICS lines in genecards. Please note that the new version of href.i needs to be merged with your copy of this file in SRSSITE
icarus/db/genecards.i
icarus/db/genecards.is
icarus/db/href.i
web/WEB-INF/jsp/views/genecardsentry/genecardsentry.jsp
2010/05/13: drugbank Fix for some stability problems when browsing through drugbank entries
icarus/db/drugbank.i
icarus/db/drugbank.is
2010/05/07: kegg system Added a field to search lcompound by pubchem sid. After applying this update you will have to index the new fields. Please note that the new version of srsgen.i needs to be merged with your copy of this file in SRSSITE
icarus/db/lcompound.i
icarus/db/lcompound.is
icarus/db/srsgen.i
2010/05/07: kegg system genbank embl ddbj refseq uniprot imgt ipi hmdb drugbank Added new views which allows for the export of references from the major sequence databases in a format suitable for reference manager software, and added a view which allows for the export of chemical structures as molfile. Please note that the new versions of views.i and loader.i need to be merged with your copy of this file in SRSSITE
icarus/db/lcommon.is
icarus/db/loader.i
icarus/db/views.i
icarus/db/seqreferences.il
2010/05/07: uniprot Corrected an error with browser display of uniprot xml
icarus/db/uniprotxml.il
2010/05/07: blast Fix for a display issue in pdf exports
icarus/db/blast.is
2010/05/07: embl uniprot ipi Fix for a problem with the parsing of volume numbers for some literature references
icarus/db/embl.is
icarus/db/swissprot.is
2010/05/07: drugbank hmdb Improved handling of page numbers when parsing literature references
icarus/db/drugbank.is
icarus/db/hmdb.is
2010/05/07: genbank embl ddbj refseq uniprot imgt ipi genpept Removed a spurious single quote from the insdseq xml output when it is displayed as a view in SRS
icarus/db/insdseqxml.il
2010/05/07: kegg latest version of the kegg species mapping file. Note that if you use prisma to keep your data up-to-date prisma will regenerate this file when appropriate
icarus/db/kegg_species.i
2010/05/04: system Added support for the new ucd-2dpage link in uniprot. Please note that you will hevato merge the new version of dbxref.i and href.i with your copies of these files in SRSSITE
icarus/db/dbxref.i
icarus/db/href.i
2010/05/04: genecards Change so prisma will pick upda the latest version of the genecards tar archive
icarus/db/genecardstar.it
2010/05/04: drugbank Changed the PDB field in drugbank to use "pid" as short name - to avoid an index file name collision between the durgbank pdb field and the link indices between drugbank and pdb. After applying this update, please index the "pid" field for drugbank, and the link between pdb and drugbank
icarus/db/drugbank.i
2010/04/28: chebi chembl drugbank hmdb kegg Added support for the use of JChemPaint for the display of chemical structures. See README.applets for more information
icarus/db/chebidatamodel.i
icarus/db/chembl_dm.i
icarus/db/drugbank.i
icarus/db/drugbank.is
icarus/db/hmdb_datamodel.i
icarus/db/hmdbsdf.is
icarus/db/lcommon.is
web/WEB-INF/jsp/views/drugbankentry/drugbankentry.jsp
2010/04/09: medline system Added a new view which allows for the display and export pf medline data in medline (text) format. Please note that the new srsgen.i file will have to be merged with your copy of that file in SRSSITE
icarus/db/medline.i
icarus/db/medline.is
icarus/db/medlinecommon.i
icarus/db/medlinenew.i
icarus/db/medlinerelease.i
icarus/db/medlineupdates.i
icarus/db/srsgen.i
icarus/db/medlineformat.il
2010/04/06: kegg Added a synonym finder for drug names from the KEGG drug database
icarus/db/ldrug.i
icarus/db/ldrug.is
2010/03/29: system Added support for the new conoserver, genolist and mint links in uniprot. Please note that the new versions of dbxref.i and href.i need to be merged with your copies of these files in SRSSITE
icarus/db/dbxref.i
icarus/db/href.i
2010/03/29: prisma Fix for a daylight saving time problem (Dates would be one day out of sync with their day names) with the calendar in the prisma report.
icarus/lion/prisma/generateCalendar.i
2010/03/10: ensembl_mysql Changes for release 57 of ensembl
icarus/db/ensemblRDB.i
icarus/db/ensembl_compara_schema.i
icarus/db/ensembl_funcgen_schema.i
icarus/db/ensemblcore_schema.i
2010/03/05: system uniprot ipi Added support for the new SUPFAM, ProtClustDB and EuPathDB links in uniprot. Please note that you will have to merge the new versions of href.i and dbxref.i with your copies of these files in SRSSITE
icarus/db/dbxref.i
icarus/db/href.i
icarus/db/swissprot.is
2010/03/03: genpept Change to allow for the fact that genpept is now distributed as multiple files (the single file available before has become too large to handle for the genpept ftp server)
icarus/db/genpeptrelease.it
2010/03/02: system chembl Added support for chembl (both oracle and mysql versions). Please read the comments in chembl.i for more information. Note that the new versions of srsgen.i and rdbaccess.i need to be merged with your copies of these files in SRSSITE
icarus/db/rdbaccess.i
icarus/db/srsdb.i
web/WEB-INF/jsp/views/chemblentry/chemblentry.jsp
icarus/db/chembl.i
icarus/db/chembl.it
icarus/db/chembl_dm.i
icarus/db/chembl_mysql_schema.i
icarus/db/chembl_oracle_schema.i
2010/03/01: chebi Fix for a problem drawing the ontology image caused by a change in ID for the root element of the ontology
icarus/db/chebidatamodel.i
2010/02/17: ccds Change to allow for a change in filenames on the download site for CCDS
icarus/db/ccds.is
icarus/db/ccdsnuc.it
2010/02/17: system kegg Change to allow for new fields (pathway, module, disease) in the kegg orthology database. Note that the new href.i and srsgen.i files need to be merged with your copy in SRSSITE
icarus/db/href.i
icarus/db/keggdisease.i
icarus/db/keggorthology.i
icarus/db/keggorthology.is
icarus/db/srsgen.i
web/WEB-INF/jsp/views/keggorthology/keggorthologyentry.jsp
2010/02/17: srscheck prisma Fixes for several problems with non-standard link names
icarus/workflows/linkPhase.i
icarus/workflows/moveIndicesPhase.i
2010/02/15: cath hmdb system Moved the definition for the PDB field from cath.i to srsgen.i, so it can be shared with other databases (like hmdb)
icarus/db/cath.i
icarus/db/hmdb.i
icarus/db/srsgen.i
2010/02/12: fasta Small fix needed for correct html linking in fasty results
icarus/db/fasta.is
2010/02/11: kegg system Important change for the kegg genome database. Please see README.KEGGGENOME for full details. Note that the new verson of href.i needs to be merged with your copy of that file in SRSSITE
icarus/db/genKeggSpecies.i
icarus/db/href.i
icarus/db/kegg_species.i
icarus/db/kegggenome.i
icarus/db/kegggenome.is
web/WEB-INF/jsp/views/kegggenomeentry/kegggenomeentry.jsp
2010/02/10: fasta Added a description field to the results databases for the fasta programs
icarus/db/fasta.is
icarus/db/fastacommon.i
icarus/db/nfasta.i
icarus/db/ssearch.i
2010/02/10: system kegg Added support for the new Kegg Disease dataset. Note that the changes in href.i, srsgen.i, srsdb.i and concepts.i need to be merged with your copies of these files in SRSSITE. concepts.i now contains a new top-level concept for diseases
icarus/db/concepts.i
icarus/db/href.i
icarus/db/srsdb.i
icarus/db/srsgen.i
icarus/db/keggdisease.i
icarus/db/keggdisease.is
web/WEB-INF/jsp/views/keggdiseaseentry/keggdiseaseentry.jsp
2010/02/02: ccds Correction for the command which extracts the release number for ccdsprot
icarus/db/ccdsprot.it
2010/02/02: kegg Some changes to improve display speed for lcompound entries (especially those which have low accession numbers which typically are involved in a large number of reactions). After applying this update you will have to build loaderCaches for lreaction, lenzyme and lglycan. srscheck/prsima will do this, but if you prefer to do it manually, use commands like "srsbuild -f id -ldrCache ".
icarus/db/lcommon.is
icarus/db/lenzyme.i
icarus/db/lglycan.i
icarus/db/lreaction.i
2010/02/01: pdb Change to speed up the display of pdb data in pdbml format in a web browser
icarus/db/pdbml.il
2010/01/27: go_mysql Change for the latest version of GO (mysql version). The updated file is compatible with earlier versions. Note that the data file containing the mysql dump for this is now called go_YYYYMMDD.seqdb-data.gz and no longer go_YYYYMMDD.seqdblite-data.gz.
icarus/db/gotermdatamodel.i
2010/01/26: system uniprot ipi Added support for new db link in Uniprot, to eggNOG. Note that the new versions of href.i and dbxref.i need to be merged with your copies of those files in SRSSITE
icarus/db/dbxref.i
icarus/db/href.i
icarus/db/swissprot.is
2010/01/26: genecards Correction for the prisma command which sets the release number of genecards after an update
icarus/db/genecards.it
2010/01/21: hmdb Added support for the new Secondary Accession Number field in hmdb. After applying this fix, you will have to index this new field
icarus/db/hmdb.i
icarus/db/hmdb.is
web/WEB-INF/jsp/views/hmdbentry/hmdbentry.jsp
2010/01/21: unigene Re-introduced the exp and rexp fields for unigene, as these fields have re-appeared in the data. After applying this update you will have to index these two fields
icarus/db/unigene.i
icarus/db/unigene.is
web/WEB-INF/jsp/views/unigeneentry/unigeneentry.jsp
2010/01/15: kegg Added support for the new INTERACTION line in the kegg drug database. After applying this update, please re-index ldrug
icarus/db/lcommon.is
icarus/db/ldrug.i
icarus/db/ldrug.is
web/WEB-INF/jsp/views/ldrugentry/ldrugentry.jsp
2010/01/15: medline The 2010 release of medline contains a newly structured Comments and Correction section. We have now taken advantage of this to add a Comments subentry for medline, which allows searching by pubmed id and comment type (retraction, comment, citation etc). After applying this update you will have to re-index the medline databases.
