Date / Databases	Files / Description
2013/06/20: medline	Change to facilitate the display of multipart abstracts (as found in MEDLINE:21710270)
	icarus/db/medline-ris.il
2013/06/10: system	Update for SignaLink links in Uniprot DBs
	icarus/db/dbxref.i icarus/db/href.i
2013/05/22: medline	Several improvements for medline: Fixed a problem with the MeshHeading subentries, changed the way keywords are indexed so keywords consisting of two words separated by a / are also searchable by those undividual words, and changed the results view for medline so it includes the first lines of the abstract, expandable to the full abstract by a + button
	icarus/db/medline.i icarus/db/medline.is icarus/db/medlinecommon.i web/WEB-INF/jsp/views/medlineentry/medlineresults.jsp
2013/04/25: ipi	updated the location of IPI data for downloads by SRS Prisma. Note that the last release of IPI was in November 2011, and that the data has been incorporated into UniProt
	icarus/db/ipi.it
2013/04/09: pdb	Fix for a problems with the PDB download link in the PDB entry view
	icarus/db/pdb.i web/WEB-INF/jsp/views/pdbentry/pdbentry.jsp
2013/03/19: system	correction to dbxref.i to support the chitars database link
	icarus/db/dbxref.i
2013/03/13: system uniprot ipi	Added support for the new ChiTaRS and SABIO-RK links in UniProtKb. Please note that the new href.i and dbxref.i files need to be merged with your copies of these files in SRSSITE.
	icarus/db/dbxref.i icarus/db/href.i icarus/db/swissprot.is
2013/03/06: rebase	Change to allow for a larger entry name in ReBase
	icarus/db/rebase.i
2013/02/27: pdb	Change so we no longer use a separate url to load the PDB structure into jmol, but use a string embedded in the applet call instead
	icarus/db/pdb.i icarus/db/pdb.is web/WEB-INF/jsp/views/pdbentry/pdbentry.jsp
2013/02/20: prisma	Change so remaining download lock files are removed between update retries
	etc/runPrisma
2013/02/18: fasta system pdb pdbfinder	Change so the nice fastaseqs view can be used with pdb and pdbfinder data. Note that the new version of loader.i needs to be merged with your copy of that file in SRSSITE
	icarus/db/fasta.il icarus/db/loader.i icarus/db/pdb.i icarus/db/pdbfinder.i
2013/02/18: prisma	Change to improve robustness to errors during the unpack/pretranslation phase
	icarus/lion/prisma/pretransPhase.i
2013/02/13: system	Added support for the new mycoClAP link in UniProtKb. Please note that the new href.i and dbxref.i files need to be merged with your copies of these files in SRSSITE
	icarus/db/dbxref.i icarus/db/href.i
2013/02/12: uniprot	Change so the cc (comment) index for UniProtKB can be larger than 4GB. We expect this to be necessary for UNIPROT_TREMBL within a few release cycles. After applying this update you should remove the existing cc indices (uniprot*_cc.i*) and re-index. This also applies to any other database which you have in UniProt like format.
	icarus/db/swisscommon.i
2013/02/12: genbank refseq ddbj	Change so the gid indices for databases in GenBank format (GenBank, RefSeq, DDBJ) can be larger than 4GB. We expect this to be needed with the next full release of GenBank. After applying this change, remove all gid indices for databases in GenBank format (genbank*_gid.i* refseq[rn]*_gid.i* ddbj*_gid.i*) and if you have the GeneSeq databases, also remove the link indices between nageneseq and the genbank/refseq family: nageneseq_genban* genbank*_nageneseq.i* refseq*_nageneseq.i* nageneseq_refseq*. Then re-index.
	icarus/db/genbankcommon.i
2013/02/12: geneseq	Change so the pat (Patent Title) index of NAGENESEQ can be larger than 4GB (it has recently started to exceed this linit). After applying this update remove the nageneseq_pat.i* indices and re-index
	icarus/db/nageneseq.i
2013/01/25: ensembl_mysql	Update for Ensembl release 70
	icarus/db/ensemblRDB.i icarus/db/ensembl_compara_schema.i icarus/db/ensembl_funcgen_schema.i icarus/db/ensemblcore_schema.i
2013/01/21: srscheck prisma	Fix for a problem with cached file listings if prismacheck is used as a standalone program
	icarus/workflows/coreCheckClasses.i
2013/01/10: genpept	Change needed so SRS Prisma can update GENPEPTNEW after another change on the GenPept download site
	icarus/db/genpeptnew.it
2013/01/10: system	Replaced various hypertext links which were pointing to the EBI srs server by links to the orginal data sources. Please note that the new href.i file needs to be merged with your copy of that file in SRSSITE
	icarus/db/href.i
2013/01/09: prisma	Fix for a crash in usage reporting if no files are downloaded during a prisma run
	icarus/lion/prisma/printUsageReport.i
2013/01/09: emboss	Removed some SRS8.3 specific code which had crept in SRS8.2 emboss definition files. Please use the EMBOSS6.5.0.tar.gz file to update your system
	EMBOSS6.5.0.tar.gz
2013/01/08: refseq	Split indexing for some REFSEQNEW links in parts to avoid memory problems
	icarus/db/refseqnew.i
2013/01/07: prisma	Fix for a problem in the Prisma reports calender if the current month does not have any reports
	icarus/lion/prisma/generateCalendar.i
2013/01/07: emboss	Improvements for the SRS integration of EMBOSS programs. We have added options for limited editing of input sequences, setting of titles for graphs and added a lot more information about the tool in the toolInfo page. Please use the EMBOSS6.5.0.tar.gz file to apply all the updates.
