Date / DatabasesFiles / Description
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: srscheck prisma Fix for some spurious warnings during the check phase of srscheck and Prisma
icarus/workflows/getSystemLibs.i
2017-05-30: 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/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/reformatPhase.i
icarus/lion/prisma/remoteConnection.i
icarus/lion/prisma/setReportPhase.i
icarus/workflows/buildPhase.i
icarus/workflows/coreCheckClasses.i
icarus/workflows/linkPhase.i
2017-05-26: rebase Fix for a problem with an authorname in rebase
icarus/db/rebase.is
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: system Fix for a problem displaying news on the SRS front page
web/WEB-INF/jsp/shared/news.jsp
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: 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 soem problems displaying Ensembl transcripts
icarus/db/ensemblcommon.i
icarus/db/ensemblcore_schema.i
icarus/db/ensembldatamodel.i
icarus/db/ensemblproteinmodel.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.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
2016-12-07: entrezgene Fix for an error in the remote search pattern for Organelle and Plasmid sections for EntrezGene Downloads
icarus/db/entrezgene.it
2016-12-05: uniprot Addjusted part sizes for links between UniParc and other databases to better handle the increased sizes of the databases
icarus/db/uniparc.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/medlinenewfiles.it
icarus/db/medlinerelease.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
2016-06-10: medline Added some missing indexing defintions which are needed for the field linking between succeeded medline entries and their successor
icarus/db/medlinecommon.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/emblwgs.i
icarus/db/emblwgs.is
icarus/db/emblwgscommon.i
icarus/db/emblwgsenv.i
icarus/db/emblwgsenvfiles.i
icarus/db/emblwgsfiles.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/emblwgsmaster.i
icarus/db/emblwgsmus.i
icarus/db/emblwgsmusfiles.i
icarus/db/emblwgsnew.i
icarus/db/emblwgsnewfiles.i
icarus/db/emblwgsnewfiles.it
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/genbankwgs.is
icarus/db/genbankwgsfiles.i
icarus/db/genbankwgsmaster.i
icarus/db/srsdb.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
2015-12-07: 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
2015-11-25: prisma srscheck Fixes for problems with dealing with compressed data files and some other bugs
icarus/lion/prisma/checkRemoteFiles.i
icarus/lion/prisma/prismaCheckClasses.i
icarus/lion/prisma/prismaCheckMain.i
icarus/workflows/buildPhase.i
icarus/workflows/coreCheckClasses.i
icarus/workflows/linkPhase.i
2015-11-19: pfam Changes for pfam, needed to access very large entries. Note that this also requires the installation of the 8.4.0.2 patch release
icarus/db/pfam.is
icarus/db/pfama.i
icarus/db/pfamhmm.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 they are indexed in parts, requiring less memory
icarus/db/uniref100.i
icarus/db/uniref50.i
icarus/db/uniref90.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: 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
2015-07-28: system uniprot Added support for UniParc - this may be needed as a large number of sequences from redundant proteomes are no longer included in UniProtKB. Be carefull when updating web/WEB-INF/config/srs/srs-export.xml, as the old file may contain edits you made to customize data exports
icarus/db/srsdb.i
icarus/db/uniparc.i
icarus/db/uniparc.is
icarus/db/xml.il
web/WEB-INF/config/srs/srs-export.xml
web/WEB-INF/jsp/views/uniparcentry/uniparcentry.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: blast hmdb Added support for several new fields in the chemical taxonomy section of HMDB
icarus/db/blast.is
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/db/quickSearch.i
icarus/util/srssection.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: iprmatches Increased the number of parts in which IPRMATCHES is build
icarus/db/iprmatches.i
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
2015-04-09: 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
2015-02-26: 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 file 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
2015-01-06: medline Correction for a missing DF_PrevAccession field needed for the 2015 version of MedLine
icarus/db/medlinecommon.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/prismaArchive.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/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/srsgen.i
web/WEB-INF/jsp/views/keggdiseaseentry/keggdiseaseentry.jsp
web/WEB-INF/jsp/views/kegggenesentry/kegggenesentry.jsp
web/WEB-INF/jsp/views/keggorthology/keggorthologyentry.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 external index specifications 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: dbsnp system 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/dbsnpvcf.i
icarus/db/dbsnpvcf.il
icarus/db/dbsnpvcf.is
icarus/db/srsdb.i
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.
