Date / Databases	Files / Description
2024-01-15: ensembl_mysql	Update for Ensembl 111
2024-01-15: ensembl_mysql	icarus/db/ensemblRDB.i icarus/db/ensembl_compara_schema.i icarus/db/ensembl_funcgen_schema.i icarus/db/ensemblcore_schema.i
2023-10-23: pfam	Added support for the Clan field
2023-10-23: pfam	icarus/db/pfam.i icarus/db/pfam.is icarus/db/pfama.i icarus/db/pfamseed.i
2023-07-24: ensembl_mysql	Updates fro Ensembl 110
2023-07-24: ensembl_mysql	icarus/db/ensemblRDB.i icarus/db/ensembl_compara_schema.i icarus/db/ensembl_funcgen_schema.i icarus/db/ensemblcore_schema.i
2023-03-15: system	Updates for the new links to AGR and GlyCosmos in UniProtKB
2023-03-15: system	icarus/db/dbxref.i icarus/db/href.i
2023-03-09: chembl	Update for ChEMBL 32
2023-03-09: chembl	icarus/db/chembl_mysql_schema.i icarus/db/chemblcompound.i icarus/db/chemblcompound_dm.i
2023-02-13: ensembl_mysql	Updates for ensembl 109
2023-02-13: ensembl_mysql	icarus/db/ensemblRDB.i icarus/db/ensembl_compara_schema.i icarus/db/ensembl_funcgen_schema.i icarus/db/ensemblcore_schema.i
2022-10-24: ensembl_mysql	updates for Ensembl 108
2022-10-24: ensembl_mysql	icarus/db/ensemblRDB.i icarus/db/ensembl_compara_schema.i icarus/db/ensembl_funcgen_schema.i icarus/db/ensemblcore_schema.i
2022-08-03: taxonomy	Allow fror a change on the ebi ftp site
2022-08-03: taxonomy	icarus/db/taxonomy.it
2022-07-22: system	Added support for the AlfaFoldDB link in uniprot
2022-07-22: system	icarus/db/dbxref.i icarus/db/href.i
2022-07-22: ensembl_mysql	Minor updates for ensemble 107
2022-07-22: ensembl_mysql	icarus/db/ensemblRDB.i icarus/db/ensembl_compara_schema.i icarus/db/ensembl_funcgen_schema.i icarus/db/ensemblcore_schema.i
2022-04-20: ensembl_mysql	Update for EnsEMBL 106
2022-04-20: ensembl_mysql	icarus/db/ensemblRDB.i icarus/db/ensembl_compara_schema.i icarus/db/ensembl_funcgen_schema.i icarus/db/ensemblcore_schema.i
2022-03-09: system	added support for the new MANE-Select link
2022-03-09: system	icarus/db/dbxref.i icarus/db/href.i
2021-12-23: ensembl_mysql	Updates for ensembl 105
2021-12-23: ensembl_mysql	icarus/db/ensemblRDB.i icarus/db/ensembl_compara_schema.i icarus/db/ensembl_funcgen_schema.i icarus/db/ensemblcore_schema.i
2021-08-09: chembl	Update for release 29 of Chembl. Note that there is no longer an oracle version of the data
2021-08-09: chembl	icarus/db/chembl_mysql_schema.i icarus/db/chemblcompound_dm.i
2021-05-17: uniprot	correction for spelling error in download directory name
2021-05-17: uniprot	icarus/db/uniprot_trembl.it
2021-05-14: uniprot	New location for downloadin uniprot data
2021-05-14: uniprot	icarus/db/uniprot_swissprot.it icarus/db/uniprot_trembl.it
2021-05-10: ensembl_mysql	Update for ensembl 104
2021-05-10: ensembl_mysql	icarus/db/ensemblRDB.i icarus/db/ensembl_compara_schema.i icarus/db/ensembl_funcgen_schema.i icarus/db/ensemblcore_schema.i
2021-03-19: rebase	Change to use the neb ftp site again, as it seems to be functional now
2021-03-19: rebase	icarus/db/rebase.it icarus/db/rebcomm.it
2021-03-10: genbank embl refseq ddbj imgt	fix for spelling error
2021-03-10: genbank embl refseq ddbj imgt	icarus/db/gbemblcommon.is
2021-02-25: chembl	update for release 28 of chembl
2021-02-25: chembl	icarus/db/chembl_mysql_schema.i icarus/db/chembl_oracle_schema.i
2021-02-23: system	Added support for the new ref to veupath in UniProt
2021-02-23: system	icarus/db/dbxref.i icarus/db/href.i
2021-02-23: ensembl_mysql	Small update for ensembl103
2021-02-23: ensembl_mysql	icarus/db/ensemblRDB.i icarus/db/ensembl_compara_schema.i icarus/db/ensembl_funcgen_schema.i icarus/db/ensemblcore_schema.i
2021-01-19: uniref	update to the partN parameters for the links between the uniref databases, and the links between those and uniprot_trembl, in order to cope with the increasing sizes of these datasets
2021-01-19: uniref	icarus/db/uniref100.i icarus/db/uniref50.i icarus/db/uniref90.i
2021-01-15: genbank embl refseq ddbj imgt	move to remove short words (up to 3 chars) from the index as the index sizes for this becomes troublesome
2021-01-15: genbank embl refseq ddbj imgt	icarus/db/gbemblcommon.is
2020-12-07: ensembl_mysql	Some minor changes for Ensembl 102
2020-12-07: ensembl_mysql	icarus/db/ensemblRDB.i icarus/db/ensembl_compara_schema.i icarus/db/ensembl_funcgen_schema.i icarus/db/ensemblcore_schema.i
2020-12-01: uniref	fix for a bug in the UniRef90 UniProtTrembl link definition
2020-12-01: uniref	icarus/db/uniref90.i
2020-10-13: system	added support for the new bmrb, cptc, pcddb and sasbdb links in UniProt
2020-10-13: system	icarus/db/dbxref.i icarus/db/href.i
2020-10-12: rebase	Update for rebase so prisma uses the rebas.neb,com site
2020-10-12: rebase	icarus/db/rebase.it icarus/db/rebcomm.it
2020-10-08: taxonomy	correction for error in link to genetic code in the new format
2020-10-08: taxonomy	icarus/db/taxonomy.i
2020-09-21: go	Change to remoe the link to GO, as it becomes impossible to build
2020-09-21: go	icarus/db/goa.i icarus/db/goa.is
2020-08-28: go	changes to allow the ever increasing size of goa
2020-08-28: go	icarus/db/goa.i
2020-08-26: system	update to suport the new glygen and pathwyacommons links in UniProt
2020-08-26: system	icarus/db/dbxref.i icarus/db/href.i
2020-08-25: ensembl_mysql	update for ensembl 101
2020-08-25: ensembl_mysql	icarus/db/ensemblRDB.i icarus/db/ensembl_compara_schema.i icarus/db/ensembl_funcgen_schema.i icarus/db/ensemblcore_schema.i