	EMBOSS6.5.0.tar.gz
2013/01/02: genecards system	Changes to allow for some new data lines in GeneCards 3.09. Note that the new version of href.i needs to be merged with your copy of this file in SRSSITE
	icarus/db/genecards.i icarus/db/genecards.is icarus/db/href.i web/WEB-INF/jsp/views/genecardsentry/genecardsentry.jsp web/WEB-INF/jsp/views/genecardsentry/genecardsexpression.jsp
2012/12/19: system	Added a missing group needed for the emboss programs sigcleave and tmap. Note that this file needs to be merged with your copy in SRSSITE
	icarus/db/applGroups.i
2012/12/18: go_xml iprmatches	Changes to build indices in more parts, needed to avoid memory problems caused by the growing size of the databases
	icarus/db/go.i icarus/db/iprmatches.i icarus/db/pdbml.i
2012/12/17: prisma	Fix for a problem where the prisma installer would hang
	icarus/lion/prisma/generateCalendar.i
2012/12/17: srscheck prisma	Fix for crashes in srscheck caused by recent code changes for SRS Prisma
	icarus/workflows/coreCheckClasses.i
2012/12/17: prisma	Implementented a more accurate estimate for actual download times in the usage report - taking parallel downloads in account
	icarus/lion/prisma/printUsageReport.i
2012/12/14: genpept	Update needed if you use SRS Prisma to mantain GenPept - the distrubuted file has changed to a compressed file
	icarus/db/genpeptnew.it icarus/db/genpeptrelease.it
2012/12/10: prisma	A large number of improvements and some fixes for SRS Prisma. See README.PRISMA.201212 for full details. Please use the prisma.latest_update.tar.gz archive to install the updates
	prisma.latest_update.tar.gz
2012/12/10: medline	Added Author affiliation and page numbers to the RIS export for medline
	icarus/db/medline-ris.il icarus/db/medlinecommon.i
2012/12/10: system	Added various hypertext link definitions needed for the new Cosmic database and the new HMDB XML format. Please note that the new version of this file needs to be merged with your copy in SRSSITE
	icarus/db/href.i
2012/12/10: genbank refseq ddbj	Change to allow the SeqVersion (sv) field of GenBank to be larger than 4GB. After applying this change, the sv field needs to be indexed for all databases in GenBank Format - all GenBank, RefSeq and DDBJ databases, and any custom databases you may have which is also in GenBank format. Prior to indexing you should remove all sv indices for these databases
	icarus/db/genbankcommon.i
2012/12/10: genpept	Changes needed to allow downloads from the newly restructured Genpept download site. Note that you will also need the latest updates of SRS Prisma in order to maintain GenPept, and that there is no longer a need to use the GPFILES helper library to remove duplicatew from the updates
	icarus/db/genpeptnew.i icarus/db/genpeptnew.it icarus/db/genpeptrelease.i icarus/db/genpeptrelease.it icarus/db/gpnewfiles.i
2012/12/10: uniprot ipi	Fix for a problem with the query string used for linking to some RESID entries
	icarus/db/swissprot.is
2012/12/04: system	Changes to allow for new links in UniProtKB, and updates for links to DNA and protein sequences at the NCBI so we use the latest url syntax for that. Update for hypertext links to LigandBox. Please note that these files need to be merged with your copies of these files in SRSSITE
	icarus/db/dbxref.i icarus/db/href.i
2012/12/04: bind	Updated the library information for BIND to reflect that it is no longer available for download by ftp
	icarus/db/bindcomplex.it icarus/db/bindinteraction.it icarus/db/bindpathway.it
2012/11/30: pdbfinder	FIx for a problem with displaying pdb sequences in the pdbfinder entry view
	icarus/db/pdbfinder.i
2012/11/28: kegg	added a --wildcard command line option to the tar command for unpacking the kegg image files - needed as the latest version of tar no longer have --wildcard as default setting
	icarus/db/pathwaytar.it
2012/11/27: enzyme	Update for change in the structure of the download location for the enzyme database. Also refreshed the annotation section
	icarus/db/enzyme.it
2012/11/21: prosite	Update to deal with the new structure of the prosite download site. Also updated the annotation of prosite
	icarus/db/prosite.it icarus/db/prositedoc.it
2012/11/12: unigene uniprot	Updatet some database display names for UniProtKB, and reorganised links to UniGene
	icarus/db/unigene.i icarus/db/uniprot.i icarus/db/uniprot_swissprot.i icarus/db/uniprot_trembl.i icarus/db/uniprotvarsplic.i
2012/10/30: uniprot uniref	Increased the number of parts in which some links are build to avoid memory problems
	icarus/db/uniprotxml.i icarus/db/uniref90.i
2012/10/30: ensembl_mysql	update for some minor schema changes in ensembl 69
	icarus/db/ensemblRDB.i icarus/db/ensembl_compara_schema.i icarus/db/ensembl_funcgen_schema.i
2012/10/16: blast	fix for a problems where SRS sometimes would populate the database name column in the blast view with sequence IDs
	icarus/db/blast.is
2012/10/02: reactome	Update for some small schema changes in Reactome release 42
	icarus/db/reactome_schema.i
2012/09/28: blast	Fix for a problem when matching hits from the results summary to the actual hits with certain fasta headers
	icarus/db/blast.is
2012/09/21: blast	Fix for a problem in a recent change in the part of the blast parser which tries to extract the database name
	icarus/db/blast.is
2012/09/14: ensembl_mysql	Fix for a display problem which occurs for some hypertexct links to databases which are not installed locally
	icarus/db/ensembldatamodel.i icarus/db/ensemblgenemodel.i icarus/db/ensemblproteinmodel.i icarus/db/exondatamodel.i
2012/09/13: blast	Fix which allows the blast parser to capture the database name from the blast summary if additional information (indexing date) is included in the database description
	icarus/db/blast.is
2012/09/11: system	Added support for the new GenomeRNAi and UniPathway links in UniProt. Note that the new versions of these files need to be merged with your copies in SRSSITE
	icarus/db/dbxref.i icarus/db/href.i
2012/09/06: medline	Added partN=16 for building links between MEDLINERELEASE_CITEDBY and MEDLINERELEASE_CITES
	icarus/db/medlinerelease.i
2012/08/14: system uniprot ipi	Fixed a problem with the hypertext links from UniProtKB to RESID. The new version of href.i needs to be merged with your copy of that file in SRSSITE