icarus/db/medline.i
icarus/db/medline.is
icarus/db/medlinecommon.i
icarus/db/medlinenew.i
icarus/db/medlinerelease.i
icarus/db/medlineupdates.i
web/WEB-INF/jsp/views/medlineentry/medlineentry.jsp
2010/01/11: genecards Change to make sure that prisma will download the correct tar archive for genecards
icarus/db/genecardstar.it
2010/01/06: system kegg Change to allow for the new DISEASE line in the Kegg gene databases. After applying this update please index the new disease field. Please note that the new href.i file needs to be merged with your copy of that file in SRSSITE
icarus/db/href.i
icarus/db/kegggenes.i
icarus/db/kegggenes.is
icarus/db/kegggenes_aa.i
icarus/db/kegggenes_na.i
web/WEB-INF/jsp/views/kegggenesentry/kegggenesentry.jsp
2009/12/22: system Added support for new db link in Uniprot, to ArachnoServer. Note that the new versions of href.i and dbxref.i need to be merged with your copies of those files in SRSSITE
icarus/db/dbxref.i
icarus/db/href.i
2009/12/18: genecards system Updates for release 2.41.1 of genecards. Please note that if you use prisma to keep your databases up to data, prisma will download the wrong tar archive if you do no apply these changes. If prisma has already downloaded the wrong tar archive, remove the Genecards.tar.gz file from the data directory to force prisma to download it again. Please note that the updated version of href.i needs to be merged with your copy of that file in SRSSITE
icarus/db/genecards.i
icarus/db/genecards.is
icarus/db/genecardstar.it
icarus/db/href.i
web/WEB-INF/jsp/views/genecardsentry/genecardsentry.jsp
2009/12/17: system Added support for new db link in Uniprot, to InParanoid. Note that the new versions of href.i and dbxref.i need to be merged with your copies of those files in SRSSITE
icarus/db/dbxref.i
icarus/db/href.i
2009/12/16: chebi Allow for a small schema change in release 63 of CheBI
icarus/db/chebi_schema.i
2009/12/15: reactome Update for some schema changes in release 31 of Reactome
icarus/db/reactome_schema.i
2009/12/14: kegg To allow for the increasing size of kegggenes we changed the link index between kegggenes and taxonomy so it is build in parts
icarus/db/kegggenes_aa.i
icarus/db/kegggenes_na.i
2009/12/10: pdb system Added two new views to allow for the export of pdb data in pdbml (xml) and mmcif format. This uses two new databases (pdbml and pdbcif, hidden from the end user) for which you will have to download and install the data (or use prisma). If you do not want to provide these export, simply do no enable these new libraries. Note that the new version of srsdb.i should be merged with your copy in SRSSITE
icarus/db/pdb.i
icarus/db/srsdb.i
web/WEB-INF/jsp/views/pdbentry/pdbentry.jsp
icarus/db/pdbcif.i
icarus/db/pdbcif.il
icarus/db/pdbcif.is
icarus/db/pdbml.i
icarus/db/pdbml.il
icarus/db/pdbml.is
2009/12/10: prisma srscheck Fix for a problem where SRS or prisma has problems linking/removing/installing datafiles where the file names contain non standard characters. Note that this not cover cases where the filename contains a ?, *, [, ] or single quote
icarus/lion/prisma/localcopyPhase.i
icarus/lion/prisma/movePrismaData.i
icarus/workflows/coreCheckClasses.i
icarus/workflows/moveData.i
icarus/workflows/srsCheckMain.i
2009/12/09: system merops Added support for the merops database. Please make sure that you read the remarks in meropspro.i before adding this dataset. Also note that the new versions of href.i, srsdb.i, srsgen.i, rdbaccess.i and concepts.i need to be merged with your copies of these files in SRSSITE
icarus/db/concepts.i
icarus/db/href.i
icarus/db/rdbaccess.i
icarus/db/srsdb.i
icarus/db/srsgen.i
icarus/db/merops.it
icarus/db/merops_schema.i
icarus/db/meropscommon_dm.i
icarus/db/meropsfam.i
icarus/db/meropsfam_dm.i
icarus/db/meropspro.i
icarus/db/meropspro_dm.i
icarus/db/meropsseq.i
icarus/db/meropsseq_dm.i
icarus/db/meropssmi.i
icarus/db/meropssmi_dm.i
web/WEB-INF/jsp/views/meropsfamentry/meropsfamentry.jsp
web/WEB-INF/jsp/views/meropsproentry/meropsproentry.jsp
web/WEB-INF/jsp/views/meropsseqentry/meropsseqentry.jsp
web/WEB-INF/jsp/views/meropssmientry/meropssmientry.jsp
2009/12/09: kegg Small change to prevent a parsing error with the new map07222 entry in the kegg pathway database
icarus/db/pathway.is
icarus/db/pathwayxml.is
2009/12/09: kegg Update for the kegg species mapping file. Note that if you use prisma to maintain your databases, this file will be generated automatically by prisma
icarus/db/kegg_species.i
2009/12/08: kegg system Added an option for export in kgml and biopax format for the pathway database. This requires the enabling of the new pathwaykgml and pathwaybiopax databases, and download of the relevant data. If you have prisma the data download is handled by the pathwaybiopaxtar and pathwaykgmltar databases. If you do not want to provide these export options, simply do not enable these databases. Note that the new version of srsdb.i needs to be merged with your copy of this file in SRSSITE
icarus/db/pathway.i
icarus/db/pathwaytar.it
icarus/db/srsdb.i
icarus/db/pathwaybiopax.i
icarus/db/pathwaykgml.i
icarus/db/pathwayxml.il
icarus/db/pathwayxml.is
2009/12/08: pfam Change needed to build read-links for pfamc
icarus/db/pfam.is
2009/12/07: prisma Added an extra safety in our new method of estimating uncompressed file sizes to prevent problems when files grow a lot between releases
icarus/lion/prisma/checkRemoteFiles.i
2009/12/07: prisma Fix for an access problem for the geneseq download site
icarus/lion/prisma/remoteConnection.i
2009/12/07: refseq lowered the part-size used for indexing refseqrelease in parts to allow for the large differences in content between different datafiles
icarus/db/refseqrelease.i
2009/12/04: prisma srscheck Fixed a problem with building links for databases with mixed case database names
icarus/lion/prisma/moveLibs.i
icarus/lion/prisma/setReportPhase.i
icarus/workflows/linkPhase.i
2009/12/04: prisma Some improvements to the usage report: we make clearer on which nodes failures occur (these node names are now in red), and we now display all failures (previously we only displayed them if they had a runtime of more than one minute). Note that short processes which failed may still be invisible as they can be hidden by subsequent successfull processes in the graph
icarus/lion/prisma/cpuslots.il
2009/12/03: dbsnp dbsts drugbank entrezgene enzyme genecards go_xml hmdb homologene kegg omim system uniprot Added a new "AllNAmes" group field which allows a user to use a single search for all name type fields, like names, synonyms, alternative names, symbols etc. Please merge the new version of srsgeni.i with your copy of that file in SRSSITE, and also re-index enzyme after applying this update
icarus/db/dbsnp.i
icarus/db/dbsts.i
icarus/db/drugbank.i
icarus/db/entrezgene.i
icarus/db/enzyme.i
icarus/db/genecards.i
icarus/db/go.i
icarus/db/hmdb.i
icarus/db/hmdbenzyme.i
icarus/db/homologene.i
icarus/db/lcompound.i
icarus/db/ldrug.i
icarus/db/lenzyme.i
icarus/db/lglycan.i
icarus/db/omim.i
icarus/db/srsgen.i
icarus/db/swisscommon.i
2009/12/03: pfam Changes for release 24 of pfam. If you have already installed that data release, please re-index all pfam databases after applying these parser updates
icarus/db/pfam.is
icarus/db/pfama.i
icarus/db/pfamc.i
2009/12/03: prisma Fix for a LONG to INT overflow which could cause wrong sizes/times to be reported in the usage reports
icarus/lion/prisma/printUsageReport.i
icarus/lion/prisma/prismaCheckClasses.i
2009/12/03: medline system Update for some small dtd changes in the 2010 release of medline. You shoukd preferably apply this update before you index the 2010 release, which is expected to become available mid December
icarus/db/medlinecommon.i
icarus/db/xml.il
2009/12/01: emboss Minor change to allow colour postscript output for EMBOSS tools that produce colour graphics
icarus/lion/emboss/charge.i
icarus/lion/emboss/dotpathn.i
icarus/lion/emboss/dotpathp.i
icarus/lion/emboss/epestfind.i
icarus/lion/emboss/hmoment.i
icarus/lion/emboss/pepinfo.i
icarus/lion/emboss/pepnet.i
icarus/lion/emboss/pepwheel.i
icarus/lion/emboss/plotorf.i
icarus/lion/emboss/prettyplotn.i
icarus/lion/emboss/prettyplotp.i
icarus/lion/emboss/syco.i
icarus/lion/emboss/tcode.i
icarus/lion/emboss/wobble.i
2009/11/27: system Parser update to include hyperlinks to phylomeDB and orthoDB in Uniprot
icarus/db/dbxref.i
icarus/db/href.i
2009/11/23: kegg system Added support for the new METABOLISM field in the kegg drug database. Please merge the new version of srsgen.i with your copy in SRSSITE
icarus/db/ldrug.i
icarus/db/ldrug.is
icarus/db/srsgen.i
web/WEB-INF/jsp/views/ldrugentry/ldrugentry.jsp
2009/11/23: interpro fix to permit parsing of 'Abstract' fields containing html layout markup
icarus/db/interpro.is
2009/11/19: kegg Fix for a problem which occurs if the sequence length is missing in the data
icarus/db/kegggenes.is
2009/11/18: chebi Update for release 62 of chebi, including support for the new Star field
icarus/db/chebi.i
icarus/db/chebi_schema.i
icarus/db/chebidatamodel.i
web/WEB-INF/jsp/views/chebientry/chebientry.jsp
2009/11/17: uniprot Following customer feedback we have changed the NCBI Taxon ID field from a numerical field to a string field, since there is really no need to search this field with numerical ranges.
icarus/db/swisscommon.i
2009/11/13: hmdb Correction to typo in printName attribute of Library definition
icarus/db/hmdbenzyme.i
2009/11/13: kegg minor fix to prevent intermittent parsing error in lglycan due to an uninitialized variable
icarus/db/lcommon.is
2009/11/09: dbsnp entrezgene go_xml homologene interpro iprmatches medline uniref system Added views to allow for data export for these databases in their native xml format, including dtd or xml schema references
icarus/db/dbsnp.i
icarus/db/entrezgene.i
icarus/db/go.i
icarus/db/homologene.i
icarus/db/interpro.i
icarus/db/iprmatches.i
icarus/db/medlinecommon.i
icarus/db/pubmedarticlesxml.il
icarus/db/unirefcommon.i
icarus/db/xml.il
2009/11/04: system uniprot ipi Added two new fields for uniprot, which allow the user to retrieve (or restrict searches to) complete proteomes by either orgainism name or ncbi taxonomy Id. Please note that the new version of general.it needs to be merged with your copy of this file in SRSSITE
icarus/db/general.it
icarus/db/swisscommon.i
icarus/db/swissprot.is
2009/11/03: prisma Fixed an issue with some proxies, and an error reporting issue which could cause a crash
icarus/lion/prisma/remoteConnection.i
2009/10/30: kegg Added support for the new literature references in the kegg orthology database. After applying this update, re-index keggorthology, and if you have medline, also build the link indices to medline
icarus/db/keggorthology.i
icarus/db/keggorthology.is
web/WEB-INF/jsp/views/keggorthology/keggorthologyentry.jsp
2009/10/30: ccds Change to allow for a difference in the layout of the human and mouse data for CCDS
icarus/db/ccds.is
2009/10/30: kegg Correction for the way authors are indexed/displayed for the kegg genome database
icarus/db/kegggenome.is
2009/10/30: geneseq genecards Small correction for the download directory used by prisma
icarus/db/aageneseqtar.it
icarus/db/genecardstar.it
icarus/db/nageneseqtar.it
2009/10/29: kegg fix for a problem with structure display in lcompound
icarus/db/lcompound.i
2009/10/27: drugbank entrezgene genecards homologene system Moved some field definitions from databases specific files to srsgen.i so they can be used by multiple databases. Please merge the new version of srsgen.i with your copy in SRSSITE
icarus/db/drugbank.i
icarus/db/entrezgene.i
icarus/db/genecards.i
icarus/db/homologene.i
icarus/db/srsgen.i
2009/10/27: hmdb system Some minor fixes for hmdb: removed a debug print from the data model script, fixed the hypertext link to BioCyc, and corrected an issue with the structure image files. Please merge the new href.i file with your copy in SRSSITE
icarus/db/hmdb.is
icarus/db/hmdb_datamodel.i
icarus/db/href.i
2009/10/22: entrezgene system Change to allow for a change in the way links to the reactome database are provided. Please note that the new href.i file needs to merged with your copy of that file in SRSSITE
icarus/db/entrezgene.is
icarus/db/href.i
2009/10/22: reactome Schema changes for release 30 of reactome
icarus/db/reactome_schema.i
2009/10/21: kegg Added a mechanism so SRS can deliver kegg images and molfiles directly via a http link instead of encoding them en sending them through the web services server. To use this, all you need to do is to link the kegg_images data directory to SRSROOT/web. This will only work if your tomcat installation has direct access to your data directories
icarus/db/lcommon.is
2009/10/21: drugbank Added links to medline, and some minor correction
icarus/db/drugbank.i
icarus/db/drugbank.is
2009/10/21: system hmdb Added support for the hmdb database. Please make sure that you read the remarks in hmdb.i before adding this dataset. Also note that the new versions of href.i, srsdb.i, srsgen.i and concepts.i need to be merged with your copies of these files in SRSSITE