2020-08-12: system taxonomy	changes to make sure the -f option works with taxonomy in xml format. Make sure you copy standard.is to SRSSITE
2020-08-12: system taxonomy	icarus/db/standard.is icarus/db/taxonomy.i icarus/db/taxonomy.is
2020-08-11: go iprmatches	Changes needed to dal with ever increasing size of the databases
2020-08-11: go iprmatches	icarus/db/goa.i icarus/db/iprmatches.i
2020-08-11: taxonomy system	switch to use the xml datafile, as the ebi no longer updates the .dat file. Please note the editing of the xml file in the .it file if you are not using SRS Prisma
2020-08-11: taxonomy system	icarus/db/taxonomy.i icarus/db/taxonomy.is icarus/db/taxonomy.it icarus/db/xml.il
2020-07-10: system	added support for the new biogrid-orcs, clae and ideal links in UniProt
2020-07-10: system	icarus/db/dbxref.i icarus/db/href.i
2020-07-10: iprmatches	updated for the increased size
2020-07-10: iprmatches	icarus/db/iprmatches.i
2020-06-11: uniprot	added missing file
2020-06-11: uniprot	icarus/db/uniprotgff.il
2020-06-03: uniest uniseq	updated file location
2020-06-03: uniest uniseq	icarus/db/uniest.i icarus/db/uniseq.i
2020-05-28: uniest unigene uniseq	change to use data in a single data directory (remove the local subdirectories after a data update) and a new species mapping file
2020-05-28: uniest unigene uniseq	icarus/db/uniest.is icarus/db/unigene.i icarus/db/unigene.is icarus/db/unigene.it icarus/db/unigenespecies.i icarus/db/uniseq.is icarus/db/uniseq.it
2020-05-28: prisma	removed debug print message left in by accident
2020-05-28: prisma	icarus/lion/prisma/printPretransPages.i
2020-05-11: ensembl_mysql	fix for spelling error
2020-05-11: ensembl_mysql	icarus/db/ensembl_compara_schema.i
2020-05-07: ensembl_mysql	Minor update for Ensembl 100. Note that canis familiaris has changed to canis lupus familiaris
2020-05-07: ensembl_mysql	icarus/db/ensemblRDB.i icarus/db/ensembl_compara_schema.i icarus/db/ensembl_funcgen_schema.i icarus/db/ensemblcore_schema.i
2020-05-06: uniprot ipi	update to avoid some parsing errors
2020-05-06: uniprot ipi	icarus/db/swissprot.is
2020-05-01: system	added support for links to antibodypedia, metosite and phi-base
2020-05-01: system	icarus/db/dbxref.i icarus/db/href.i
2020-05-01: blast	added workaround for customer case
2020-05-01: blast	icarus/db/blast.is
2020-04-16: chembl	update for release 26 of Chembl
2020-04-16: chembl	icarus/db/chembl.i icarus/db/chembl_mysql_schema.i icarus/db/chembl_oracle_schema.i
2020-03-31: uniprot ipi	update for a change in the feature lines: they no longer contain a feature id
2020-03-31: uniprot ipi	icarus/db/swisscommon.i icarus/db/swissprot.is
2020-03-25: prisma	correction
2020-03-25: prisma	icarus/lion/prisma/remoteConnection.i
2020-03-25: go	update for an error in an earlier update
2020-03-25: go	icarus/db/goa.is
2020-03-17: irefindex prisma	New location for irefindex and some hacks for Prisma to handle https urls
2020-03-17: irefindex prisma	icarus/db/irefindex.i icarus/db/irefindex.is icarus/lion/prisma/pretransPhase.i icarus/lion/prisma/printPretransPages.i icarus/lion/prisma/remoteConnection.i
2020-03-09: go	workaroud for some malformed lines in the latest version of goa
2020-03-09: go	icarus/db/goa.is
2020-03-03: go	Added missing acc production
2020-03-03: go	icarus/db/go_obo.is
2020-03-03: go	Suppression of a spurious error message during indexing
2020-03-03: go	icarus/db/goref.is
2020-03-03: go	Workaround for a malformed dataline in the data
2020-03-03: go	icarus/db/goa.is
2020-02-21: go	update for new location of go, which we hope will be better maintained
2020-02-21: go	icarus/db/go_obo.i
2020-02-14: prisma	Workaround for a problem in gmake with filenames exposed by a recent change in irefindex
2020-02-14: prisma	icarus/lion/prisma/remoteConnection.i
2020-02-10: irefindex	upafet for the new location of the irefindex file
2020-02-10: irefindex	icarus/db/irefindex.i
2020-02-05: ensembl_mysql	Correction for a spelling error in the latest update for Ensembl 99
2020-02-05: ensembl_mysql	icarus/db/ensembl_compara_schema.i
2020-01-31: system uniprot ipi	added support vor hypertext links to plantreactome and RNAct and fixed a prblem with single amino acid features
2020-01-31: system uniprot ipi	icarus/db/dbxref.i icarus/db/href.i icarus/db/swissprot.is
2020-01-23: ensembl_mysql	Update for Ensembl 99
2020-01-23: ensembl_mysql	icarus/db/ensemblRDB.i icarus/db/ensembl_compara_schema.i icarus/db/ensembl_funcgen_schema.i icarus/db/ensemblcore_schema.i
2019-09-24: system	Added support fro the new DrugCentral, Massive and Pharos links in uniprot
2019-09-24: system	icarus/db/dbxref.i icarus/db/href.i
2019-08-06: system	Addedsupport for the new CPTAC and NIAGADS links in UnuProtKB
2019-08-06: system	icarus/db/dbxref.i icarus/db/href.i
2019-07-08: system	Added support for the new ABCD link in UniProt
2019-07-08: system	icarus/db/dbxref.i icarus/db/href.i
2019-07-05: ensembl_mysql	Update for ENSEMBL release 97
2019-07-05: ensembl_mysql	icarus/db/ensemblRDB.i icarus/db/ensembl_funcgen_schema.i icarus/db/ensemblcore_schema.i
2019-05-20: chembl	Fix for a type on the chembl mysql schema definition
2019-05-20: chembl	icarus/db/chembl_mysql_schema.i
2019-04-15: ensembl_mysql	Update for ensembl 96
2019-04-15: ensembl_mysql	icarus/db/ensemblRDB.i icarus/db/ensembl_funcgen_schema.i
2019-04-08: chembl	Update for ChEMBL release 25
2019-04-08: chembl	icarus/db/chembl_mysql_schema.i
2019-04-03: iprmatches	devided the building of the link between IPRMATCHES and PFAMA in 16 parts to accomodate the increasing sizes of these databases