	icarus/db/href.i icarus/db/swissprot.is
2012/08/13: embl genbank refseq ddbj imgt system	Added support for sample origin (country,region,locality), longitude and lattitude as searchable fields to facilitate search by geographical location in the main DNA sequence databases. Also added a small Google map in the entry view which displays the location (if available). Note that the new versions of general.it, href.i and srsgen.i need to be merged with your copies of these files in SRSSITE
	icarus/db/embl.is icarus/db/emblcommon.i icarus/db/gbemblcommon.is icarus/db/genbank.is icarus/db/genbankcommon.i icarus/db/href.i icarus/db/srsgen.i
2012/08/13: hssp	Added support for the new dbref lines in hssp
	icarus/db/hssp.i icarus/db/hssp.is web/WEB-INF/jsp/views/hsspentry/hsspentry.jsp
2012/08/10: blast fasta fastasequence	Fix for a database name assignment problem if multiple database names are associated with an identifier in localApplicationOptions.i
	icarus/db/blast.is icarus/db/fasta.is icarus/db/fastaseq.is
2012/08/09: system	Removed a debug print statement which would show up during indexing of xml files. Plases note that the new version of standard.is needs to be merged with your copy of this file in SRSSITE
	icarus/db/standard.is
2012/08/03: genecards system	Update for new data lines in GeneCards 3.08 - note that there are three new fields to index (frnadb, reacd and genego). The new version of href.i needs to be merged with your copy of that file in SRSSITE
	icarus/db/genecards.i icarus/db/genecards.is icarus/db/href.i web/WEB-INF/jsp/views/genecardsentry/genecardsentry.jsp
2012/08/03: ensembl_mysql	Update for some Ensembl release 68
	icarus/db/ensemblRDB.i icarus/db/ensembl_compara_schema.i icarus/db/ensembl_funcgen_schema.i icarus/db/ensemblcore_schema.i
2012/07/26: geneseq	Fixes for various inconsistencies in concepts used for the various patent databases, which affected the places where these databases show up in the query builder
	icarus/db/aageneseq.i icarus/db/aageneseqsupp.i icarus/db/nageneseq.i icarus/db/nageneseqsupp.i
2012/07/17: system	Fix for a problem where the icarus based xml parser would not see attributes in a empty tag without a separate closing tag. Note that the new version of stardard.is needs to be merged with your copy of that file in SRSSITE
	icarus/db/standard.is
2012/07/17: dbsts	Improved the display of citations in dbsts entries
	web/WEB-INF/jsp/views/dbstsentry/references.jsp
2012/07/17: ddbj	Removed link from DDBJ to IMGT, as it is also defined in imgt.i
	icarus/db/ddbj.i
2012/07/17: kegg	Update for kegg species mapping file. Note that it you have prisma, this file will be regenrated automatically when the kegggome database is updated
	icarus/db/kegg_species.i
2012/07/17: emboss	Upgraded emboss support to emboss 6.5.0. For your convenience we make this upgrade available as a separate tarball: EMBOSS6.5.0.tar.gz. If you upgrade from emboss 6.4, simply untar this file in SRSROOT, and run srssection. If you upgrade from an eearlier version of emboss, please have a look at the various Emboss README files
	EMBOSS6.5.0.tar.gz
2012/07/16: refseq	Added a command so SRS Prisma will set the release number of RefSeq(P). Note that applying this update will trigger a re-indeing if RefSeq(P), so it is best done if there is a real data update available
	icarus/db/refseqprelease.it icarus/db/refseqrelease.it
2012/07/16: uniref	Increased the number of parts in which the uniref - uniprot_trembl links are build to prevent memory problems during indexing
	icarus/db/uniref100.i icarus/db/uniref50.i icarus/db/uniref90.i
2012/07/04: pfam	Fix for a wrong link definition between PfamA and UniProtSwissprot. After applying this update you will have to build the indices for this link: srsbuild -l pfama -xl uniprot_swissprot
	icarus/db/pfama.i
2012/07/02: reactome	Updates for release 41 of Reactome
	icarus/db/reactome.i icarus/db/reactome_schema.i web/WEB-INF/jsp/views/reactomeentry/notevent.jsp
2012/06/26: kegg	Made date unpack commands for Pathway and Kegg Genome more robust
	icarus/db/kegggenome.it icarus/db/pathway.it
2012/06/25: embl	Added a command so SRS Prisma can set the release number for EMBLWGSRELEASE, and modified the search path so SRS will index EMBLWGSRELEASE from subdirectories (this is the way the data is now organised on the EBI ftp server)
	icarus/db/emblwgsrelease.i icarus/db/emblwgsrelease.it
2012/06/22: ccds	Change to allow for some name changes for CCDS on the ncbi ftp server
	icarus/db/ccdsnuc.it
2012/06/20: hssp	Fix to prevent problems caused by garbage in some of the compressed hssp data files
	icarus/db/hssp.is
2012/06/18: kegg	Change needed for the Kegg Genes database after a change in the ftp structure on the Kegg downloads site
	icarus/db/kegggenes_na.it
2012/06/18: geneseq	Changes so we index the patent number in GeneSeq with and without the kind (-A, -A1 etc) extension
	icarus/db/aageneseq.i icarus/db/geneseq.is icarus/db/nageneseq.i
2012/06/18: pdb	Fix for a problem wich occurs if one wants to display the pdb.is file in the web interface
	icarus/db/pdb.is
2012/06/15: kegg	Correction for the link defintion between the Kegg Genes databases and Taxonomy - we now use the more precice Taxon (scientific name) field in taxonomy
	icarus/db/kegggenes_aa.i icarus/db/kegggenes_na.i
2012/06/12: blast	Fix for a problems where SRS might skip the second entry in a blast result during indexing
	icarus/db/blast.is
2012/06/07: kegg	updated citation information for some Kegg ligand database, replacing medline Ids for PubMed IDs
	icarus/db/lcompound.it icarus/db/lenzyme.it icarus/db/lglycan.it icarus/db/lreaction.it
2012/06/07: pdb	updated web and citation information for PDB
	icarus/db/pdb.it
2012/05/30: embl	Change so Prisma will be able to download emblwgs with the next full update of EMBL, when the directory structure for the WGS files will change. Note that untill that data Prisma will throw errors when it is chacking for the EMBL WGS section, but these errors are harmless if your current EMBLWGS data is up-to-date. If not, you should apply this update with the next full release of EMBL (expected in June).