icarus/db/concepts.i
icarus/db/hmdb.i
icarus/db/hmdb.is
icarus/db/hmdb_datamodel.i
icarus/db/hmdbenzyme.i
icarus/db/hmdbenzyme.is
icarus/db/hmdbsdf.i
icarus/db/hmdbsdf.is
icarus/db/hmdbspectra.i
icarus/db/href.i
icarus/db/srsdb.i
icarus/db/srsgen.i
web/WEB-INF/jsp/views/hmdbentry/hmdbentry.jsp
2009/10/21: ddbj embl genbank refseq Changed part sizes for the major sequence databases so less parts need to be build and merged. This should be suitable for most modern hardware configurations
icarus/db/ddbjrelease.i
icarus/db/ddbjwgs.i
icarus/db/emblnew.i
icarus/db/emblrelease.i
icarus/db/emblwgsnew.i
icarus/db/emblwgsrelease.i
icarus/db/genbanknew.i
icarus/db/genbankrelease.i
icarus/db/genbankwgs.i
icarus/db/refseqnew.i
icarus/db/refseqp.i
icarus/db/refseqpnew.i
icarus/db/refseqprelease.i
icarus/db/refseqrelease.i
icarus/db/ddbjnew.i
2009/10/21: prisma Implemented a better way of estimating the size of uncompressed datafiles, using older versions of those files (if available) as a template. This should ensure more evenly distributed part sizes when indexing large databases in parts
icarus/lion/prisma/checkRemoteFiles.i
2009/10/21: prisma Small change to correct a proxy setting for wgetPrisma
icarus/lion/prisma/remoteConnection.i
2009/10/21: kegg latest kegg species mapping file. Note that if you have prisma this file will be automatically re-generated when the kegg databases are updated
icarus/db/kegg_species.i
2009/10/19: pfam Allow for a new line in the pfamA data, and change the download location for the pfam databases to use ftp.sanger.ac.uk. Note that we do not yet download the hmm data for HMMER version 3, as we do not yet support that version
icarus/db/pfam.is
icarus/db/pfama.it
icarus/db/pfamb.it
icarus/db/pfamc.it
icarus/db/pfamhmm.it
icarus/db/pfamseed.it
2009/10/15: system Added support for the new genevestigator link in uniprot. Please note that the new dbxref.i and href.i need to be merged with your copies of those files in SRSSITE
icarus/db/dbxref.i
icarus/db/href.i
2009/10/14: kegg fix for a jsp coding error which would break the lcompound view
web/WEB-INF/jsp/views/lcompoundentry/lcompgeneral.jsp
2009/10/07: chebi kegg system Added support for the marvin chemical structure viewing applet for chebi, kegg compound and kegg drug database. See README.applets for information about marvin. Please note that the new version of srsgen.i needs to be merged with your copy of that file in SRSSITE
icarus/db/chebi.i
icarus/db/chebidatamodel.i
icarus/db/lcommon.is
icarus/db/lcompound.i
icarus/db/ldrug.i
icarus/db/srsgen.i
web/WEB-INF/jsp/views/chebientry/chebientry.jsp
web/WEB-INF/jsp/views/lcompoundentry/lcompgeneral.jsp
web/WEB-INF/jsp/views/ldrugentry/ldrugentry.jsp
2009/10/06: ensembl_mysql system There have been significant changes with ensembl release 56. Please see README.ensembl56 for full details
icarus/db/ensemblRDB.i
icarus/db/ensemblRDBconfig.i
icarus/db/ensembl_compara_schema.i
icarus/db/ensembl_funcgen_schema.i
icarus/db/ensemblaffy.i
icarus/db/ensemblaffymodel.i
icarus/db/ensemblaffymosquitomodel.i
icarus/db/ensemblcommon.i
icarus/db/ensemblcore_schema.i
icarus/db/ensembldatamodel.i
icarus/db/ensemblgene.i
icarus/db/ensemblmosquito.i
icarus/db/ensemblseq.i
icarus/db/ensembltranscript.i
icarus/db/rdbaccess.i
icarus/db/srsdb.i
icarus/lion/packages/ensemblRDB.ip
web/WEB-INF/jsp/views/ensemblaffyentry/affymosquitoentry.jsp
2009/10/02: entrezgene Added a test which checks if the entrezgene xml file is properly terminated. This will prevent prisma from moving the data online in case the conversion from ASN1 has failed, but the gene2xml program has exited cleanly
icarus/db/entrezgene.it
2009/09/17: refseq Change so prisma will not download the refseq wgs master record files, as these do not contain sequence information
icarus/db/refseqrelease.it
2009/09/16: dbsnp Fix for a problem with some links to refseq in the entryview for dbsnp
icarus/db/dbsnp.is
2009/09/15: refseq Change so we build the link between refseqrelease and refseqprelease in parts, as building the link in one part now requires more than 4GB of memory
icarus/db/refseqrelease.i
2009/09/14: system entrezgene Change to handle 12 digit refseq accession numbers in the transcript and products cartoon in the entrezgene entry view
web/WEB-INF/tags/geneproductimage.tag
2009/09/14: interpro Fix for a display problem with interpro entries which have embedded an CDATA tag in the abstract field
icarus/db/interpro.is
2009/09/14: entrezgene removed a spurious debug print statement from the entrezgene parser
icarus/db/entrezgene.is
2009/09/08: kegg Change to allow for the fact that the kegg drug database is now provided in a separate tar archive
icarus/db/kegg_images.i
2009/09/08: blast Small change to prevent a parsing error with some bl2seq output
icarus/db/bl2seq.is
2009/09/04: system Change to allow for the new STRING link in the uniprot DR lines. Please note that you wil have to merge the new dbxref.i and href.i files with your versions of these files in SRSSITE
icarus/db/dbxref.i
icarus/db/href.i
2009/08/28: genbank embl refseq ddbj imgt Changed the way we do hypertext links to refseq for coded_by features in refseqp - this should result in better performance when following that hypertext link
icarus/db/gbemblcommon.is
2009/08/28: system kegg Changes needed for the latest version of the kegg pathway database. There have been significant changes in the way references to other kegg databases are provided, and without this update these will not work in SRS. Note that the new pathway.is file is not backwards compatible with previous versions of the pathway data, so you will need to ensure that no old data is left in your pathway data directories (if you have SRS prisma, prisma will do that automatically). Please note that the new href.i file needs to be merged with your copy of that file in SRSSITE. After applying this update you will have to re-index pathway, and rebuild links to other kegg databases.
icarus/db/href.i
icarus/db/pathway.i
icarus/db/pathway.is
2009/08/27: system embl genbank ddbj uniprot Change to add html names to references, so we can refer/link to them in entryviews
web/WEB-INF/tags/referencetable.tag
2009/08/24: kegg Change so we no longer try to extract gif image files from the pathway tar archive, as pathway has now fully switched to png images
icarus/db/pathwaytar.it
2009/08/24: dbsts Corrected a misconfigured sort parameter for the source fields in dbsts
icarus/db/dbsts.i
2009/08/24: drugbank Correction for an error in the display of target names
web/WEB-INF/jsp/views/drugbankentry/drugbankentry.jsp
2009/08/24: prisma srscheck Implemented a new way of removing partial index files after index merging, in order to prevent performence problems due to NFS congestion
icarus/lion/prisma/prismaCheckMain.i
icarus/workflows/buildPhase.i
icarus/workflows/linkPhase.i
icarus/workflows/srsCheckMain.i
2009/08/21: drugbank Small change so the PDB field in drugbank uses a field definition available in srsgen.i
icarus/db/drugbank.i
2009/08/17: system drugbank Added support for the DrugBank database. For SRS we have configured this as two databases: drugbank, which contains the drug information, and drugbanktarget, which gives information about the targets for the drugs (and their protein sequences). Please ensure that you merge the new version of srsdb.i, srsgen.i, href.i and concepts.i with your copies of these files in SRSSITE
icarus/db/concepts.i
icarus/db/drugbank.i
icarus/db/drugbank.is
icarus/db/href.i
icarus/db/srsdb.i
icarus/db/srsgen.i
web/WEB-INF/jsp/views/drugbankentry/drugbankentry.jsp
2009/08/17: genbank refseq ddbj Correction for a wrongly configured setting for sorting by moleculetype in databases in GenBank format
icarus/db/genbankcommon.i
2009/08/04: system Added hypertext link support for the new CTD reference in uniprot. Please note that the new dbxref.i and href.i files need to be merged with your copies in SRSSITE
icarus/db/dbxref.i
icarus/db/href.i
2009/07/29: unigene uniprot Change made to unigene, uniprot_swissprot and uniprot_trembl to fix problem with read links
icarus/db/unigene.i
icarus/db/uniprot_swissprot.i
icarus/db/uniprot_trembl.i
2009/07/28: reactome Update for release 29 of reactome
icarus/db/reactome.i
icarus/db/reactome_schema.i
web/WEB-INF/jsp/views/reactomeentry/intercept.jsp
web/WEB-INF/jsp/views/reactomeentry/notevent.jsp
web/WEB-INF/jsp/views/reactomeentry/referenceentity.jsp
2009/07/27: ensembl_mysql Updates for ensembl release 55
icarus/db/ensemblRDB.i
icarus/db/ensembl_compara_schema.i
icarus/db/ensemblcore_schema.i
2009/07/24: prisma Changed the getFastaSequence.i script so it will also construct contig sequences. This script is used by the built in fastaconverters in prisma
icarus/lion/prisma/getFastaSequence.i
2009/07/23: homologene system Moved the EntrezGeneId field defintion from homologene.i to to srsgen.i as it is also used for unigene. Please note that the new version of srsgen.i needs to be merged with your copy of srsgen.i in SRSSITE
icarus/db/homologene.i
icarus/db/srsgen.i
2009/07/23: unigene Removed the link between unigene and entrezgene we recently added, as that link was already defined in entrezgene.i
icarus/db/unigene.i
2009/07/21: system uniprot ipi Added support for new UCSC link in Uniprot, and updated links to Gene3D, ArrayExpress, GeneCards, PDBsum. Note that the new versions of href.i and dbxref.i need to be merged with your copies of those files in SRSSITE
icarus/db/dbxref.i
icarus/db/href.i
icarus/db/swissprot.is
2009/07/21: cath update for the new download site for cath data
icarus/db/cath.it
2009/06/24: uniprot Added a link for SRS 3D (visible if SRS3D is installed)
web/WEB-INF/jsp/views/swissentry/swissentry.jsp
2009/06/23: unigene Replaced the redundant/obsolete LocusLink field with a EntrezGeneId field, and removed some other fields which are no longer used. After applying this update you may want to rename the unigene loc indices to egid, and remove the pla, exp, rexp, gn and per indices
icarus/db/unigene.i
icarus/db/unigene.is
web/WEB-INF/jsp/views/unigeneentry/unigeneentry.jsp
2009/06/18: embl genbank refseq ddbj imgt genpept uniprot ipi system We have added two new views (TinySeqXML and INSDSeqXml) which allow for export of sequence data in XML format according to the INSD v.14 and NCBI TinySeq specifications. INSDSeqXML and TinySeqXML are available for EMBL, GenBank, DDBJ. RefSeq, RefSeqP and IMGT. TinySeqXML is further available for UniProt, GenPept and IPI. Note that the new versions of loader.i and views.i need to be merged with your copies of these files in SRSSITE
icarus/db/embl.is
icarus/db/emblcommon.i
icarus/db/gbemblcommon.i
icarus/db/gbemblcommon.is
icarus/db/genbank.is
icarus/db/genbankcommon.i
icarus/db/genpept.is
icarus/db/genpeptnew.i
icarus/db/genpeptrelease.i
icarus/db/insdseqxml.il
icarus/db/loader.i
icarus/db/swissprot.is
icarus/db/tinyseqxml.il
icarus/db/views.i
2009/06/11: hmmer Change to handle entry IDs which contain a ":"
icarus/db/hmmsearch.is
2009/06/10: hmmer Change for more reliable hypertext linking with hmmsearch hits
icarus/db/hmmsearch.is
2009/06/09: hmmer Change to keep hmmsearch hit names short
icarus/db/hmmsearch.is
2009/06/05: srscheck prisma Change to fix a problem with calculating partsizes if the partsize is set to very hight values (there was an error in th earlier fix)
icarus/workflows/linkPhase.i
2009/06/02: medline Change to handle a new layout used for some EC numbers in medline
icarus/db/medline.is
2009/06/01: system Added support for the new PMAP-CutDB link in uniprot. Note that the new versions of href.i and dbxref.i need to be merged with your copies of those files in SRSSITE
icarus/db/dbxref.i
icarus/db/href.i
2009/05/28: kegg Fixes for some inedxing errors for the kegg pathway database. After applying this update, please re-index pathway
icarus/db/pathway.is
2009/05/28: system kegg pathway Some more improvements for kegg pathway: added a field for glycan IDs, which are now also displayed and hypertext linked in the entry view. Fixed hypertext links in the new Metabolic Pathways entries. Made sure that png image files are unpacked from the pathway tar archive which prisma downloads. Please note that the new version of href.i needs to be merged with your copy in SRSSITE
icarus/db/href.i
icarus/db/pathway.i
icarus/db/pathway.is
icarus/db/pathwaytar.it
web/WEB-INF/jsp/views/pathwayentry/pathwayentry.jsp
2009/05/21: srscheck prisma Chanage to fix a problem with calculating partsizes if the partsize is set to very hight values
icarus/workflows/buildPhase.i
icarus/workflows/linkPhase.i
2009/05/21: srscheck prisma Improved the removal of symlinked index (and other srs files) from the off-line index directory. They could be left in the off-line index directory after a crash, and a subsequent srscheck or prisma run could try to install them in the online index directory, resulting in self-referential links. The removal of these links at the start of a run (during the check phase for a library) should prevent this.