2019-04-03: iprmatches	icarus/db/iprmatches.i
2019-03-26: refseq	Increased the maximum name length for RefSeq entries, as entries with an 18 character ID have appeared in release 93
2019-03-26: refseq	icarus/db/refseqnew.i icarus/db/refseqrelease.i
2019-01-21: system	Added support for the new jPost references in uniprot
2019-01-21: system	icarus/db/dbxref.i icarus/db/href.i
2019-01-17: ensembl_mysql	Fix for a spelling error in a column name
2019-01-17: ensembl_mysql	icarus/db/ensembl_compara_schema.i
2019-01-16: ensembl_mysql	Some corrections for errors in the update for Ensembl 95
2019-01-16: ensembl_mysql	icarus/db/ensembl_compara_schema.i icarus/db/ensembl_funcgen_schema.i
2019-01-15: ensembl_mysql	update for ensembl 95
2019-01-15: ensembl_mysql	icarus/db/ensemblRDB.i icarus/db/ensembl_compara_schema.i icarus/db/ensembl_funcgen_schema.i
2019-01-15: medline	update for medline/pubmed 2019
2019-01-15: medline	icarus/db/medlinecommon.i icarus/db/medlineformat.il
2019-01-07: pubchem	Update for some recent datasource additions to PubChem
2019-01-07: pubchem	icarus/db/pubchem.is
2018-12-05: patch	A new patch release for SRS (8.4.0.4) is now available from http://downloads.biowisdomsrs.com/srs84_dist/
2018-12-05: patch	See http://downloads.biowisdomsrs.com/srs84_dist/README.8.4.0.4
2018-11-30: pfam	Fix for a parsing error caused by a misaligned end of record line in one of the entries in the latest PFAMC data file
2018-11-30: pfam	icarus/db/pfamc.is
2018-11-30: go	Improved stability of parser so it will not hang when accessing some parts of the data
2018-11-30: go	icarus/db/goa.is
2018-11-12: genbank embl refseq ddbj imgt	Fix for a parsing error in some refseq entries
2018-11-12: genbank embl refseq ddbj imgt	icarus/db/gbemblcommon.is
2018-11-06: prosite	Fix for an indxing error thrown by some book titles in prositedoc
2018-11-06: prosite	icarus/db/prositedoc.is
2018-11-06: system	fix for a typo in the definition of hypertext links to the Zebrafish Information Network (zfin)
2018-11-06: system	icarus/db/href.i
2018-10-23: system	Remove an extra [ character which had crept in
2018-10-23: system	icarus/db/srsdb.i
2018-10-15: genbank embl refseq ddbj imgt	Added some measures to prevent memory problems with refseq entries (human chromosomes) which contain millions of sequence variations
2018-10-15: genbank embl refseq ddbj imgt	icarus/db/gbemblcommon.is icarus/db/genbank.is
2018-10-15: ensembl_mysql	update for ENSEMBL release 94
2018-10-15: ensembl_mysql	icarus/db/ensemblRDB.i icarus/db/ensembl_compara_schema.i icarus/db/ensembl_funcgen_schema.i icarus/db/ensemblcore_schema.i
2018-10-10: go	Corrections for comiplation errors
2018-10-10: go	icarus/db/go_obo.i icarus/db/goa.i
2018-10-05: geneseq ensembl_mysql genecards hmdb resid uniprot	Changed link definitions so the use the new OBO based GO database instead of the XML GO database. Only apply these changes once you have disabled GO_XML, and enabled GO_OBO
	icarus/db/aageneseq.i icarus/db/ensemblRDB.i icarus/db/ensemblgene.i icarus/db/ensembltranscript.i icarus/db/genecards.i icarus/db/hmdbprotein.i icarus/db/nageneseq.i icarus/db/resid.i icarus/db/uniprot.i icarus/db/uniprot_swissprot.i icarus/db/uniprot_trembl.i
2018-10-01: go system taxonomy	We have added a complete new implementation of GO, using the GO OBO data, as the data provision of GO in legacy formats has become indreasingly erratic. See README.GO for full details
2018-10-01: go system taxonomy	icarus/db/go_obo.i icarus/db/go_obo.is icarus/db/go_obo_datamodel.i icarus/db/goa.i icarus/db/goa.is icarus/db/goref.i icarus/db/goref.is icarus/db/href.i icarus/db/srsdb.i icarus/db/taxonomy.is web/WEB-INF/jsp/views/goentry/go_obo_entry.jsp web/WEB-INF/jsp/views/goentry/go_obo_general.jsp web/WEB-INF/jsp/views/goentry/go_obo_relatives.jsp
2018-09-27: uniprot ipi	Fix for a problem with the indexing of the ptxi (proteome tax id) field
2018-09-27: uniprot ipi	icarus/db/swissprot.is
2018-07-26: system	Added support for the new UniLectin link in UniProtKB
2018-07-26: system	icarus/db/dbxref.i icarus/db/href.i
2018-07-26: dbest	fixed a problem with indexing the organism field in some entries in DBEST
2018-07-26: dbest	icarus/db/dbest.is
2018-07-20: ensembl_mysql	Updates for ensembl 93
2018-07-20: ensembl_mysql	icarus/db/ensemblRDB.i icarus/db/ensembl_compara_schema.i icarus/db/ensembl_funcgen_schema.i icarus/db/ensemblcore_schema.i
2018-06-25: system	Update for new database references/hypertext links in UniprotKB release 2018_06
2018-06-25: system	icarus/db/dbxref.i icarus/db/href.i
2018-06-20: dbsnp system	Complete overhaul of the dbsnp libraries - for size/performance reasons we split them into several taxonomic divisions. Note that non-human DBSNP are no longer updated by the NCBI
2018-06-20: dbsnp system	icarus/db/dbsnp.i icarus/db/dbsnp.is icarus/db/dbsnp.it icarus/db/dbsnp_dm.i icarus/db/dbsnp_human.i icarus/db/dbsnp_human1.i icarus/db/dbsnp_human2.i icarus/db/dbsnp_mammal.i icarus/db/dbsnp_other.i icarus/db/dbsnp_primate.i icarus/db/dbsnp_rodent.i icarus/db/dbsnplocation.i icarus/db/dbsnplocation.is icarus/db/dbsnplocation.it icarus/db/dbsnplocation_human.i icarus/db/dbsnplocation_mammal.i icarus/db/dbsnplocation_other.i icarus/db/dbsnplocation_primate.i icarus/db/dbsnplocation_rodent.i icarus/db/dbsnpss_dm.i icarus/db/srsdb.i
2018-06-11: embl genbank refseq ddbj system	Added a separate library for EMBL TSA records, as they are no longer included in the full EMBL release