	icarus/db/emblwgsrelease.it
2012/05/28: embl	Change needed to allow for the fact the the EMBL Sequence version (sv) field soon will be larger than 4GB. This change requires re-indexing of the sv field for all databases in EMBL Format and users will not be able to query this field until this has been done. It is probbaly a good idea to apply this change with the next full release of EMBL (expected in June)
	icarus/db/emblcommon.i
2012/05/28: entrezgene	Change needed to allow for the fact the the EntrezGene All text field is now larger than 4GB. This change requires re-indexing of the Alltext field and users will not be able to query this field until this has been done
	icarus/db/entrezgene.i
2012/05/28: genbank refseq ddbj	Change needed to allow for the facts that index for the GenBank Sequence version (sv) field soon will be larger than 4GB, and that the indices for the CountedItam (cti) and CountedN (ctn) are already larger than 4GB. This change requires re-indexing of the sv,cti and ctn fields for all databases in GENBANK Format (GenBank, RefSeq, DDBJ) and users will not be able to query these fields until this has been done.
	icarus/db/genbankcommon.i
2012/05/28: geneseq	Change needed to allow for the facts that index for the Keyword (key) field soon will be larger than 4GB, and that the indices for the Patent Title (pat) are already larger than 4GB. This change requires re-indexing of the key and pat fields for NAGENESEQ and users will not be able to query these fields until this has been done.
	icarus/db/nageneseq.i
2012/05/28: iprmatches	Change of IdType for iprmatches so we can accomodate the 2.2 million entries of this database. This Change requries re-indexinf of iprmatches. Note that srscheck/prisma will not notice that re-indexing is neede, so you need to use a -force flag (or delete the iprematches_id index files)
	icarus/db/iprmatches.i
2012/05/28: uniprot	Change to allow for the fact that the indices for the Author (aut) and DBXref (dr) fields in UNIPROT_TREMBL will soon be larger than 4GB in size. This change requires re-indexing of the aut and dr fields for all databases in UNiProt/Swissprot format, and users will not be able to query these fields until this has been done
	icarus/db/swisscommon.i
2012/05/28: fasta	Changes needed to parse the output of the GLSEARCH and GGSEARCH programs from the Fasta Suite
	icarus/db/fasta.is
2012/05/28: fasta	Changes to allow for a changes in command line options for fastx, fasty, tfastx and tfasty in fasta 3.6.5 - Do not install these updates if you are using fasta 3.6.4 or older
	icarus/db/fastacommon.i icarus/db/fastx.i icarus/db/fasty.i icarus/db/tfastx.i icarus/db/tfasty.i
2012/05/16: prisma	Change to prevent prisma from hanging on gibberish in the command timing records
	icarus/lion/prisma/prismatime.i
2012/05/14: ensembl_mysql	Updates for Ensembl 67. There have been some significant from release 66, and you should apply these updates at the same time as you bring the new data on-line. We also fixed some performance problems for sequence display/export views
	icarus/db/ExonsandIntrons.il icarus/db/OutputExons.il icarus/db/OutputTranscripts.il icarus/db/UTRandCDS.il icarus/db/ensemblRDB.i icarus/db/ensembl_compara_schema.i icarus/db/ensembl_funcgen_schema.i icarus/db/ensemblcommon.i icarus/db/ensemblcore_schema.i icarus/db/ensemblproteinmodel.i icarus/db/exondatamodel.i web/WEB-INF/jsp/views/ensemblgeneentry/geneentry.jsp web/WEB-INF/jsp/views/ensemblproteinentry/proteinentry.jsp web/WEB-INF/jsp/views/transcriptentry/transcriptentry.jsp
2012/05/10: chebi	Updated comments about the loading of chebi in mysql and oracle. No functional changes
	icarus/db/chebi.i icarus/db/chebi_schema_mysql.i
2012/05/10: medline	removed the from medline to pdb, as that link is now defined from pdb in pdb.i
	icarus/db/medline.i icarus/db/medlinenew.i icarus/db/medlinerelease.i icarus/db/medlineupdates.i
2012/05/08: kegg	Change so that the three letter organism part of the entry identifier in KEGGGENES is obtained from the organism field, and no longer from the file name
	icarus/db/kegggenes.is
2012/05/02: genecards	Fix for a table display problem with diseases, genes and compounds from BioAlma lines in genecards
	icarus/db/genecards.i icarus/db/genecards.is
2012/05/01: system	Added support for the new EvolutionaryTrace link in uniprot. Note that dbxref.i and href.i need to be merged with your copies of these files in SRSSITE
	icarus/db/dbxref.i icarus/db/href.i
2012/04/30: embl system	Change so that for EMBL records the link to a genome project points to the EBI, and not to the NCBI. Note that the updated href.i file needs to be merged with your copy of this file in SRSSITE
	icarus/db/embl.is icarus/db/href.i
2012/04/30: embl imgt	Change so we coorectly index the release number for imgt, and added a command so SRS Prisma will be able to set the imgt release number after installing new data
	icarus/db/embl.is icarus/db/imgt.it
2012/04/30: uniref	Change to the ID type used for the UniRef databases, needed to accomodate the increased number of entries in UniRef100 (more than 256^3 - which no longer fits in the standard 3 byte ID type in SRS). After applying this update you will have to re-index the UniRef databases
	icarus/db/unirefcommon.i
2012/04/30: prisma	Fixed some usage/options display issues for the -help option
	etc/runPrisma
2012/04/13: imgt	Update to allow for some changes on the imgt download site
	icarus/db/imgt.it
2012/04/11: kegg	Removed unnecessary content from the kegg species mapping file (no longer needed due to changes in kegg databases)
	icarus/db/genKeggSpecies.i icarus/db/kegg_species.i
2012/03/29: omim	Added information for use with OMIM data at omim.org. File needs to be edited to activate omim.org information.