icarus/workflows/coreCheckClasses.i
icarus/workflows/getSystemLibs.i
icarus/workflows/srsCheckMain.i
2009/05/14: geneseq Changes in the names used for the geneseq archives and megapatent files to ensure that both are downloaded. After applying this update it is recommended to remove all contents from the geneseq_tmp data directory, as not all files with old names will be automatically removed
icarus/db/aageneseq.i
icarus/db/aageneseqtar.it
icarus/db/nageneseq.i
icarus/db/nageneseqtar.it
2009/05/14: ensembl_mysql updates for ensembl release 54
icarus/db/ensemblRDB.i
icarus/db/ensembl_compara_schema.i
icarus/db/ensemblcore_schema.i
2009/05/11: prisma Fix for a problem when detecting a time window for installing new data
icarus/lion/prisma/checkTimeWindow.i
2009/05/11: dbsnp removed some debug print commands
icarus/db/dbsnp.is
icarus/db/dbsnplocation_dm.i
2009/05/08: system Added support for the new oma hypertext link in uniprot. Please note that the new version of dbxref.i and href.i need to be merged with your copies of these files in SRSSITE
icarus/db/dbxref.i
icarus/db/href.i
2009/04/30: pdb Change to handle a slight format change in the resolution remark line. After applying this fix, please re-index the resolution (res) field
icarus/db/pdb.is
2009/04/30: uniprot ipi Made sure that we do not insert a splice variant hypertext link for the actual variant which is used in the uniprot entry
icarus/db/swissprot.is
2009/04/23: prisma Change so we will not use a username and password for anonymous http access, as this can cause problems with some proxy servers
icarus/lion/prisma/remoteConnection.i
2009/04/23: prisma Fix for a problem where prisma would not run reformat commands with the -forceReformat option if there is nothing else to update
icarus/lion/prisma/prismaCheckMain.i
2009/04/16: system Added support for the new CAZy links in uniprot. Please note that the new dbxref.i and href.i files need to be merged with your copies of those files in SRSSITE
icarus/db/dbxref.i
icarus/db/href.i
2009/04/16: uniprot Changes to handle changes in the structure of the description line in UNIPROTVARSPLICE. We have also added a Organism and Gene field. After applying this update, please re-index uniprotvarsplice
icarus/db/uniprotvarsplic.i
icarus/db/uniprotvarsplic.is
2009/04/08: blast system Added a facility to provide hypertext links from a blast result to external (non-SRS) data. These need to be specified in the externalRefs list in localApplicationOptions.i, and a matching href definition should be provided in SRSSITE/href.i
icarus/db/blast.is
icarus/db/localApplicationOptions.i
2009/04/08: system uniprot Added support for data export using uniprot xml - see the notes in uniprotxml.i for details. Note that the new version of srsdb.i needs to me merged with your copy of that file in SRSSITE
icarus/db/srsdb.i
icarus/db/uniprot_swissprot.it
icarus/db/uniprot_trembl.it
icarus/db/uniprotxml.i
icarus/db/uniprotxml.il
icarus/db/uniprotxml.is
2009/04/07: geneseq Change for a more robust recognition of the start of an entry
icarus/db/geneseq.is
2009/04/06: prosite Fix to handle a situation in prositedoc where the entry contains two PDOC start lines
icarus/db/prositedoc.is
2009/04/06: geneseq fix for an issue with html display of gi values
icarus/db/geneseq.is
2009/04/02: fasta Change for better handling of fasta output without any hits found
icarus/db/fasta.is
2009/03/23: genecards system Added support for the new NOVUS line in genecards. Note that the new version of href.i needs to be merged with your copy of that file in SRSSITE
icarus/db/genecards.i
icarus/db/genecards.is
icarus/db/href.i
web/WEB-INF/jsp/views/genecardsentry/genecardsentry.jsp
2009/03/16: refseq embl genbank Added a hypertext link the the NCBI revision history in the modification date line
web/WEB-INF/jsp/views/dnadbentry/dnadbentry.jsp
2009/03/16: embl implemented a slightly more robust method of identifying the start of an entry in embl
icarus/db/embl.is
2009/03/12: ensembl_mysql update for release 53 of ensembl
icarus/db/ensemblRDB.i
icarus/db/ensembl_compara_schema.i
icarus/db/ensemblcore_schema.i
2009/03/11: prints A small parser change for release 39 of PRINTS, and added support for the latest version of Jalview
icarus/db/prints.i
icarus/db/prints.is
2009/03/11: clustalw Fix for a problem with the display of sequence names in table views, fixed for a problem where wrong sequence names could be assigned, and improved htmlization of sequence names
icarus/db/clustalw.is
2009/03/11: system some changes to improve linking back to SRS from JalView
icarus/db/srsgen.i
2009/03/10: fasta Fix for a parsing problem with fasta results from databases with more than 2.1 billion residues (this results in a slightly different Library line in the output)
icarus/db/fasta.is
2009/03/09: system Added hypertext link support for the new tcdb and pathway interaction references in uniprot. Note that you will have to merge the new copies of these files with your versions in SRSSITE
icarus/db/dbxref.i
icarus/db/href.i
2009/03/09: genbank refseq ddbj embl Changes to allow for the new DBLINK link in GenBank. Since this line will replace the existing PROJECT line, we have merged these two, and use the GenomeProject field for its content (this to keep the differences between the EMBL and GenBank implementations in SRS to a minimum. There is no need to re-index after applying this update.
icarus/db/genbank.is
icarus/db/genbankcommon.i
web/WEB-INF/jsp/views/dnadbentry/dnadbentry.jsp
2009/03/09: kegg Fix for an indexing problem with mass field of lcompound. After applying this fix, please rebuild the mass index with a command like srsbuild -f mass lcompound
icarus/db/lcompound.i
2009/03/04: rebase Change to ensure that each entry has a single value in the prototype field, so sorting by prototype is possible
icarus/db/rebase.is
2009/03/04: go_mysql Fix for a display issue with the march 2009 version of go
icarus/db/gotermdatamodel.i
2009/03/02: genbank refseq ddbj Fix for a display issue with complete refseqp entries
icarus/db/genbankcommon.i
2009/02/24: prisma Two major changes in prisma reporting. We now also report the results of the remote checking in the main prisma report page (previously this was in other files, making it difficult to see if there was a problem with access to remote sites), and we now sort the entries in the report so that failures and errors are at the top of the various lists, so you no longer have to scroll through the entire report to find problems
icarus/lion/prisma/PrismaToolsTestDb/prismaToolTest
icarus/lion/prisma/checkRemoteFiles.i
icarus/lion/prisma/dbSync.i
icarus/lion/prisma/printBuildPages.i
icarus/lion/prisma/printDownloadPages.i
icarus/lion/prisma/printLinkPages.i
icarus/lion/prisma/printMainPage.i
icarus/lion/prisma/printMovePages.i
icarus/lion/prisma/printPretransPages.i
icarus/lion/prisma/printReformatPages.i
icarus/lion/prisma/prismaCheckClasses.i
icarus/lion/prisma/prismadata.i
icarus/lion/prisma/prismastatus.is
icarus/lion/prisma/qualityReport/checkidsize.i
icarus/lion/prisma/qualityReport/checkindexsize.i
icarus/lion/prisma/qualityReport/indicesTest.i
icarus/lion/prisma/report_resources/images/check_compErrors.gif
icarus/lion/prisma/report_resources/images/check_completed.gif
icarus/lion/prisma/report_resources/images/check_failed.gif
icarus/lion/prisma/report_resources/images/check_white.gif
icarus/lion/prisma/report_resources/images/local_copy2_compErrors.gif
icarus/lion/prisma/report_resources/images/local_copy2_completed.gif
icarus/lion/prisma/report_resources/images/local_copy2_failed.gif
icarus/lion/prisma/report_resources/images/local_copy2_running.gif
icarus/lion/prisma/report_resources/images/local_copy2_skipped.gif
icarus/lion/prisma/report_resources/images/local_copy2_waiting.gif
icarus/lion/prisma/report_resources/images/local_copy2_white.gif
icarus/lion/prisma/setReportPhase.i
2009/02/23: genbank Change so prisma will no download the wgs master record files, as they do not contain sequence information
icarus/db/genbankwgs.it
2009/02/23: entrezgene Fix for a display issue with entrezgene entries for which there is no sequence cartoon
icarus/db/entrezgene_dm.i
2009/02/23: dbsts Workaround for a few parsing errors during indexing
icarus/db/dbsts.is
2009/02/19: clustalw Correction for a wrong setting for the input file name for nlcustalw
icarus/db/nclustalw.i
2009/02/17: entrezgene Fix for a problem where some transcript IDs were not displayed in the gene cartoon
icarus/db/entrezgene_dm.i
2009/02/13: system Change to handle some uniprot entries which have more than 4000 external library references (DR lines). No re-indexing is required, but the new version of srsgen.i needs to be merged with your copy of this file in SRSSITE
icarus/db/srsgen.i
2009/02/12: entrezgene Added a link to the new primary entry for obsolete entries, Extended the amount of information displayed in the refseq section, and fixed a few issues with the sequence cartoon
icarus/db/entrezgene.i
icarus/db/entrezgene.is
icarus/db/entrezgene_dm.i
web/WEB-INF/jsp/views/entrezgeneentry/entrezgeneentry.jsp
2009/02/11: system Changes to allow for the new links to Bgee and IPI in uniprotKB. Note that the new dbxref.i and href.i files need to be merged with your copies of these files in SRSSITE
icarus/db/dbxref.i
icarus/db/href.i
2009/02/11: prisma Fix for a problem where the usage history in the prisma reports would not display statistics (CPU etc) of previous prisma runs. Note that prisma will start to build up a usage history after applying this fix