2018-06-11: embl genbank refseq ddbj system	icarus/db/embltsa.i icarus/db/gbemblcommon.i icarus/db/loader.i icarus/db/srsdb.i
2018-06-08: chembl	Update for ChEMBL release 24
2018-06-08: chembl	icarus/db/chembl_mysql_schema.i icarus/db/chembl_oracle_schema.i icarus/db/chemblcompound.i
2018-06-04: prisma	Fixes for some small bugs, and added a provision to skip dbsnp and go xml files which are too small to contains any data
2018-06-04: prisma	icarus/lion/prisma/checkRemoteFiles.i icarus/lion/prisma/dbSync.i icarus/lion/prisma/movePrismaData.i icarus/lion/prisma/remoteConnection.i
2018-06-04: go_xml	Recently the provision of go rdf-xml files has become unreliable, with sometimes empty datafiles available on the ftp server. We have modified the go configuration for prisma so it will download the latest good file. Note that you will also have to update your prisma system files for this to work. We are looking into using a different data source for the provision of go data in SRS
2018-06-04: go_xml	icarus/db/go.it
2018-05-02: system	Added support for the new GlyConnect link in UniProtKB
2018-05-02: system	icarus/db/dbxref.i icarus/db/href.i
2018-04-11: ensembl_mysql	update for ENSEMBL release 92
2018-04-11: ensembl_mysql	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
2018-04-04: system	Added support for the new VGNC link in UniProt
2018-04-04: system	icarus/db/dbxref.i icarus/db/href.i
2018-03-05: system	Added support for the new carbonylDB references in UniProt
2018-03-05: system	icarus/db/dbxref.i icarus/db/href.i
2017-12-22: kegg	Added support for the new NETWORK field in the Kegg Genes (KEGGGENES_NA dn KEGGGENES_AA) databases
2017-12-22: kegg	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
2017-12-22: medline	Correction for an error in the last update for Medline 2018
2017-12-22: medline	icarus/db/medlinerelease.it
2017-12-20: medline	Updates for Medline release 2018
2017-12-20: medline	icarus/db/medlinecommon.i icarus/db/medlineformat.il icarus/db/medlinenew.it icarus/db/medlinenewfiles.i icarus/db/medlinenewfiles.it icarus/db/medlinerelease.it icarus/db/striptags.pl web/WEB-INF/jsp/views/medlineentry/medlineentry.jsp
2017-12-18: ensembl_mysql	Updates for ensembl release 91
2017-12-18: ensembl_mysql	icarus/db/ensemblRDB.i icarus/db/ensembl_compara_schema.i icarus/db/ensembl_funcgen_schema.i icarus/db/ensemblaffymodel.i icarus/db/ensemblcommon.i icarus/db/ensemblcore_schema.i
2017-12-06: kegg	Added support for the new network field in KeggDisease and the new Efficacy field in LDRUG
2017-12-06: kegg	icarus/db/keggdisease.i icarus/db/keggdisease.is icarus/db/ldrug.i icarus/db/ldrug.is web/WEB-INF/jsp/views/keggdiseaseentry/keggdiseaseentry.jsp web/WEB-INF/jsp/views/ldrugentry/ldrugentry.jsp
2017-11-15: pdbfinder	Fix for some error messages during indexing
2017-11-15: pdbfinder	icarus/db/pdbfinder.is
2017-10-02: system	Chang to allwo for the new CORUM references in UniProtKB
2017-10-02: system	icarus/db/dbxref.i icarus/db/href.i
2017-09-20: system kegg	Added support for the new DBLINKS field in lreaction
2017-09-20: system kegg	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
2017-09-11: emboss	icarus/lion/emboss/needlealln.i icarus/lion/emboss/needleallp.i
2017-09-06: ensembl_mysql	Update for some minor schema changes in EnsEMBL 90
2017-09-06: ensembl_mysql	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
2017-09-04: system	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)
2017-08-10: genpept	icarus/db/genpept.is
2017-08-04: kegg	Update to support the new Created field in the Kegg genome database
2017-08-04: kegg	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
2017-07-03: ccds system	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
2017-07-03: epd	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
2017-07-03: prisma	icarus/lion/prisma/remoteConnection.i
2017-06-23: kegg	Inproved stability of the unpacking of Kegg pathway images
2017-06-23: kegg	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
2017-06-23: prisma	icarus/lion/prisma/pretransPhase.i
2017-06-14: chembl	Update for some minor schema changes in ChEMBL 23
2017-06-14: chembl	icarus/db/chembl_mysql_schema.i icarus/db/chembl_oracle_schema.i
2017-06-13: ensembl_mysql	update for EnsEMBL 89
2017-06-13: ensembl_mysql	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
2017-06-06: epd	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
2017-05-31: srscheck 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
2017-05-30: prisma srscheck	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
2017-05-26: rebase	icarus/db/rebase.is
2017-05-22: geneseq	Added support for the new Kind Code field in geneseq supplements and fastalert
2017-05-22: geneseq	icarus/db/geneseqsupp.is icarus/db/geneseqsuppcommon.i
2017-05-22: pdbfinder	Fixes for some problems with entry boundaries and sorting in prbfinder
2017-05-22: pdbfinder	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
2017-05-15: genbank refseq ddbj	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
2017-05-08: uniprot	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
2017-05-08: genbank refseq ddbj	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
2017-04-18: genbank refseq ddbj	icarus/db/genbank.is
2017-04-06: ensembl_mysql	update for Ensembl release 88
2017-04-06: ensembl_mysql	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