	icarus/db/omim.it
2012/03/29: system	Added support for dnasu link in Uniprot
	icarus/db/dbxref.i icarus/db/href.i
2012/03/19: kegg	Change to allow for the new ORGANISM line in the Kegg Genes database
	icarus/db/kegggenes.is icarus/db/kegggenes_aa.i icarus/db/kegggenes_na.i icarus/db/kegggenes_na.it
2012/03/13: ensembl_mysql	Changes for ensembl version 66
	icarus/db/ensemblRDB.i icarus/db/ensembl_funcgen_schema.i icarus/db/ensemblcore_schema.i icarus/db/ensemblgenemodel.i
2012/03/08: system	removed link to PDB from hypertext link for the Sequence CRC Digest field, as a bug in SRS results in a broken query for that
	icarus/db/href.i
2012/03/02: geneseq system	Change in the way prisma handles GeneSeq data - it will no longer keep copies of the downloaded tar archivs in the offline data directory. The AAGENESEQTAR and NAGENESEQTAR helper databases (used for downloading the data) are now obsolete and have been removed from srsdb.i
	icarus/db/aageneseq.it icarus/db/nageneseq.it icarus/db/srsdb.i
2012/03/02: geneseq	Fix for the handling of the entry creation and revision dates in GeneSeq
	icarus/db/aageneseq.i icarus/db/geneseq.is icarus/db/nageneseq.i web/WEB-INF/jsp/views/aageneseqentry/aageneseq.jsp web/WEB-INF/jsp/views/nageneseqentry/nageneseq.jsp
2012/03/01: pdb	Added a pubmed id field to PDB, and links to medline, and display of DOI literature links in the entry display
	icarus/db/pdb.i icarus/db/pdb.is
2012/03/01: embl genbank refseq ddbj	retired Medline ID as in indexed field in EMBL/Genbank/Refseq/DDBJ, as it is empty in EMBL and the few entries in GenBank and RefSeq which have a MedlineID also have a PubMed ID
	icarus/db/emblcommon.i icarus/db/genbankcommon.i
2012/02/29: prisma	Change so SRS Prisma will not descend into all subdirectories during recursive downloads if it is clear from the wanted filename patterns that a path can never match those patterns. When applying this update also update the dbsnp.it and dbsnplocation.it files, otherwise prisma will not be able to download dbsnp data
	icarus/lion/prisma/remoteConnection.i
2012/02/29: genpept	Correction for the retrieval of the GenPept accession number field
	icarus/db/genpeptcommon.i
2012/02/29: prisma srscheck	Fix for a problem where Prisma would try to re-index dependent databases without first having linked the online data to teh offline directories
	icarus/lion/prisma/localcopyPhase.i icarus/lion/prisma/pretransPhase.i icarus/workflows/buildPhase.i
2012/02/29: srscheck prisma	Fix for a problem where prisma would not index data files in the correct order if only a few fields need re-indexing
	icarus/workflows/checkLocalFiles.i icarus/workflows/coreCheckClasses.i
2012/02/29: srscheck prisma	Fixes for various problems where SRS would build unneccesary virtual link sets, or would not move them online
	icarus/workflows/getSystemLibs.i icarus/workflows/linkPhase.i
2012/02/29: uniprot	Increased the partsize paramter for parallel indexing of uniprot_trembl, as we are now hitting the common 1024 filehandles limit when merging link indices for this database
	icarus/db/uniprot_trembl.i
2012/02/29: system pdb	Various changes for pdb: We have added fields (NCBI taxon ID, Genbank accession, sequence CRC digest, obsolete date), we added links to the taxonomy database and the major DNA sequence databases. We also changed the way SRS Prisma updates the PDB data, so it will include obsolete and model records (this can be controlled by editing pdb.it). With this change the separate PDBMODEL database is now no longer necessary. This change also requires that SRS Prisma needs to traverse recursively through the ftp direcories on the PDB download site and to stop Prisma from taking too much time going through irrelevant subdirectories, we have also an update for SRS Prisma (remoteConnection.i) which will limit the subdirectories SRS Prisma is traversing. After applying this update PDB will have to be re-indexed. Note that the new href.i file needs to be merged with your copy in SRSSITE
	icarus/db/href.i icarus/db/pdb.i icarus/db/pdb.is icarus/db/pdb.it web/WEB-INF/jsp/views/pdbentry/pdbdescription.jsp web/WEB-INF/jsp/views/pdbentry/pdbsequence.jsp
2012/02/29: embl genbank refseq ddbj	We moved the NCBI taxon ID field (which is available in the "source" feature) from the feature subentry database to the main part of the data for EMBL/Genbank/DDBJ/RefSeq/Refseqp. This will allow for easier querying by taxon ID. This update requires re-indexing of the taxon id (txi) field. After applying this update the old txi indices will return errors, and srscheck or prisma will not be able to detect that the indices need rebuilding. Therefore the best way of handling this update is to renove all _txi.i* for all embl/genbank/ddbj/refseq/refseqp datasets you have and than use srscheck of prisma to build the new indices. You may also have to look at other code you have (for instance to build blast datasets) which use taxon ids in queries
	icarus/db/embl.is icarus/db/emblcommon.i icarus/db/gbemblcommon.i icarus/db/genbank.is icarus/db/genbankcommon.i web/WEB-INF/jsp/views/dnadbentry/dnadbentry.jsp