icarus/lion/prisma/printUsageReport.i
2009/02/11: prisma fix for a spurious error thrown by rm during the archiving of prisma reports
icarus/lion/prisma/prismaArchive.i
2009/02/10: emboss Fix for a problem which results in situations where a 0 would be used instead of the default value for an option if the user has not set a value for that option
icarus/lion/emboss/consn.i
icarus/lion/emboss/consp.i
icarus/lion/emboss/edialignn.i
icarus/lion/emboss/edialignp.i
icarus/lion/emboss/infoalignn.i
icarus/lion/emboss/infoalignp.i
icarus/lion/emboss/matchern.i
icarus/lion/emboss/matcherp.i
icarus/lion/emboss/mergern.i
icarus/lion/emboss/mergerp.i
icarus/lion/emboss/needlen.i
icarus/lion/emboss/needlep.i
icarus/lion/emboss/prettyplotn.i
icarus/lion/emboss/prettyplotp.i
icarus/lion/emboss/showalignn.i
icarus/lion/emboss/showalignp.i
icarus/lion/emboss/stretchern.i
icarus/lion/emboss/stretcherp.i
icarus/lion/emboss/supermatchern.i
icarus/lion/emboss/supermatcherp.i
icarus/lion/emboss/watern.i
icarus/lion/emboss/waterp.i
icarus/lion/emboss/wordfindern.i
icarus/lion/emboss/wordfinderp.i
2009/02/09: iprmatches Change to make sure prisma will not download an erroneous datafile from the interpro download site
icarus/db/iprmatches.it
2009/02/04: genecards Fix for some issues with genecards images
icarus/db/genecards.i
icarus/db/genecards.is
web/WEB-INF/jsp/views/genecardsentry/genecardsexpression.jsp
2009/01/28: emboss Added applet based tree viewer for display of output from (Emboss/Embassy) Phylip programs. Note that the applet (forester.jar) must be obtained separately from http://www.phylosoft.org/atv/, and installed in SRSROOT/web/java
web/WEB-INF/jsp/views/emboss/embossTreeView.jsp
2009/01/28: quicktree Change so we remove ":" from sequence names, as these are causing problems with the tree viewer applet
icarus/db/quicktree.i
2009/01/28: clustalw correction for an issue with displaying muscle output where sequence identifiers contain "_" characters
icarus/db/clustalw.is
2009/01/27: system uniprot ipi Changes to allow for the new reference to brenda in UniProt - note that the new href.i and dbxref.i files need to merged with your copies of these files in SRSSITE
icarus/db/dbxref.i
icarus/db/href.i
icarus/db/swissprot.is
2009/01/20: blast fasta Change to improve the way sequences are extracted from blast and fasta results for further processing, for instance in seuqnece alignment programs
icarus/db/blast.is
icarus/db/fasta.is
2009/01/20: bind Change to reflect the fact that BIND is no longer available for download
icarus/db/bindcomplex.it
icarus/db/bindinteraction.it
icarus/db/bindpathway.it
2009/01/20: pfam Change to reflect the fact that swisspfam is no longer available for download
icarus/db/swisspfam.it
2009/01/20: system Changed the JalView view to use the latest version of jalview, which allows for correctly linking back of sequences in the view to the SRS installation. Note that you will need to obtain the new jalview applet from www.jalview.org, and install it in SRSROOT/web/java. Also note that the new version of srsgen.i needs to be merged with your version of this file in SRSSITE
icarus/db/srsgen.i
2009/01/20: clustalw Changed the way clustalw is run, so it no longer builds a list of sequences at the top of the output, but simply presents the plain clustalw output file. Increased support to version 2.0 (you will have to comment out some lines if you (want to) continue to use version 1.83, and made some changes to support the new JalView view
icarus/db/clustalw.i
icarus/db/clustalw.is
icarus/db/nclustalw.i
2009/01/20: Changed the way muscle is run, so it no longer builds a list of sequences at the top of the output, but simply presents a plain clustalw formatted output file and made some changes to support the new JalView view
icarus/db/nmuscle.i
icarus/db/pmuscle.i
2009/01/14: transfac Change to eliminate some parsing errors during link-indexing of the tffactor database
icarus/db/transfaccommon.is
2009/01/14: ensembl_mysql Changes for ensembl release 52
icarus/db/ensemblRDB.i
icarus/db/ensembl_compara_schema.i
icarus/db/ensemblcore_schema.i
2008/12/17: system Added support for PRIDE and GeneCards hypertext links in uniprot
icarus/db/dbxref.i
icarus/db/href.i
2008/12/16: genbank embl refseq ddbj imgt Change to allow for a PrimaryAccession (pac) index of more than 4GB. Following customer request we have also added a new TissueType field. Note that after applying this change all databases in GENBANK_FORMAT will become inaccesible and require a complete re-index, and that the TissueType field also needs to be indexed for REFSEQPRELEASE/REFSEQPNEW
icarus/db/gbemblcommon.is
icarus/db/genbankcommon.i
2008/12/09: embl genbank refseq ddbj imgt Change to allow for a PrimaryAccession (pac) index of more than 4GB. Following customer request we have also added a new TissueType field. Note that after applying this change all databases in EMBL_FORMAT will become inaccesible and require a complete re-index.
icarus/db/emblcommon.i
icarus/db/gbemblcommon.is
2008/12/09: geneseq Fix for a problem which was throwing a few parser errors each time aageneseq/nageneseq was indexed
icarus/db/geneseq.is
2008/12/09: srscheck prisma Fix for an issue where prisma sometimes would build link-indices on-line
icarus/workflows/linkPhase.i
2008/12/09: system removed an erroneous inclusion of ensembl_compara_48_schema.i from the ensembl compara LibLoc
icarus/db/srsdb.i
2008/12/08: biogrid dip intact mint Small change the to perl script for pre-processing intact data, so it wil not erroneously report that no interactions were found
icarus/db/intactProcessData.pl
2008/12/03: embl genbank refseq ddbj imgt Some changes to prevent memory problems when indexing large genomic entries: Smaller parts for refseq, and a more efficient parsing of the feature table, as full chromosome entries have well over a million features in the feature table
icarus/db/embl.is
icarus/db/gbemblcommon.is
icarus/db/genbank.is
icarus/db/refseqnew.i
icarus/db/refseqrelease.i
2008/12/01: geneseq FIx to make sure srs knows that the aageneseqtar is a helper library which should not be indexed
icarus/db/aageneseqtar.it
2008/11/28: iprmatches Fix for a problem in SRS83, where iprmactches hits would be displayed multiple times in the iprmatchesGraph and iprmatchesTable views
web/WEB-INF/jsp/views/iprmatchesentry/iprmatcheslist.jsp
web/WEB-INF/jsp/views/iprmatchesentry/iprmatchestable.jsp
2008/11/27: fasta system blast Fix for a problem (actually a crash) when trying to use the related information browser from a blast or fasta result displayed with the graphical homolgy view. Note that the new version of loader.i needs to be merged with your copy of this file in SRSSITE
icarus/db/fasta.is
icarus/db/loader.i
web/WEB-INF/jsp/views/blastentry/blastgraphic.jsp
2008/11/25: dbsnp Change needed to handle the increasing growth of dbsnp: The id index of the dbsnplocation database is now larger than 4GB, which requires a different file access mechanism. After applying this change, the current id index will become unreadable (causing disruption for the user), and you will have to re-index this database
icarus/db/dbsnplocation.i
2008/11/25: dbest Change needed to handle the increasing size of dbest. The comments field (cc) is now larger than 4GB, and the author (aut) field will be in the near future. After applying this update, the existing dbest_cc and dbest_aut indices will become unreadable. We would recommand to remove the existing dbest_cc.* and dbest_aut.* files and re-index. To minimize impact for your users, you could set the ignoreMissingIndices parameter in SRSICA/parameter.i to 1
icarus/db/dbest.i
icarus/db/dbest.is
2008/11/20: prisma Fix for a problem where in some cases a missing offline data directory could cause prisma to crash
icarus/lion/prisma/movePrismaData.i
2008/11/20: ensembl_mysql Update for Ensembl 51. Note that there is a small schema change which affects the way SRS displays proteins so make sure you apply this update at the same time you install the Ensembl 51 data
icarus/db/ensemblRDB.i
icarus/db/ensembl_compara_schema.i
icarus/db/ensemblcommon.i
icarus/db/ensemblcore_schema.i
icarus/db/ensemblproteinmodel.i
web/WEB-INF/jsp/views/ensemblproteinentry/proteinentry.jsp
web/WEB-INF/jsp/views/ensemblproteinentry/proteinrefs.jsp
2008/11/14: biogrid dip intact mint Fixed a problem with the uniprot references and made data pre-processing (we prcess the data using a perl script prior to indexing) more robust
icarus/db/intactProcessData.pl
icarus/db/intactdata.it
icarus/db/intactinteractor.i
2008/11/13: system prisma Changes to make maintenance easier by reducing the number of changes made to these files when ensembl, prisma or emboss are installed. In order to reduce the risk of system confusion about what changes have been made by these packages, we would recommend to first uninstall these packages by running "srspackage -remove srsprisma/emboss/EnsemblRD" (whatever is appropriate in your situation), update srsgen.i and srsdb.i (in you SRSSITE directory), and then reinstalling the packages. For prisma this is done by running "srspackage -install $SRSLION/packages/srsprisma.ip" (make sure you get the latest version of this file). For ensembl this is done by running "srspackage -install $SRSLION/packages/ensembl.ip". For emboss this is done by running "srssetup -emboss" - but see also the notes on upgrading to EMBOSS 6. After applying this update all these packages do is setting the enabled:y flag for the relevant libraries in srsdb.i file, and no changes are made to srsgen.i.