icarus/db/embl.is
icarus/db/emblwgs.i
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/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
icarus/db/srsdb.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 Some text field re-definitions needed to make DrugBank 4 work with SOLR in SRS 8.4, and a fix for an xml parsing problem. Note that the new copy of standard.is needs to be installed in SRSSITE
icarus/db/drugbank.i
icarus/db/drugbank.is
icarus/db/drugbankpartner.i
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
2014-06-18: 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. This update is not needed if you have applied the recent update for SRSICA/field_mod.i
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. This update is not needed if you have applied the recent update for SRSICA/field_mod.i
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
2014-05-01: 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
2014-05-01: 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
2014-05-01: 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
2014-05-01: genbank refseq ddbj 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/genbankcommon.i
icarus/db/swisscommon.i
2014-05-01: system Change so all indices can be larger than 4GB. After applying this update, remove all index (and other files) from SRSINX, and re-index everything. Once this has been done, it will no longer be necessary to change indexsettings and reindindex a field if the index gets larger than 4GB. This update is not included in the updates tar ball, as it could seriuously disrupt SRS if it was accidentally applied
icarus/util/field_mod.i
2014-05-01: system We added some dummy IdType to prevent problems when reading indwxfiles after a index size limit change. Please note that the new version of srsgen.i needs to be merged with your copy of this file in SRSSITE
icarus/db/srsgen.i
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
2014-03-27: refseq embl genbank Fix for a problem in SRS 8.4 with the link to sequence features in entries in the major DNA databases which have too many features to be displayed in the main entry view
web/WEB-INF/jsp/views/dnadbentry/features.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 seacrh 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: uniprot ipi Fix for a size related problem with the index files for the link field in uniprot_trembl. After updating this file re-index the link field for all databases in uniprot format - but only if you use regular SRS indices and not Lucene indices for these databases
icarus/db/swisscommon.i
icarus/db/swissprot.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 changes 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: system Fixes for a number of prblems with annotations in SRS8.4. If you have already installed annotations in SRS8.4, please add a LibLic for AnnotationUsers_DB in SRSSITE/srsdb.i
icarus/lion/annotations/annotations_common.i
icarus/lion/annotations/installAnnotations.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
2014-02-24: 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
2014-02-24: pfam Fox for a display probelsm with pfamhmm entries
web/WEB-INF/jsp/views/pfamhmmentry/pfamhmmentry.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: 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: prisma Fix for a command line option interpretation problems with srsinspect
icarus/lion/prisma/srsinspect.i
2014-01-09: system Fix for a problem where SRS8.4 specific code had been lost from this file in an earlier update, causing index failures for tool results
icarus/util/appl.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 Removed some tests from the Prisma quality report which are irrelevant for SRS8.4, and 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/indicesTest.i
icarus/lion/prisma/qualityReport/resourceObjectCheck.i
icarus/lion/prisma/qualityReport/toolTests.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 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: srscheck prisma Fix for a problem with srscheck and SRS Prisma when it would detect a discrepance between SRS indices and solr/lucene, call for re-indexing of the database involved, but not move the new indices on-line
icarus/workflows/checkLocalFiles.i
2013-12-02: dbgss Fix for a problem with the sortsets for DBGSS. After applying this update is would be recommended to re-index DBGSS
icarus/db/dbgss.i
2013-12-02: dbgss 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 is would be recommended to re-index both GENPEPTNEW and GENPEPTRELEASE
icarus/db/dbgss.i
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 IREFSINDEX 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: hmmer Added missing hmmscan.is file in SRS8.4 distribution
icarus/db/hmmscan.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
2013-10-15: refseq Fixed a permission problem with a utility used for the indexing of REFSEQVARIATIONS
icarus/db/findrefseqacc.is
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.srs84.tar.gz
interface_updates_Oct_2013.srs84.tar.gz
2013-10-04: system Fixed a problem with the sequence text box on the tool launch page if one arrives on that page without a selected sequence. We have alse added this update to interface_updates_Oct_2013.srs84.tar.gz
interface_updates_Oct_2013.srs84.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. Also included is a fix for a problem with launching tools using an entry from a database. For your convenience we supply this update as a single tar archive: interface_updates_Oct_2013.srs84.tar.gz. Note that you also should update SRSDB/localApplicationOptions.i, readseq.i, loader.i and views.i - which is are notincluded in the tar archive
interface_updates_Oct_2013.srs84.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. This update is also needed as part of a fix for a problem wich can sporadicly occur when launching tools with sequences selected from queries. 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. This update is also needed as part of a fix for a problem wich can sporadicly occur when launching tools with sequences selected from queries.
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
2013-10-02: srscheck prisma Fix for a problem in srscheck, where it would try to move virtual library files online before they have been build, occuring when the -force option is usd to rebuild the virtual library
icarus/workflows/moveIndicesPhase.i