2012/02/29: kegg	updated species mapping file for Kegg. Note that if you use prisma, this file will be generated by prisma and there is no need to update this file
	icarus/db/kegg_species.i
2012/02/28: system	Change to allow of the new pomBase references in uniprot (they replace the GeneDB_Spombe references)). Please note that the new dbxref.i and href.i files need to be merged with your copies in SRSSITE
	icarus/db/dbxref.i icarus/db/href.i
2012/02/28: kegg	Changes to allow for the new MODULE line in the Kegg Genes database. Also some changes to improve robustness for downloads of the Kegg Genes data by Prisma
	icarus/db/kegggenes.i icarus/db/kegggenes.is icarus/db/kegggenes_aa.i icarus/db/kegggenes_na.i icarus/db/kegggenes_na.it icarus/db/lcommon.is web/WEB-INF/jsp/views/kegggenesentry/kegggenesentry.jsp
2012/02/28: genecards system	Update to allow for the new BIOTIME (cell lines) in GeneCards. Note that the new href.i file needs to be merged with your copy of that file in SRSSITE
	icarus/db/genecards.i icarus/db/genecards.is icarus/db/href.i web/WEB-INF/jsp/views/genecardsentry/genecardsentry.jsp
2012/02/20: kegg	fix for a parsing error during indexing of the Kegg Glycan database, caused by a malformed authors line in a single entry
	icarus/db/lcommon.is
2012/02/15: reactome	Update for some minor schema changes in REACTOME release 29
	icarus/db/reactome_schema.i
2012/01/31: uniprot	Fix for a display problem with features in uniprot text entries, introduced with the recently added FtResidKey field
	icarus/db/swisscommon.i
2012/01/30: imgt	Changed the name of the IMGT database to IMGTLIGM to avoid confusion with the other IMGT databases. Please note that fater applying this update you need to rename the imgt indices to imgtligm (or reindex imgtligm)
	icarus/db/imgt.i icarus/db/imgt.it
2012/01/20: fasta system	Changed the fastaseqs view (for the export of sequences in fasta format) so the output is more in line with the format used by the NCBI. The header line now includes a gi number (when available) and an accession number which includes the version number (when available). We also extended the database name/abbrviation mappings we use, which you may want to modify to reflect your local setup. Please note that the new version of loader.i needs to be merged with your copy in SRSSITE
	icarus/db/fasta.il icarus/db/loader.i
2012/01/20: genbank embl refseq ddbj imgt	Some fixes for the insertion of hypertext links in EMBL/GenBank/RefSeq/DDBJ feature tables
	icarus/db/gbemblcommon.is
2012/01/04: geneseq ccds system	Added support for the CRC sequences digest field to the ccds and geneseq databases. Please note that the new href.i file needs to be merged with your copy of this file in SRSSITE
	icarus/db/aageneseq.i icarus/db/ccds.i icarus/db/ccds.is icarus/db/geneseq.is icarus/db/geneseqsupp.is icarus/db/geneseqsuppcommon.i icarus/db/href.i icarus/db/nageneseq.i web/WEB-INF/jsp/views/aageneseqentry/aageneseq.jsp web/WEB-INF/jsp/views/ccdsentry/ccdsentry.jsp web/WEB-INF/jsp/views/nageneseqentry/nageneseq.jsp
2011/12/20: hssp	Fix to allow for a change in the format of the date line in hssp
	icarus/db/hssp.is
2011/12/20: system	support added for PATRIC and DMDM links in UniProt libraries
	icarus/db/dbxref.i icarus/db/href.i
2011/12/19: ensembl_mysql	Updates for Ensembl release 65
	icarus/db/ExonsandIntrons.il icarus/db/OutputExons.il icarus/db/OutputPeptides.il icarus/db/OutputTranscripts.il icarus/db/UTRandCDS.il icarus/db/ensemblRDB.i icarus/db/ensembl_compara_schema.i icarus/db/ensembl_funcgen_schema.i icarus/db/ensemblcommon.i icarus/db/ensemblcore_schema.i icarus/db/ensembldatamodel.i icarus/db/ensemblgenemodel.i icarus/db/ensemblproteinmodel.i icarus/db/exondatamodel.i
2011/12/16: embl genbank refseq ddbj imgt	Correction for the Sequence CRC Digest hypertext link for protein sequences
	icarus/db/emblcommon.i icarus/db/gbemblcommon.is icarus/db/genbankcommon.i
2011/12/16: genpept	Fix for a display problem in GenPept
	web/WEB-INF/jsp/views/genpeptentry/genpeptentry.jsp
2011/12/16: srscheck prisma	Fix for a problem where partial link databases for uniprot_trembl where not removed during indexing due too a removal command which was too long for the shell (resulting in an "Argument list too long" error
	icarus/workflows/linkPhase.i
2011/12/14: system ipi	Added support for the new Sequence CRC Digest field to IPI. Please merge the new version of href.i with your copy in SRSSITE
	icarus/db/href.i icarus/db/ipi.i
2011/12/14: uniprot ipi	Additional changes needed to link to RESID
	icarus/db/swissprot.is web/WEB-INF/jsp/views/swissentry/swissentry.jsp
2011/12/13: genpept kegg	Added a new Sequence CRC digest field, which allows the user to quickly identify identical sequences
	icarus/db/genpept.is icarus/db/genpeptcommon.i icarus/db/kegggenes.i icarus/db/kegggenes.is icarus/db/kegggenes_aa.i icarus/db/kegggenes_na.i web/WEB-INF/jsp/views/genpeptentry/genpeptentry.jsp web/WEB-INF/jsp/views/kegggenesentry/kegggenesentry.jsp
2011/12/13: uniprot ipi	Added a new Sequence CRC digest field, which allows the user to quickly identify identical sequences and added links to RESID, UniRef100, UniParc (only if UniParc or UniRef is installed locally) and a link to the UniProt version archive (UniSave).