icarus/db/srsdb.i
icarus/db/srsgen.i
icarus/lion/packages/srsprisma.ip
2008/11/12: biogrid dip intact mint Change so prisma will not accidentally remove the active datafiles during a data update
icarus/db/intactProcessData.pl
icarus/db/intactexperiment.i
icarus/db/intactinteraction.i
icarus/db/intactinteractor.i
2008/11/12: transpath Corrections for some link names which might cause confusion when data is updated by prisma
icarus/db/transpath_gene.i
icarus/db/transpath_molecule.i
icarus/db/transpath_pathway.i
icarus/db/transpath_reaction.i
icarus/db/transpath_reference.i
2008/11/12: entrezgene Improvement in the way gene symbols are indexed - we were missing a few gene symbols which are located in an alternative location in the data
icarus/db/entrezgene.i
icarus/db/entrezgene.is
2008/11/12: emboss Upgraded emboss support to emboss 6.0.1. For your convenience we make this upgrade available as a separate tarball: EMBOSS6.0.1.tar.gz. Before applying this update make sure you read README.EMBOSS6
EMBOSS6.0.1.tar.gz
2008/11/12: system update tool package versions supported by SRS
icarus/db/packages.i
2008/11/11: prisma Added a new feature in prisma reports: the usage report will now contain a graph showing the usage of each cpu slot during a prisma run. This can be useful in locating bottlenecks during data processing
icarus/lion/prisma/printUsageReport.i
icarus/lion/prisma/prismaGui.i
icarus/lion/prisma/cpuslots.il
icarus/lion/prisma/report_resources/wz_tooltip.js
2008/11/11: prisma Added an option to runPrisma to ignore data move scheduling conditions (-ignoreMoveDataConditions), and improved verbosity indicating why prisma is waiting with moving data online
etc/runPrisma
icarus/lion/prisma/checkTimeWindow.i
2008/11/11: srscheck prisma Change so srscheck and prisma will remove symbolic links in the offline index directory when checking on a library. This will prevent the srsbuild process from writing to these links, and will also prevent these links being moved online, which could result in these files ending up being self-referential links
icarus/workflows/coreCheckClasses.i
2008/11/11: prisma fixes for some minor tool testing issues in prisma reports
icarus/lion/prisma/PrismaToolsTestDb/testdata.is
icarus/lion/prisma/PrismaToolsTestDb/testdb.i
icarus/lion/prisma/PrismaToolsTestDb/testdb/distmat.testdata
icarus/lion/prisma/PrismaToolsTestDb/testdb/hmm.testdata
icarus/lion/prisma/generateCalendar.i
icarus/lion/prisma/inspectClasses.i
icarus/lion/prisma/inspectReport.i
icarus/lion/prisma/qualityReport/toolTests.i
icarus/lion/prisma/srsinspect.i
icarus/lion/prisma/toolsTestSets.i
2008/11/10: genecards Change so genecards no longer relies on a linf/directory in SRSROOT/data to display images
icarus/db/genecards.is
2008/11/10: uniprot Change to ensure that the reldate.txt file is downloaded with uniprot_swissprot and uniprot_trembl
icarus/db/uniprot_swissprot.it
icarus/db/uniprot_trembl.it
2008/11/10: kegg system Change to make sure all kegg data is in sync with eachother (when prisma is used to keep the data up-to-date) - we no longer download the individual ligand sets (lenzyme, lcompound, ldrug, lglycan and lreaction), but use the tar archive we download to obtain the images for these datasets (kegg_images). Note that for this to work the off-line data directory for these datasets in srsdb.i needs to be set to the data directory used for the keggimages dataset. We also changed the way the images are retrieved so it is no longer necessary to have a kegg_images directory linked to SRSROOT/data (unless you do not have the keggimages database enabled)
icarus/db/kegg_images.i
icarus/db/lcommon.is
icarus/db/lcompound.is
icarus/db/lcompound.it
icarus/db/ldrug.is
icarus/db/ldrug.it
icarus/db/lenzyme.i
icarus/db/lenzyme.it
icarus/db/lglycan.is
icarus/db/lglycan.it
icarus/db/lreaction.is
icarus/db/lreaction.it
icarus/db/srsdb.i
2008/11/10: kegg Change to make sure we can handle some hidden files which may be present in the kegggenome tar archive
icarus/db/kegggenome.it
2008/11/10: dbest dbgss Fix for a problem where SRS might mistake gzipped datafiles for actual datafiles, and a fix for a problem where SRS could not build the link between the dbest and taxonomy databases
icarus/db/dbest.i
icarus/db/dbest.it
icarus/db/dbgss.i
icarus/db/dbgss.it
2008/11/10: kegg Latest kegg species mapping file. Note that it you have prisma, this file will be regenrated automatically when the kegggome database is updated
icarus/db/kegg_species.i
2008/11/10: geneseq Modification so prisma will also download the megapatent data with geneseq (comment out the relevant sections in [na]aageneseqtar.it if you do not want this), reorganised links so no more readlinks are build (the merge phase for this could cause problems on systems with filehandle restrictions). Note that with the addition of the megapatent data, we needed to change the structure of nageneseq indices. This will mean that after applying the updated icarus files, you will have to re-index nageneseq (preferably after first removing the old nageneseq indices
icarus/db/aageneseq.i
icarus/db/aageneseqtar.it
icarus/db/geneseq.is
icarus/db/nageneseq.i
icarus/db/nageneseqtar.it
2008/11/10: hmmer fasta userdna userprotein Some changes so prisma tool testing will not faile on these tools
icarus/db/hmmpfam.it
icarus/db/hmmsearch.it
icarus/db/ssearch.it
icarus/db/userdna.i
icarus/db/userprotein.i
2008/11/10: entrezgene added an alternative unpackcommand which strips out the xml indentation for entrezgene - this will save about 35% on diskspace, but will make the raw xml less readable. Edit the file to comment in/out the command you would like to use
icarus/db/entrezgene.it
2008/11/06: system Added support for nextbio and xenbase hypertext links in uniprot - note that the new versions of href.i and dbxref.i need to be merged with your copies of these files in SRSSITE
icarus/db/dbxref.i
icarus/db/href.i
2008/11/04: genecards system Changes for release 2.39 of GeneCards. Note that the new version of href.i needs to merged with your copy in SRSSITE
icarus/db/genecards.i
icarus/db/genecards.is
icarus/db/href.i
web/WEB-INF/jsp/views/genecardsentry/genecardsentry.jsp
2008/11/03: chebi Changes for release 29 of Chebi
icarus/db/chebidatamodel.i
2008/11/03: srscheck prisma Fix so prisma will correctly handle failures occurring during the merging of read-link indices
icarus/workflows/linkPhase.i
2008/10/16: uniprot ipi Fix for a problem with displaying subentry IDs
icarus/db/swissprot.is
2008/10/10: go_xml Small change to work around a dodgy data problem in the 20081005 release of go
icarus/db/go.is
2008/10/08: fasta Change to handle a small data output change between fasta3.5.3 and fasta3.5.4
icarus/db/fasta.is
2008/10/06: embl Fix so we do not download the tpa cumulative file ( we use the relevant sections instead ) . Note that for emblnew without emblnewfiles enabled, this also fixes a problem where the tpa/cumulative file was taking precendence over the main new/cumulative file, resulting in missing entries
icarus/db/emblnew.it
icarus/db/emblnewfiles.it
2008/10/02: system Added views for vectorNTI export to the distribution. Note that to enable export to vectorNTI functionality, you will have to comment in the relevant parts in web/WEB-INF/config/srs/srs-export.xml. The new versions of loader.i and views.i need to be merged with your versions of these files in SRSSITE
icarus/db/loader.i
icarus/db/views.i
icarus/lion/vectorNTI/genbankstyle.il
icarus/lion/vectorNTI/vectorNTI_AAGENESEQ.il
icarus/lion/vectorNTI/vectorNTI_DBEST.il
icarus/lion/vectorNTI/vectorNTI_EMBL.il
icarus/lion/vectorNTI/vectorNTI_FASTAGEN.il
icarus/lion/vectorNTI/vectorNTI_GENBANK.il
icarus/lion/vectorNTI/vectorNTI_GENPEPT.il
icarus/lion/vectorNTI/vectorNTI_NAGENESEQ.il
icarus/lion/vectorNTI/vectorNTI_PIR.il
icarus/lion/vectorNTI/vectorNTI_REFSEQP.il
icarus/lion/vectorNTI/vectorNTI_UNIEST.il
icarus/lion/vectorNTI/vectorNTI_UNIPROT.il
icarus/lion/vectorNTI/vectorNTI_UNISEQ.il
2008/10/02: prisma change so the prisma test databases no longer show up in the web interface
icarus/lion/prisma/PrismaToolsTestDb/testdb.i
2008/09/24: system kegg Added internal hypertext links to the kegg orthology database from pathway entries. Note that the new href.i file needs to be merged with your copy in SRSSITE
icarus/db/href.i
icarus/db/pathway.is
2008/09/23: blast fasta Added a direct hypertext link from the blast graphical view to the hit entry
icarus/db/blastgraphicdatamodel.i
2008/09/19: system embl genbank ddbj uniprot Added display of comment and consortium with references in the main sequence databases
web/WEB-INF/tags/referencetable.tag
2008/09/19: kegg Various changes for lenzyme - removed the no longer present motif and disease fields, and allow for better processing and display of the now highly structured reference field(s) - note that after this update you will have to re-index lenzyme
icarus/db/lenzyme.i
icarus/db/lenzyme.is
web/WEB-INF/jsp/views/lenzymeentry/lenzymeentry.jsp
2008/09/15: embl Change to allow for the TSA (Transcriptome Shotgun Assembly) section
icarus/db/embl.is
2008/09/15: chebi ensembl_mysql genecards go_mysql system Replaced hardcoded external hypertext links by proper Hlink references. Note that you will have to merge the new version of href.i with your copy of that file in SRSSITE
icarus/db/chebidatamodel.i
icarus/db/ensembldatamodel.i
icarus/db/genecards.is
icarus/db/gogenproddatam.i
icarus/db/href.i
2008/09/11: prints prosite rebase Change to suppress irrelevant output to STDERR when processing datafiles for emboss usage
icarus/db/prints.it
icarus/db/prosite.it
icarus/db/rebase.it
2008/09/11: embl Corrections for the annotated contig location and filenames used for deleted entries
icarus/db/emblnew.it
icarus/db/emblnewfiles.it
2008/09/10: kegg Changes to allow for the new PRDUCTS field in the kegg drug database
icarus/db/ldrug.i
icarus/db/ldrug.is
web/WEB-INF/jsp/views/ldrugentry/ldrugentry.jsp
2008/09/08: emboss Fix for an image display problem for the dan emboss tool
icarus/lion/emboss/dan.is
2008/09/04: prisma Fix for a problem where prisma would not honour all timewindows for data installation
icarus/lion/prisma/checkTimeWindow.i
2008/08/22: emboss Fix so showalign and remap will correctly use the colors specified by the user to color sequence regions
icarus/lion/emboss/remap.i
icarus/lion/emboss/showalignn.i
icarus/lion/emboss/showalignp.i
2008/08/22: system genbank embl refseq ddbj imgt some minor parser improvements
icarus/db/ftseq.is
icarus/db/gbemblcommon.is
icarus/db/genbank.is
2008/08/19: chebi Fix for a problem where SRS would not always retrieve the matching structure image from lcompound to be displayed with a chebi entry
icarus/db/chebidatamodel.i
2008/08/18: reactome Changes for release 25 of the reactome database. Note that we have changed the database name as used in the interaction with mysql to Reactome
icarus/db/reactome.i
icarus/db/reactome_schema.i
2008/08/13: pdb added a new field providing chain Ids (combining entry name and chain designation)
icarus/db/pdb.i
icarus/db/pdb.is
2008/08/12: uniprot Change to allow for a change in the header line in uniprot splice variant data (uniprotvarsplice)
icarus/db/uniprotvarsplic.is
2008/08/08: prisma Changes needed for correctly moving link indices online if there are multiple links between two databases
icarus/lion/prisma/moveLibs.i
2008/08/08: prisma Fix for a problem where prisma would not pick up an update scheduled to run on Sundays
icarus/lion/prisma/prismaCheckClasses.i
2008/08/08: prisma Some fixes for importing settings from older srs installations when installing Prisma
icarus/lion/prisma/importPrismaProperties.i
2008/08/07: system uniprot ipi Changes to handle the new format of the DE lines in uniprot. We have added new fields: Name, AltName,Contains, Includes and Flag, but have kept the old Description field in order to query the entire contents of the DE lines. We also added a new synonym finder which uses the Name and AltName fields. Note that the new srsgen.i file needs to be merged with your copy of that file in SRSSITE
icarus/db/srsgen.i
icarus/db/swisscommon.i
icarus/db/swissprot.is
icarus/db/uniprot.i
web/WEB-INF/jsp/views/swissentry/swissentry.jsp
2008/08/04: enzyme removed the disease (reference to omim) field, as it is no longer used
icarus/db/enzyme.i
icarus/db/enzyme.is