2017-03-30: genpept	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
2017-03-30: blast fasta	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)
2017-03-30: pdb	icarus/db/pdb.i
2017-03-14: system	Fix for a problem displaying news on the SRS front page
2017-03-14: system	web/WEB-INF/jsp/shared/news.jsp
2017-03-14: genbank refseq ddbj	Some tweaking of sort sets and links to inprove indexing performance
2017-03-14: genbank refseq ddbj	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
2017-02-24: medline	icarus/db/medline.is
2017-02-22: system	Update for the changed URL for imgt links in UniProt
2017-02-22: system	icarus/db/dbxref.i icarus/db/href.i
2017-02-20: system	Update for the new Araport link in UniProtKB
2017-02-20: system	icarus/db/dbxref.i icarus/db/href.i
2017-02-08: geneseq	Added two useful parsing elements fro GeneSeq - no functional changes
2017-02-08: geneseq	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
2017-02-08: uniprot	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
2017-02-06: 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
2017-02-02: entrezgene	icarus/db/entrezgene.i
2017-02-02: prosite	Fix for some changes in the data field in Prosite
2017-02-02: prosite	icarus/db/prosite.is
2017-01-23: system	Added support for the new SFLD link in UniProt
2017-01-23: system	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
2017-01-17: entrezgene	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
2017-01-16: refseq	icarus/db/refseqnew.i
2017-01-13: ensembl_mysql	Fixes for soem problems displaying Ensembl transcripts
2017-01-13: ensembl_mysql	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
2017-01-11: fasta	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
2017-01-11: entrezgene	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)
2017-01-09: fasta system	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
2017-01-05: ensembl_mysql	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
2016-12-20: medline system	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
2016-12-09: ensembl_mysql	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
2016-12-07: entrezgene	icarus/db/entrezgene.it
2016-12-06: patch	A new patch release for SRS (8.4.0.3) is now available from http://downloads.biowisdomsrs.com/srs84_dist/
2016-12-06: patch	See http://downloads.biowisdomsrs.com/srs84_dist/README.8.4.0.3
2016-12-05: uniprot	Addjusted part sizes for links between UniParc and other databases to better handle the increased sizes of the databases
2016-12-05: uniprot	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
2016-11-24: entrezgene	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
2016-11-15: uniref	icarus/db/uniref50.i icarus/db/uniref90.i icarus/db/unirefcommon.i
2016-11-14: chembl	Fix for missing DF_PValue field definition
2016-11-14: chembl	icarus/db/chembl.i
2016-11-07: system	Added support for the new PhosphoSitePlus, DisGeNet and OpenTargets references in UniProt
2016-11-07: system	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
2016-11-07: medline	icarus/db/medlinenewfiles.it icarus/db/medlinerelease.it
2016-11-02: chembl	Update for Chembl release 22
2016-11-02: chembl	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.
2016-10-20: ncbi-nr	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
2016-10-11: go_xml	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
2016-10-10: kegg	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
2016-09-30: embl	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
2016-09-14: kegg	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
2016-09-14: embl	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
2016-09-13: kegg	icarus/db/lcommon.is
2016-08-26: system kegg	Added support for the Brite classification in the Kegg Glycan library
2016-08-26: system kegg	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
2016-07-29: genecards	icarus/db/genecardstar.it
2016-07-26: ensembl_mysql	update for for Ensembl release 85
2016-07-26: ensembl_mysql	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)
2016-07-05: kegg	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
2016-07-04: kegg	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
2016-06-15: blast	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
2016-06-15: medline	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
2016-06-10: medline	icarus/db/medlinecommon.i
2016-06-02: pubchem	Fixes for some parsing errors caused by data errors in the PubChem files
2016-06-02: pubchem	icarus/db/pubchem.is
2016-05-13: system	Added support if the new SIGNOR link in UniProtKB
2016-05-13: system	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
2016-05-09: genpept	icarus/db/genpeptnew.i
2016-04-22: prosite	Change to allow for a new line format in the comments field of prosite
2016-04-22: prosite	icarus/db/prosite.is
2016-04-22: pdb	Fix for some parsing errors generated during indexing of PDB
2016-04-22: pdb	icarus/db/pdb.is
2016-04-15: hmdb	Update for release 3.6 of HMDB, incuding a change in the download location
2016-04-15: hmdb	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
2016-04-14: prisma	icarus/lion/prisma/dbSync.i
2016-04-14: reactome	Update for Reactome release 56
2016-04-14: reactome	icarus/db/reactome.i icarus/db/reactome_schema.i
2016-04-13: ensembl_mysql	Update for some minor schema changes in Ensembl release 84
2016-04-13: ensembl_mysql	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.