	icarus/db/swisscommon.i icarus/db/swissprot.is web/WEB-INF/jsp/views/swissentry/swissentry.jsp web/WEB-INF/tags/featuretable.tag
2011/12/13: embl genbank refseq ddbj imgt	Added a new Sequence CRC digest field, which allows the user to quickly identify identical sequences, and added links to the EMBL or NCBI version archives for EMBL, GenBank and RefSeq entries
	icarus/db/embl.is icarus/db/emblcommon.i icarus/db/gbemblcommon.i icarus/db/gbemblcommon.is icarus/db/genbank.is icarus/db/genbankcommon.i web/WEB-INF/jsp/views/dnadbentry/dnadbentry.jsp web/WEB-INF/jsp/views/dnadbentry/sequence.jsp
2011/12/13: system	Changes needed for the new Sequence CRC Digest field - please note that these files need to be merged with your copies of these files in SRSSITE
	icarus/db/general.it icarus/db/href.i icarus/db/srsgen.i
2011/12/09: unigene	Change so building links from UniGene to EMBL/GenBank is done in more parts, so less memory is used
	icarus/db/unigene.i
2011/12/03: pfam	Correction to fix broken pfamhmm entry view.
	icarus/db/pfamhmm.i web/WEB-INF/jsp/views/pfamhmmentry/pfamhmmentry.jsp
2011/12/03: emboss	Fix to correct output error that breaks viewing of plot.
	icarus/lion/emboss/polydotp.i
2011/12/01: embl genbank refseq ddbj	Change to allow for non-numerical characters in Genomic project identifiers
	icarus/db/embl.is icarus/db/genbank.is
2011/12/01: system	Change to allow for the new ko (Kegg Orthology) link in UniProt records. Please note that the updated dbxref.i file needs to be merged with your copie of this file in SRSSITE
	icarus/db/dbxref.i
2011/12/01: unigene	Fix for a parsing error in some unigene entries for Danio Rerio
	icarus/db/unigene.is
2011/12/01: omim	Updated omim.it so SRS Prisma will download the frozen (Frebrary 2011) version available from the NCBI. If you have access to the up-to-date omim data, then you will have to modify omim.it so Prisma will download the correct data. As we have not been able to get access to that, we cannot guarantee that our implementation of omim in SRS will continue to work with the latest omim data
	icarus/db/omim.it
2011/12/01: hssp	Updates for HSSP parser files to work with bz2 compression and add new ftp and www info.
	icarus/db/hssp.i icarus/db/hssp.it
2011/11/30: enzyme	getReleaseCommand add for ENZYME database.
	icarus/db/enzyme.it
2011/11/29: hmmer	Note added to remind admin that PFAMHMM is required when enabling HMMSCAN
	icarus/db/hmmscan.i
2011/11/29: system	added ProteinProperties group that was causing error in a few EMBOSS libraries.
	icarus/db/applGroups.i
2011/11/28: hmmer	Add missing .is file for hmmscan from the HMMER3 package update
	icarus/db/hmmscan.is
2011/11/27: geneticcode	Minor change to add in release command for geneticcode
	icarus/db/geneticcode.it
2011/11/15: kegg	The Kegg Pathway KGML distribution does not include files for the reference pathways (mapXXXXX entries). To ovecome problems with external data linking to these we now create the relevant entries from the "ko" (ortology) entries. The ko entries are indexed twice, once as "ko" and once as "map". Note that this still does not entirely eliminate the dead link problem, as "ko" data is only available for regular metabolic pathways
	icarus/db/pathway.is
2011/11/15: system	Updated the package information for various tools to reflect the latest versions we support. Please note that this file needs to be merged with your copy of this file in SRSSITE
	icarus/db/packages.i
2011/11/15: hmmer system pfam	Upgraded the SRS integration of the HMMER package to version 3.0 - Please note that the hhmpfam tool has been replaced by hmmscan. The changes in href.i, srsgen.i, localApplicationOptions.i and srsdb.i need to be merged with your copies of these files in SRSSITE
	icarus/db/hmmbuild.i icarus/db/hmmbuild.it icarus/db/hmmpfam.i icarus/db/hmmpfam.it icarus/db/hmmscan.i icarus/db/hmmsearch.i icarus/db/hmmsearch.is icarus/db/hmmsearch.it icarus/db/href.i icarus/db/localApplicationOptions.i icarus/db/pfamhmm.i icarus/db/pfamhmm.is icarus/db/pfamhmm.it icarus/db/srsdb.i icarus/db/srsgen.i web/WEB-INF/jsp/views/pfamhmmentry/pfamhmmentry.jsp
2011/11/14: fasta	Change needed to handle sequences from the new refseqvariations database with the fastaseqs view - as this database can return multiple sequences for the same entry
	icarus/db/fasta.il
2011/11/14: system	Fix for crashes with readseq.i - the sequence format conversion script available in SRS
	icarus/db/readseq.i
2011/11/14: fasta	Fix for spelling error in the description of ssearch
	icarus/db/ssearch.i
2011/11/14: kegg	Latest Kegg species mapping file. Note that if you use SRS prisma this file will be generated by Prisma
	icarus/db/kegg_species.i
2011/11/03: prisma srscheck	Added a new option (-novirtual), which will exclude virtual libraries from checking. This is useful in combination with the -nolinks option during first time updates
	etc/runPrisma icarus/lion/prisma/prismaCheckClasses.i icarus/lion/prisma/prismaCheckMain.i icarus/workflows/getSystemLibs.i icarus/workflows/srsCheckClasses.i icarus/workflows/srsCheckMain.i
2011/11/03: srscheck prisma	Change to ensure that (memory intensive) sort operations are done sequentially and not simultaneously
	icarus/workflows/buildPhase.i
2011/11/03: prisma	Change which should result in better parallization if there are multiple unpack commands
	icarus/lion/prisma/pretransPhase.i
2011/11/03: srscheck prisma	Fix for a problem in srscheck which occurs if the -L option is used in combination with -nolinks
	icarus/workflows/moveData.i
2011/11/03: srscheck	Fix for a problem with makefile target names when using srscheck with libraries which have dependencies
	icarus/workflows/srsCheckMain.i
2011/11/03: srscheck prisma	Fix to ensure that all links for relational databases with a staticlinks setting are build
	icarus/workflows/getSystemLibs.i icarus/workflows/linkPhase.i
2011/11/01: ensembl_mysql	Fix for a sequence display problem with some Ensembl Pufferfish transcripts
	icarus/db/exondatamodel.i
2011/10/27: kegg	Added support for the new Molecular weight, Sequence and Structure Map fields in the Kegg Drug database
	icarus/db/lcompound.i icarus/db/ldrug.i icarus/db/ldrug.is web/WEB-INF/jsp/views/ldrugentry/ldrugentry.jsp
2011/10/24: system uniprot	Another fix for the links subemtries in UniProt (our apologies for these multiple updates). The new version of srsgen.i will need to be merged with your copy of that file in SRSSITE, and you will have to re-index all databases in uniprot format.