icarus/db/enzyme.it
web/WEB-INF/jsp/views/enzymeentry/enzymeentry.jsp
2008/07/29: ensembl_mysql Changes for release 50 of ensembl
icarus/db/ensemblRDB.i
icarus/db/ensembl_compara_schema.i
icarus/db/ensemblcore_schema.i
2008/07/29: uniprot ipi Changes needed to make sure we correctly link to the enzyme database with the new format of the uniprot description line. You may have to rebuild the links between uniprot_swissprot/trembl and enzyme after applying this update
icarus/db/swissprot.is
icarus/db/uniprot_swissprot.i
icarus/db/uniprot_trembl.i
2008/07/29: system Changes to allow for the new references to BindingDB in uniprot. Please note that you will need to merge href.i and dbxref.i with your copies of these files in SRSSITE
icarus/db/dbxref.i
icarus/db/href.i
2008/07/28: iprmatches fix for links to prodom entries in iprmatches
icarus/db/iprmatches.is
2008/07/02: kegg Added support for the new Source and Component fields in the kegg drugs database (ldrug)
icarus/db/ldrug.i
icarus/db/ldrug.is
web/WEB-INF/jsp/views/ldrugentry/ldrugentry.jsp
2008/07/02: chebi Update for small chebi schema change in release 46
icarus/db/chebi_schema.i
2008/06/24: genecards Change to allow for the mew MilliPore references in GeneCards
icarus/db/genecards.i
icarus/db/genecards.is
web/WEB-INF/jsp/views/genecardsentry/genecardsentry.jsp
2008/06/19: emboss Fix for a display problem with the feature files created by diffseq
icarus/lion/emboss/diffseq.is
icarus/lion/emboss/diffseqview.il
icarus/lion/emboss/diffseqn.i
icarus/lion/emboss/diffseqp.i
2008/06/19: emboss fix for an display issue when more than one sequence is submitted (note that sixpack will only work on the first sequence)
icarus/lion/emboss/sixpack.is
icarus/lion/emboss/sixpack.i
2008/06/18: blast Fix for a problem with the BlastLoader, which would result in missing values for Blast Evalue and Scores with this loader
icarus/db/blastcommon.i
2008/06/12: system Added support for the new hogenom and hovergen hypertext links in uniprot
icarus/db/dbxref.i
icarus/db/href.i
2008/06/09: prisma Fixed various minor issues with prisma reporting, and fixed links to the prisma documentation (the prisma 4.3 documention is included in the SRS8.3.0.1 patch release)
icarus/lion/prisma/decisionReport.i
icarus/lion/prisma/dumpTarget.i
icarus/lion/prisma/generateKey.i
icarus/lion/prisma/generateLinkReports.i
icarus/lion/prisma/inspectReport.i
icarus/lion/prisma/printBuildPages.i
icarus/lion/prisma/printDownloadPages.i
icarus/lion/prisma/printLinkPages.i
icarus/lion/prisma/printMainPage.i
icarus/lion/prisma/printMovePages.i
icarus/lion/prisma/printPretransPages.i
icarus/lion/prisma/printReformatPages.i
icarus/lion/prisma/printUsageReport.i
icarus/lion/prisma/prismaArchive.i
icarus/lion/prisma/prismaGui.i
icarus/lion/prisma/prismaGuiCal.i
icarus/lion/prisma/prismaPage.i
icarus/lion/prisma/prismatime.is
icarus/lion/prisma/tracePhase.i
2008/06/09: kegg fix for a problem with hypertext links from lenzyme to lcompound
icarus/db/lenzyme.is
2008/06/06: chebi Better checking for recursion when traversing the chebi ontology, so the drawing of the ontology graph does not end in a loop
icarus/db/chebidatamodel.i
2008/06/05: system Added some annotations related code. You will have to merge the new concept.i and srsgen.i with your copies of these files in SRSSITE. This update should be done at the same time as you install the 8.3.0.1 patch release
icarus/db/concepts.i
icarus/db/srsgen.i
2008/06/05: chebi Fixed some issues with the ontology tree displayed with chebi entries, and added colorcoding (with a legend) for the relationship between entitities
icarus/db/chebi.i
icarus/db/chebidatamodel.i
2008/06/02: ddbj embl genbank Change needed to cope with the increasing sizes of EMBLRELEASE, GENBANKRELEASE and DDBJRELEASE. After applying this update you will have to re-index the primary accession number (pac) field. It is important that you apply this change before you install the next (June 2008) full releases of these databases, as otherwise you will not be able to access all entries
icarus/db/ddbjrelease.i
icarus/db/emblrelease.i
icarus/db/genbankrelease.i
2008/06/02: ddbj Change to allow for a change in the directory structure of the DDBJ ftp site
icarus/db/ddbjnew.it
icarus/db/ddbjnewfiles.it
icarus/db/ddbjrelease.it
icarus/db/ddbjwgs.it
2008/06/02: pdbfinder Change to make sure that we can launch sequences from pdbfinder as input for analysis tools
icarus/db/pdbfinder.i
2008/06/02: system kegg Fixed a parsing issue with the description line in some entries, and changed the hypertext to kegggenes to use a srs83 style url. Note that you will have to merge the updated href.i file with your copy of that file in SRSSITE
icarus/db/href.i
icarus/db/pathway.is
2008/05/27: system Change needed to handle the new links to the Candidia Genome Database in uniprot. Please merge the changed dbxref.i file with your copy in SRSSITE
icarus/db/dbxref.i
2008/05/27: system reformatted srsgen.i so it matches the layout of srsgen.i after the installation of emboss tools. There are no functional changes
icarus/db/srsgen.i
2008/05/22: srscheck prisma Changes needed to handle cases where there are multiple links defined between two libraries
icarus/workflows/linkPhase.i
2008/05/14: hmmer Improvements for the HMMPfam tool - a view showing description, Evalue and Score, and added a searchable description field
icarus/db/hmmpfam.is
icarus/db/hmmpfam.i
2008/05/13: fasta Change needed to handle some cases of output from fasta3.5
icarus/db/fasta.is
2008/05/13: system Change so the Sequence Version field (sv) is also included in an All Identifier search. Note that you will have to merge the updated srsgen.i file with your copy in SRSSITE
icarus/db/srsgen.i
2008/05/13: blast Change to make sure blast honours a user request to use ungapped aligments
icarus/db/blastn.i
icarus/db/blastp.i
icarus/db/blastx.i
icarus/db/tblastn.i
icarus/db/tblastx.i
2008/05/13: go_mysql Changed linkidentifiers for some databases. Without this change recent version of gogeneprodcts will not link correctly to uniprot
icarus/db/gogeneproducts.i
2008/05/12: kegg system Added support for the new ANNOTATION line in kegggenome. Note that you will have to merge the new srsgen.i file with your copy of this file in SRSSITE
icarus/db/kegggenome.i
icarus/db/kegggenome.is
icarus/db/srsgen.i
web/WEB-INF/jsp/views/kegggenomeentry/kegggenomeentry.jsp
2008/05/12: intact uniprot Changed the names of the uniprot splice variants database and the various intact databases to all uppercase as mixed case databases names can cause problems when doing databases updates with prisma
icarus/db/intactexperiment.i
icarus/db/intactinteraction.i
icarus/db/intactinteractor.i
icarus/db/uniprotvarsplic.i
2008/05/12: kegg latest update for kegg species mapping file
icarus/db/kegg_species.i
2008/05/07: genbank embl refseq ddbj imgt system Added special handling for Korean patent numbers when including a hypertext link to the European patent Office. Note that the new version of href.i needs to be merged with your copy of this file in SRSSITE
icarus/db/gbemblcommon.is
icarus/db/href.i
2008/05/06: system Added support for the new nmpdr link in uniprot
icarus/db/dbxref.i
icarus/db/href.i
2008/05/06: dbsnp Fox for a probem with indexing the organis field of dbsnp
icarus/db/dbsnp.is
2008/04/29: system Change needed to handle a change in the way unknown gaps are specified in EMBL/GenBank/DDBJ Feature tables and contig construction representations
icarus/db/ftseq.is
2008/04/24: hssp Some changes to make display of hssp entries in the default view, or any table view faster for entries which contain a large number of sequence references
icarus/db/hssp.is
2008/04/23: blast fasta Removed some debugging code from the blast graphical view
icarus/db/blastgraphicdatamodel.i
2008/04/22: rebase Better handling of rebase where there are multiple entries for the same enzyme - we now combine thes into a single entry, so there are no longer duplicate id warnings when indexing. Also some minor display improvements, and a fix for a spurious parsing error when indexing the commdata (commercial vendors) file
icarus/db/rebase.i
icarus/db/rebase.is
icarus/db/rebcomm.is
web/WEB-INF/jsp/views/rebaseentry/rebaseentry.jsp
2008/04/21: epd removed some obsolete code
icarus/db/epd.is
2008/04/18: prisma Change so prisma will honour a defaultBatchCommand if no specific batch command is defined for a task
icarus/lion/prisma/prismaCheckClasses.i
2008/04/17: prisma Fix for a problem where prisma would not execute a reformat command for a dependend library when the -forceReformat option is specified
icarus/lion/prisma/checkDependentDbs.i
2008/04/17: genecards system Updates for version 2.38 of genecards
icarus/db/genecards.i
icarus/db/genecards.is
icarus/db/href.i
web/WEB-INF/jsp/views/genecardsentry/genecardsentry.jsp
2008/04/15: system Fix for a problem when using a batch queue system to run a tool on a host on which the SRS partition is not mounted
icarus/util/appl.i
2008/04/15: blast fasta system Updates for blast: Fix so the blast graphical view (HomologyView) will behave correctly when browsing through multiple blast results. Brought the psiblast implementation in sync with the other blast programs - all views applicable to blast now also work for psiblast. Note that the new loader.i file must be merged with your copy of this file in SRSSITE
icarus/db/blast.is
icarus/db/blastcommon.i
icarus/db/blastgraphicdatamodel.i
icarus/db/loader.i
icarus/db/psiblast.i
icarus/db/psiblast.is
icarus/db/psiblast.it
web/WEB-INF/jsp/views/blastentry/blastgraphic.jsp
2008/04/09: srscheck prisma Change so the fileCountTolerance used by srscheck and prisma is also applied if the nunber of files decreases
icarus/workflows/checkLocalFiles.i
2008/04/08: pdb Added support for the structure viewers jmol and chime in the pdb entry view. See comments at the top of pdb.i on how to enable jmol
icarus/db/pdb.i
web/WEB-INF/jsp/views/pdbentry/pdbentry.jsp
2008/04/01: prisma Change so the prisma installation procedure will no longer hardcode the full path to the icarus include files for the prisma test databases in srsdb.i
icarus/lion/packages/srsprisma.ip
2008/04/01: fasta Changes needed to handle output from fasta 3.5. Our fasta parser should now be able to handle output generated by fasta 3.3, 3.4 and 3.5
icarus/db/fasta.is
2008/04/01: interpro Fix for an issue with literature reference counting within interpro entries
icarus/db/interpro.is
2008/03/31: embl refseq Correction in the instructions on how to use these files with GCG formatted data. There are no functional changes
icarus/db/emblcontigs.i
icarus/db/emblwgsnew.i
icarus/db/emblwgsrelease.i
icarus/db/refseqnew.i
icarus/db/refseqrelease.i
2008/03/31: pathway Fix for a problem with the imagemap for pathway entries
web/WEB-INF/jsp/views/pathwayentry/pathwayentry.jsp
2008/03/27: prisma Fix for a problem with recursive traversion of directories on a remote ftp site
icarus/lion/prisma/remoteConnection.i
2008/03/27: prisma Fix to ensure we remove old content from the current report directory, and an extra check so prisma will not accidentally wipe out all prisma directories
icarus/lion/prisma/prismaArchive.i
icarus/lion/prisma/prismaCheckMain.i
2008/03/26: system Added support for the new ProMEX hypertext link in uniprot. Note that you will have to merge the new versions of href.i and dbxref.i with your copies in SRSSITE
icarus/db/dbxref.i
icarus/db/href.i
2008/03/26: geneseq Correction for the (variable)name for the gswpi resource object. Without this SRS will not display dataabses information, and prisma will not download the data
icarus/db/gswpi.it
2008/03/26: prisma Fix to ensure we remove old content from the prisma reports
icarus/lion/prisma/prismaCheckMain.i
2008/03/26: dbsnp system Some minor corrections for dbsnp. Note that you will have to merge the new copies of srsdb.i and loader.i with your copies of these files in SRSSITE
icarus/db/dbsnp.i
icarus/db/dbsnp.is
icarus/db/dbsnp_dm.i
icarus/db/dbsnplocation.is
icarus/db/loader.i
icarus/db/srsdb.i
2008/03/20: ensembl_mysql Changes for ensembl release 49
icarus/db/ensemblRDB.i
icarus/db/ensemblcore_schema.i
icarus/db/ensembl_compara_schema.i
2008/03/19: system A few changes to what are acceptable input patterns for blast/fasta sequence database selections. Note that this change needs to be merged with your copie of this file in SRSSITE