2016-04-12: embl genbank refseq ddbj system	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
2016-03-23: system uniprot ipi	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
2016-03-23: chembl	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)
2016-03-18: kegg	icarus/db/genKeggSpecies.i icarus/db/kegg_species.i
2016-03-03: system	Added support for the new SwissPalm links in UniProtKB
2016-03-03: system	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
2016-02-26: medline	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
2016-02-11: ncbi-nr	icarus/db/gimap.i
2016-02-11: ncbi-nr	Change to make sure the link between NR and UNIPROT_TREMBL is build -in parts
2016-02-11: ncbi-nr	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
2016-02-11: refseq	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)
2016-02-10: kegg	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
2016-01-29: system	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)
2016-01-22: kegg	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
2016-01-18: blast	icarus/db/blast.is
2016-01-13: patent_prt	Correction for the download location for the PATENT_PRT Patent Protein database
2016-01-13: patent_prt	icarus/db/patent_prt.i
2016-01-13: pfam	Fix for a problem with PfamC caused by recent optimizations for PfamA
2016-01-13: pfam	icarus/db/pfamc.i icarus/db/pfamc.is
2015-12-23: srscheck prisma	Fixed some issues with chunk and chunksize parallelization
2015-12-23: srscheck prisma	icarus/workflows/buildPhase.i icarus/workflows/linkPhase.i
2015-12-17: system	Added support for the new SwissLipids and MalaCard references in UniProtKB
2015-12-17: system	icarus/db/dbxref.i icarus/db/href.i
2015-12-15: genpept	Fixed a misconfigation of indexing parallelization in GENPEPTRELEASE
2015-12-15: genpept	icarus/db/genpeptrelease.i
2015-12-15: uniref	Fixed a misconfigation of indexing parallelization in UNIREF90
2015-12-15: uniref	icarus/db/uniref90.i
2015-12-07: embl	Fix for some parsing errors during indxing of IMGTLIGM
2015-12-07: embl	icarus/db/embl.is
2015-11-27: ensembl_mysql	Update for some minor schema changes in Ensembl 82
2015-11-27: ensembl_mysql	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
2015-11-26: uniprot ipi	icarus/db/swissprot.is
2015-11-25: prisma srscheck	Fixes for problems with dealing with compressed data files and some other bugs
2015-11-25: prisma srscheck	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: pacth	A new patch release for SRS (8.4.0.2) is now available from http://downloads.biowisdomsrs.com/srs84_dist/
2015-11-19: pacth	http://downloads.biowisdomsrs.com/srs84_dist/README.8.4.0.2
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
2015-11-19: pfam	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
2015-10-29: genbank refseq ddbj	icarus/db/genbank.is
2015-10-27: system	Added support for the new WBParaSite link in UniProtKB
2015-10-27: system	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
2015-10-27: prisma	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
2015-10-23: genpept	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
2015-10-22: uniref	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
2015-10-19: go_xml	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
2015-10-19: uniprot ipi	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
2015-10-16: drugbank system	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
2015-10-06: hmmer	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
2015-10-06: pfam	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
2015-09-23: embl	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
2015-09-23: uniprot	icarus/db/uniprot_trembl.i
2015-09-14: pubchem	Fix to handle very long lines in resent PubChem assaey results data
2015-09-14: pubchem	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.
2015-08-24: genpept uniprot ipi	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
2015-08-24: refseq	icarus/db/refseqrelease.i
2015-08-13: prisma	fix for a problem with creating blast indices from file which is already in fasta format
2015-08-13: prisma	icarus/lion/prisma/reformatPhase.i
2015-08-07: drugbank	Update for some small changes in DrugBank 4.3
2015-08-07: drugbank	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
2015-07-28: system uniprot	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
2015-07-27: merops	icarus/db/merops_schema.i
2015-07-27: reactome	Updates for Reactome release 53
2015-07-27: reactome	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
2015-07-24: ensembl_mysql	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
2015-07-22: biogrid dip intact mint	icarus/db/intactProcessData.pl
2015-07-21: embl	Fix for indexing problems with some deleted EMBL records which have incomplete molecule and division iformation
2015-07-21: embl	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
2015-07-13: system	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
2015-07-13: embl	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
2015-07-09: system uniprot ipi	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)
2015-06-19: kegg	icarus/db/keggorthology.i
2015-06-16: blast hmdb	Added support for several new fields in the chemical taxonomy section of HMDB
2015-06-16: blast 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
2015-06-09: system	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
2015-06-09: medline	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
2015-05-15: system	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
2015-05-07: pdb	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
2015-04-29: uniprot ipi	icarus/db/swissprot.is
2015-04-24: iprmatches	Added a bew Signature field to IPRMATCHES
2015-04-24: iprmatches	icarus/db/iprmatches.i icarus/db/iprmatches.is
2015-04-24: refseq	Added parallization for building the link between REFSEQRELEASe and REFSEQPNEW
2015-04-24: refseq	icarus/db/refseqrelease.i
2015-04-24: drugbank	Fix for a porblem caused by very long lines in Drgbank SDF files
2015-04-24: drugbank	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
2015-04-24: go_xml taxonomy	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
2015-04-24: ncbi-nr	icarus/db/nr.is
2015-04-24: iprmatches	Increased the number of parts in which IPRMATCHES is build
2015-04-24: iprmatches	icarus/db/iprmatches.i
2015-04-24: intact	Increased the number of parts in which intactinteractions is build
2015-04-24: intact	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)
2015-04-24: chemicalsearch	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
2015-04-24: chemicalsearch chembl hmdb drugbank kegg	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
2015-04-24: kegg	icarus/db/kegg_species.i
2015-04-22:	A new patch release for SRS (8.4.0.1) is now available from http://downloads.biowisdomsrs.com/srs84_dist/
2015-04-22:	http://downloads.biowisdomsrs.com/srs84_dist/README.8.4.0.1
2015-04-22: embl genbank refseq ddbj	Speedup and fix for a memory problem when trying to retrieve contig information from large genomic records
2015-04-22: embl genbank refseq ddbj	icarus/db/embl.is icarus/db/genbank.is