icarus/db/localApplicationOptions.i
2008/03/19: interpro Added a link between interpro and refseqp
icarus/db/interpro.i
2008/03/19: pfam Added code so prisma can set the release number after a data update
icarus/db/pfama.it
icarus/db/pfamb.it
icarus/db/pfamc.it
icarus/db/pfamseed.it
icarus/db/swisspfam.it
2008/03/19: pfam Correction for sorting pfamhmm by description
icarus/db/pfamhmm.i
2008/03/19: kegg Latest version of the kegg species mapping file. Note that if you have prisma, and use it to update the kegggeeome database, it will create this file automatically
icarus/db/kegg_species.i
2008/03/19: system dbsnp taxonomy We have added support for dbsnp. It comes in two libraries: dbnsp, which provides Reference SNP information, and dbsnplocation, which allows you to search for SNPs by location. Note that you will have to merge the changes in concepts.i, srsdb.i and loader.i with your versions of these files in SRSSITE
icarus/db/concepts.i
icarus/db/dbsnp.i
icarus/db/dbsnp.is
icarus/db/dbsnp.it
icarus/db/dbsnp_dm.i
icarus/db/dbsnplocation.i
icarus/db/dbsnplocation.is
icarus/db/dbsnplocation.it
icarus/db/dbsnplocation_dm.i
icarus/db/dbsnpss_dm.i
icarus/db/loader.i
icarus/db/srsdb.i
icarus/db/taxonomy.is
web/WEB-INF/jsp/views/dbsnpentry/dbsnpentry.jsp
web/WEB-INF/jsp/views/dbsnpentry/dbsnplocentry.jsp
web/WEB-INF/jsp/views/dbsnpentry/dbsnpssentry.jsp
2008/03/18: chebi Fixes for a few hypertext link problems in chebi entry display
icarus/db/chebidatamodel.i
2008/03/14: chebi Changes for release 42 of chebi. A mass and charge field have been added
icarus/db/chebi.i
icarus/db/chebi_schema.i
icarus/db/chebidatamodel.i
web/WEB-INF/jsp/views/chebientry/chebientry.jsp
2008/03/13: genecards Change so we do not include the synomyn origin (EG/HGNC) in the synonym index
icarus/db/genecards.is
2008/03/12: go_mysql kegg reactome system Added an internal link for reactome, and moved some field definitions from reactome.i, goterms.i and lcompound.i to srsgen.i for increased stability during srssection. Note that you will have to merge the new srsgen.i with your version of that file in SRSSITE
icarus/db/goterms.i
icarus/db/lcompound.i
icarus/db/reactome.i
icarus/db/srsgen.i
2008/03/12: geneseq system Added support for a geneseq patent number database. This dataset allwos you to find geneseq entries by alternative (issued by other patent offices) patent numbers by querying this database directly, or by using the synonym finder based on this database. Also a few small changes to the views used by geneseq (direct listing of patent nymbers in the default view). Note that you will have to merge the changes in srsdb.i, loader.i and concepts.i with your copies in SRSSITE
icarus/db/aageneseq.i
icarus/db/concepts.i
icarus/db/geneseq.is
icarus/db/gswpi.i
icarus/db/gswpi.is
icarus/db/gswpi.it
icarus/db/gswpi_dm.i
icarus/db/loader.i
icarus/db/nageneseq.i
icarus/db/srsdb.i
web/WEB-INF/jsp/views/gswpi/gswpi.jsp
2008/03/12: embl Small change so the patent number is indexed with and without the -A (or similar) extension
icarus/db/embl.is
2008/03/10: prisma Change needed so prisma tools testing will not fail on the userprotein/dna tools
icarus/lion/prisma/toolsTestSets.i
2008/03/10: system Chnage needed to handle the more rigourous input checking used in SRS83
icarus/db/localApplicationOptions.i
2008/03/10: clustalw quicktree userdna userprotein tacg Various changes to prevent erroneous error reporting by prisma tool testing
icarus/db/nclustalw.i
icarus/db/nmuscle.it
icarus/db/pmuscle.it
icarus/db/quicktree.i
icarus/db/quicktree.it
icarus/db/userdna.it
icarus/db/userprotein.it
icarus/db/restrictionmap.i
2008/03/10: emboss Various changes to prevent erroneous error reporting by prisma tool testing and handle the more rigourous imput testing in SRS8.3
icarus/lion/emboss/tmap.it
icarus/lion/emboss/dreg.i
icarus/lion/emboss/fuzznuc.i
icarus/lion/emboss/fuzzpro.i
icarus/lion/emboss/fuzztran.i
icarus/lion/emboss/patmatdb.i
icarus/lion/emboss/vectorstrip.i
2008/03/10: prisma Workaround for a case where the calender generation mechians gets confused by daylight savings time
icarus/lion/prisma/generateCalendar.i
2008/03/10: emboss removed options which are no longer valid in EMBOSS 5.0
icarus/lion/emboss/prettyplotn.i
icarus/lion/emboss/prettyplotp.i
icarus/lion/emboss/restover.i
2008/03/05: system Change so hypertxt links from displayed icarus files to the SRS documentation work again
icarus/util/colicarus.i
2008/03/05: embl genbank refseq ddbj medline Changes needed to handle the increasing growth of several indices in EMBL, GenBank and Medline. Applying these changes requires re-indexing and will cause major disruption. Please read instructions in http://downloads.biowisdomsrs.com/parser/srs83/UPDATE.20080503 before applying these updates
icarus/db/emblcommon.i
icarus/db/genbankcommon.i
icarus/db/medlinecommon.i
2008/03/05: prisma Various fixes for prisma quality reporting: Fix for a possible crash during tool testing, fixed various hypertext links in prisma reports, and removed an obsolete test for relational databases
icarus/lion/prisma/getappls.i
icarus/lion/prisma/inspectReport.i
icarus/lion/prisma/qualityReport/rdbTests.i
2008/02/29: system Added support for the new 2d-ecoli and phosphosite hypertext references. Note that you will need to merge the new versions of dbxref.i and href.i with your copies of these files in SRSSITE
icarus/db/dbxref.i
icarus/db/href.i
2008/02/28: prisma Fixes for various minor inconsistencies with images in prisma reports
icarus/lion/prisma/decisionReport.i
icarus/lion/prisma/dumpTarget.i
icarus/lion/prisma/generateCalendar.i
icarus/lion/prisma/inspectReport.i
icarus/lion/prisma/printBuildPages.i
icarus/lion/prisma/printDownloadPages.i
icarus/lion/prisma/printLinkPages.i
icarus/lion/prisma/printMainPage.i
icarus/lion/prisma/printPretransPages.i
icarus/lion/prisma/printReformatPages.i
icarus/lion/prisma/printUsageReport.i
icarus/lion/prisma/prismaGui.i
icarus/lion/prisma/prismaGuiCal.i
icarus/lion/prisma/prismaTreeImage.i
icarus/lion/prisma/report_resources/images/DecisionReport_up.png
icarus/lion/prisma/report_resources/images/PrismaReport_up.png
icarus/lion/prisma/report_resources/images/QualityReport_up.png
icarus/lion/prisma/report_resources/images/QuickReference.gif
icarus/lion/prisma/report_resources/images/UsageReport_up.png
icarus/lion/prisma/report_resources/images/backMainPage_down.png
icarus/lion/prisma/report_resources/images/backMainPage_up.png
icarus/lion/prisma/report_resources/images/bw_logo.gif
icarus/lion/prisma/report_resources/images/bwfavicon.ico
icarus/lion/prisma/report_resources/images/loadersTest_up.png
icarus/lion/prisma/report_resources/images/suggested_action.gif
icarus/lion/prisma/report_resources/images/toolsTest_up.png
icarus/lion/prisma/report_resources/images/viewReport_up.png
2008/02/21: emboss fix to prevent sixpack indexing to hang on an empty results file, which in some cases can bring down an SRS server
icarus/lion/emboss/sixpack.is
2008/02/18: prisma Fix to prevent crashes during tool tests
icarus/lion/prisma/getappls.i
2008/02/14: medline The 2008 release of medline has 16880015 entries, which is about 100000 more than can be accomodated by the 3 byte id space we allocate by default for a database. The result is that for the final 100000 entries in medlinerelease, wrong entries (from the beginning of the database are returned). The updated medlinecommon.i file will correct this, allocating 4 bytes for entry identifiers. Note that you must re-index both medlinerelease and medlinenew for this to take effect. Note that after applying this update, and while re-indexing is in progress, the old indices will still be working, so there is no need to take medline offline (unless you are concerned about those 100000 wrong entries)
icarus/db/medlinecommon.i
2008/02/07: system Added support for the new world-2dpage link in uniprot
icarus/db/dbxref.i
icarus/db/href.i
2008/02/01: uniprot ipi Change to make sure that we can still extract the EC number from the uniprot description line after the description line structure changes announced for late February (see http://beta.uniprot.org/docs/sp_soon.htm). The new structure should not cause problems for the current handling of the description line in SRS, but once the data in the new format is available, we will provide additional changes to take advantage of the new structure
icarus/db/swissprot.is
2008/02/01: system Fix for a problem when trying to use sequence tools with pdb sequences. Note that with this change the long name of the pdb sequence field changes from Sequence to FtSequence. Please merge the new srsgen.i file with your copy in SRSSITE
icarus/db/srsgen.i
2008/01/31: go_xml Added an internal link (go_children/go_parent) to allow querying the go hierarchy using the hierarchical link operators >_ and >^. For this link the information of both the "Is a" and "Part off" fields are combined in a new parentId field
icarus/db/go.i
2008/01/29: prisma Fix for a problem with dependent databases when a local re-indexing is done
icarus/lion/prisma/localcopyPhase.i
2008/01/25: system Added support for the new pdbsum and vectorbase links in uniprot. Please note you will have to merge the new href.i and dbxref.i files with your files in SRSSITE
icarus/db/dbxref.i
icarus/db/href.i
2008/01/24: system Corrected some mistakes in srsdb.i
icarus/db/srsdb.i
2008/01/21: prisma Removed icaIsDebug parameter as it is obsolete
icarus/lion/prisma/prismaCheckMain.i
2008/01/18: quicktree system Added support for quicktree - a tool for constructing phylogentic trees. Trees are displayed using the ATV tree viewing applet. See treeview.i for additional installation notes. Note that the changes in srsgen.i and srsdb.i need to be merged with your copy of these file in SRSSITE
icarus/db/quicktree.i
icarus/db/quicktree.is
icarus/db/quicktree.it
icarus/db/srsdb.i
icarus/db/srsgen.i
web/WEB-INF/jsp/views/atvview/atvview.jsp
2008/01/18: emboss Changed the TMAP tool (EMBOSS) to take alignments as input. Note that if you have already installed EMBOSS, you have to change the association of TMAP from sequence data input to alignment data input. This is easiest done by editing SRSSITE/packChanges.i, and change "PROTSEQ_DATA.applications.app:$TMAP_APP" to "PROTALI_DATA.applications.app:$TMAP_APP".
icarus/lion/packages/emboss.ip
icarus/lion/emboss/tmap.i
2008/01/18: kegg Fixes for some issues with image maps when multiple pathway images are displayed
icarus/db/pathway.is
2008/01/17: system genbank embl refseq ddbj imgt Added hypertext links for imgt/gene-db dbxrefs, and suppressed hypertext links for imgt/lims from refseq, as the values currently used in refseq do not provide a usefull way for linking. Note that you will need to merge the new versions of dbxref.i and href.i with your versions of these files in SRSSITE
icarus/db/dbxref.i
icarus/db/gbemblcommon.is
icarus/db/href.i
2008/01/17: userprotein userdna Fix for a hypertext link problem with user supplied sequences
icarus/db/usersequence.is
2008/01/17: kegg Fix to remove the duplicate display of map numbers
icarus/db/pathway.is
2008/01/15: prisma Changes needed to handle the fact the general.it is now residing in SRSSITE
icarus/lion/prisma/configUpdate/srssection_off
icarus/lion/prisma/configUpdate/srssection_off.i
2008/01/04: system correction for a file definition which was causing erooneous warnings in prisma
icarus/db/srsgen.i
2008/01/03: genecards kegg Added searchnames to some hidden helper libraries so prisma will not throw confusing error messages about missing data files for these
icarus/db/genecards.i
icarus/db/kegg_images.i
icarus/db/lenzyme.i
2008/01/03: geneseq Change to make sure prisma will download geneseq tar files, even if the size of the file has not changed
icarus/db/aageneseqtar.it
icarus/db/nageneseqtar.it
2008/01/02: pdbfinder Added support for the new compound lines in the chains subsections. Note that after this update you will have to index the new chaincompound field.
icarus/db/pdbfinder.i
icarus/db/pdbfinder.is
web/WEB-INF/jsp/views/pdbfinderentry/pdbfindersequence.jsp
2008/01/02: kegg Changed .Z to .gz to fix a few error/info messages
icarus/db/pathway.i
2007/12/20: prisma Added SRSFLAGS setting preservation for use with integrated config file updates
etc/runPrisma