2015-04-20: drugbank	Small change to prevent some parsing warnings in DrugBank 4.2
2015-04-20: drugbank	icarus/db/drugbankpartner.is
2015-04-09: system kegg	Added support for the new Brite classification data in the KEGG disease database
2015-04-09: system kegg	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
2015-04-09: ncbi-nr	icarus/db/nt.i
2015-04-08: drugbank	Added support for the new product data in DrugBank 4.2
2015-04-08: drugbank	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
2015-04-08: ensembl_mysql	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
2015-04-07: refseq	icarus/db/refseqvariations.is
2015-04-02: dssp	Fix for some parsing arrers caused by malformed data lines in some dssp entries
2015-04-02: dssp	icarus/db/dssp.is
2015-04-02: hssp	Fix for some parsing errors in some hssp entries
2015-04-02: hssp	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
2015-04-02: pfam	icarus/db/swisspfam.i
2015-04-02: domo	Removed sorting for the keyword field of DOMO
2015-04-02: 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
2015-03-26: prosite	icarus/db/prositedoc.is
2015-03-25: system	Added missing hypertext definition needed to navigate Brite hierarchies in KEGG data
2015-03-25: system	icarus/db/href.i
2015-03-25: srscheck prisma	Fix for errors thrown during the removal of partial link indices
2015-03-25: srscheck prisma	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
2015-03-04: dbsnp system	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.
2015-02-26: embl	icarus/db/emblnewfiles.it icarus/db/emblrelease.it
2015-02-10: chembl	Update for ChEMBL release 20
2015-02-10: chembl	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
2015-01-23: prisma srscheck	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.
2015-01-21: system	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
2015-01-19: system	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
2015-01-06: 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
2014-12-19: medline	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
2014-12-17: dbsnp	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
2014-12-08: prisma srscheck	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
2014-12-01: kegg system	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 !
2014-11-28: blast	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
2014-11-25: system	web/WEB-INF/config/srs/srs-export.xml
2014-11-25: embl	Correction for some misspelled names for EMBLWGSMUS subentry libraries
2014-11-25: embl	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
2014-11-25: system	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
2014-11-24: dbsnp system	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
2014-11-24: system	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
2014-11-18: system	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.
2014-11-17: embl system	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
2014-11-10: 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
2014-10-24: medline	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
2014-10-22: chembl	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
2014-09-30: genecards	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
2014-09-18: uniprot	icarus/db/uniprot_trembl.i
2014-09-18: ensembl_mysql	Update for Ensembl release 76
2014-09-18: ensembl_mysql	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
2014-09-15: 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
2014-09-15: system	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
2014-09-12: pdb	icarus/db/pdb.is
2014-09-10: system	Corrected some wrong examples of dividers in blast/fasta database listings
2014-09-10: system	icarus/db/localApplicationOptions.i
2014-09-10: genpept	Fix for a Genpept data download problem with SRS Prisma
2014-09-10: genpept	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
2014-09-09: cosmic	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
2014-09-04: system	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
2014-08-20: embl	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
2014-08-11: pubchem	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
2014-08-08: system	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
2014-08-04: dbsnp	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)
2014-08-04: prisma	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
2014-08-04: genpept	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
2014-07-25: hmdb	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
2014-07-24: irefindex	icarus/db/irefindex.i
2014-07-24: merops	Updated for some small schema changes in Merops release 9.11
2014-07-24: merops	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
2014-07-23: reactome	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
2014-07-17: embl	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
2014-07-15: drugbank system	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
2014-07-10: prisma srscheck	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
2014-07-10: drugbank system	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
2014-06-24: prositesearch	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
2014-06-24: system	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
2014-06-18: system	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
2014-06-12: 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
2014-06-02: system	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
2014-05-08: genpept	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
2014-05-08: ncbi-nr	icarus/db/gimap.i
2014-05-06: refseq	Fix for a problem with the construction of variant sequences from contig specifications
2014-05-06: refseq	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
2014-05-01: embl	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
2014-05-01: dbsnp	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
2014-05-01: genbank refseq ddbj	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
2014-05-01: genbank refseq ddbj uniprot	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
2014-05-01: system	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
2014-05-01: system	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
2014-04-29: 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/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
2014-04-16: pfam	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
2014-04-14: srscheck 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.
2014-03-31: ddbj embl genbank	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
2014-03-28: genecards	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
2014-03-27: refseq embl genbank	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
2014-03-21: drugbank	icarus/db/drugbankpartner.i
2014-03-20: srscheck prisma	Fix for a problem in srscheck with database dependencies if only link indices are build
2014-03-20: srscheck prisma	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
2014-03-18: system	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.
2014-03-18: srscheck prisma	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
2014-03-18: blast	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
2014-03-17: intact prisma	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
2014-03-17: ncbi-nr	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
2014-03-14: genbank embl refseq ddbj imgt	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
2014-03-13: uniprot ipi	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
2014-03-13: genbank embl refseq ddbj imgt	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
2014-03-11: drugbank	icarus/db/drugbank.i
2014-03-11: uniprot	Fix for a problem with unzipping if Prisma decides only to download the release text file
2014-03-11: uniprot	icarus/db/uniprot_swissprot.it icarus/db/uniprot_trembl.it
2014-03-10: ensembl_mysql	Update for some minor schema changes in EnsEMBL 75
2014-03-10: ensembl_mysql	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
2014-03-10: 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
2014-03-05: chebi	icarus/db/chebidatamodel.i
2014-03-04: ncbi-nr	Fixed some display problems and a tool type association problem
2014-03-04: ncbi-nr	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
2014-03-03: system	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
2014-02-28: system	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
2014-02-28: refseq embl genbank	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
2014-02-28: pubchem	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
2014-02-28: uniref	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
2014-02-24: ncbi-nr system	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
2014-02-24: pfam	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)
2014-02-19: system	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
2014-02-13: kegg	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
2014-02-11: quicktree emboss	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
2014-02-10: embl	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
2014-02-03: 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
2014-01-28: prisma	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
2014-01-28: prisma	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
2014-01-28: prisma	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
2014-01-28: 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
2014-01-21: system	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
2014-01-20: chemicalsearch	icarus/db/chemicalsearch.i
2014-01-13: prisma	Fix for a problems with the Prisma test databases if blast is not enabled
2014-01-13: prisma	icarus/lion/prisma/PrismaToolsTestDb/testdb.i
2014-01-10: system	Fix for a problem with the display of database names on the link page
2014-01-10: system	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
2014-01-09: system	icarus/db/dbxref.i icarus/db/href.i
2014-01-09: ensembl_mysql	Changes needed for Ensembl release 74
2014-01-09: ensembl_mysql	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
2014-01-09: prisma	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
2014-01-09: system	icarus/util/appl.i
2014-01-09: nrpat	Fix for stability problems with sequence display in the nr patent databases 9NRPL1 NRPL2 NRNL1 NRNL2)
2014-01-09: nrpat	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
2014-01-08: prisma	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
2014-01-08: prisma	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
2014-01-07: 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)
2013-12-24: pubchem chemicalsearch	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
2013-12-24: embl system	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
2013-12-23: system	icarus/util/appl.i
2013-12-23: system	Some changes to improve stability for batch jobs listed on the tools results page
2013-12-23: system	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
2013-12-09: chembl	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
2013-12-06: prisma	icarus/lion/prisma/getFastaSequence.i
2013-12-06: chembl	Changes needed for schema changes in ChEMBL release 17
2013-12-06: chembl	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
2013-12-06: pfam	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
2013-12-05: chebi	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
2013-12-04: ccds embl genbank refseq ddbj geneseq nrpat	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
2013-12-02: srscheck prisma	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
2013-12-02: 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
2013-12-02: dbgss genpept	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
2013-12-02: embl genbank refseq ddbj	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
2013-11-29: prisma	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
2013-11-28: refseq	icarus/db/refseqvariations.i
2013-11-28: irefindex	Correction for the construction of links from IREFSINDEX to other Protein-Protein interaction databases
2013-11-28: irefindex	icarus/db/irefindex.i icarus/db/irefindex.is
2013-11-28: prosite	Fix to allow for days in the data update date field
2013-11-28: prosite	icarus/db/prosite.is
2013-11-27: pubchem	Fix for an indexing problem with the Target Species in PUBCHEMASSAY
2013-11-27: pubchem	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
2013-11-26: system	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.
2013-11-26: pubchem	icarus/db/createpubchemassaydata.pl
2013-11-26: prosite	Fix for a parsing problems with one of the literature refrences
2013-11-26: prosite	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
2013-11-26: uniref	icarus/db/unirefcommon.i
2013-11-26: blocks	fix for a problem with hypertext links to UniProt in BLOCKS entries
2013-11-26: blocks	icarus/db/blocks.is
2013-11-25: hmmer	Added missing hmmscan.is file in SRS8.4 distribution
2013-11-25: hmmer	icarus/db/hmmscan.is
2013-11-25: genbank refseq ddbj	Fix for a display problem with the contig specification for GenBank and RefSeq entries
2013-11-25: genbank refseq ddbj	icarus/db/genbank.is
2013-11-25: dbgss	Fix for a problem with the link to GenBank in DBGSS entry display
2013-11-25: dbgss	icarus/db/dbgss.is
2013-11-25: genbank embl refseq ddbj	Fix for a sequence display problem with RefSeqP entries
2013-11-25: genbank embl refseq ddbj	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
2013-11-25: go_xml go_mysql go	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)
2013-11-19: system	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
2013-11-14: blast	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
2013-11-14: omim	icarus/db/omim.is icarus/db/omim.it
2013-11-14: quicktree	Fix for an input sequence reformatting problem with QuickTree
2013-11-14: 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
2013-11-12: clustalw system	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
2013-11-05: clustalw	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
2013-11-04: kegg	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
2013-11-04: reactome	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
2013-11-01: system	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
2013-11-01: blast	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
2013-11-01: system	icarus/db/loader.i icarus/db/views.i
2013-11-01: system	Improved autorefresh and messaging if batch jobs are running
2013-11-01: system	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
2013-11-01: blast fasta system	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
2013-10-24: cosmic	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
2013-10-24: prisma	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
2013-10-23: uniprot ipi	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
2013-10-18: uniprot ipi	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
2013-10-18: kegg pathway	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
2013-10-17: system	web/javascript/queryresults.js
2013-10-15: refseq	Fixed a permission problem with a utility used for the indexing of REFSEQVARIATIONS
2013-10-15: refseq	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
2013-10-11: system	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
2013-10-04: system	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
2013-10-04: system	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
2013-10-03: system	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
2013-10-03: system	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
2013-10-03: kegg	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.
2013-10-03: system	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
2013-10-03: system	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
2013-10-02: srscheck prisma	icarus/workflows/moveIndicesPhase.i
--:	A new patch release for SRS () is now available from http://downloads.biowisdomsrs.com/srs84_dist/
--:	http://downloads.biowisdomsrs.com/srs84_dist/README.