	icarus/db/srsgen.i icarus/db/swisscommon.i
2011/10/19: system uniprot	Fix for an error in the ID type used for the uniprot link subentry libraries. After applying this update, please re-index all libraries which are in Uniprot format (uniprot_swissprot, uniprot_trembl). Note that the new version of srsgen.i needs to be merged with your copy of that file in SRSSITE
	icarus/db/srsgen.i icarus/db/swisscommon.i
2011/10/14: ipi	Added a note to the library information for IPI explaining that IPI is now retired and that the data is available via UniProtKB
	icarus/db/ipi.it
2011/10/12: prosite	Change to prevent a parsing error on a non-standard date value in a certain prosite entry
	icarus/db/prosite.is
2011/10/10: intact	Change for the link between IntactInteractor and UniProt, so we now use the primary accession number instead of the ID to link. After applyig this update you will have to re-index the links between IntactInteractor and the UniProt databases
	icarus/db/intactinteractor.i
2011/10/10: kegg	Changes so SRS Prisma can work with the new structure of the Kegg download site. Note that even if you do not use Prisma, there are some changes as we now require the renaming of some data files. See README.KEGG_NEW_STRUCTURE for details
	icarus/db/kegg_images.i icarus/db/kegggenes_aa.i icarus/db/kegggenes_na.i icarus/db/kegggenes_na.it icarus/db/kegggenome.i icarus/db/kegggenome.it icarus/db/keggorthology.i icarus/db/keggorthology.it icarus/db/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.it icarus/db/lglycan.i icarus/db/lglycan.is icarus/db/lglycan.it icarus/db/lreaction.i icarus/db/lreaction.is icarus/db/lreaction.it icarus/db/pathway.i icarus/db/pathway.is icarus/db/pathway.it icarus/db/pathwaybiopax.i icarus/db/pathwaytar.it
2011/10/10: system	Removed the now obsolete keggimages, pathwaykgml and pathwaybiopax databases, and set an offline data directory for pathway. Note that these changes need to be merged with your copy of srsdb.i in the SRSSITE directory
	icarus/db/srsdb.i
2011/10/07: srscheck prisma	Fix for a problem where srscheck correctly detects offline data files which need indexing, but then fails to use the offline settings in the resulting indexing and data move commands
	icarus/workflows/moveData.i icarus/workflows/srsCheckMain.i
2011/10/03: uniprot	Changed the ID type used for databases in uniprot format from using a 3 byte identifier to a 4 byte internal identifier, so SRS can accomodate the more than 16.7 million entries which are available in the current release of uniprot_trembl. After this update you will have to re-index uniprot_tremblxml
	icarus/db/uniprotxml.i
2011/09/30: uniprot	Changed the ID type used for databases in uniprot format from using a 3 byte identifier to a 4 byte internal identifier, so SRS can accomodate the more than 16.7 million entries which are available in the current release of uniprot_trembl. After this update you will have to re-index uniprot_trembl
	icarus/db/swisscommon.i
2011/09/29: imgt	Change to allow for the fact the imgt is now provided a .gz file, and no longer as a .Z file
	icarus/db/imgt.it
2011/09/28: iprmatches	Added code so Prisma wil set the release number for the iprmatches database after a data update
	icarus/db/iprmatches.it
2011/09/28: interpro	Fix so prisma can correctly extrat the InterPro version number from the datafile
	icarus/db/interpro.it
2011/09/28: iprmatches	Split the building of links between interpro and iprmatches in parts, as it becomes difficult to build th link in one indexing command
	icarus/db/iprmatches.i
2011/09/19: ensembl_mysql	Update for some small schema chanegs in Ensembl 64
	icarus/db/ensemblRDB.i icarus/db/ensembl_compara_schema.i icarus/db/ensembl_funcgen_schema.i icarus/db/ensemblcore_schema.i
2011/09/07: embl	Fix for a problem during indexing which could result in SRS not returning sequences for contig entries
	icarus/db/embl.is
2011/08/19: prodom	Removed sorting on the keyword field of prodom, as it contains multiple values per entry
	icarus/db/prodom.i
2011/08/18: kegg	Correction for the handling of the molecular weight fields in Kegg Compound
	icarus/db/lcompound.i
2011/08/18: kegg	Some updates for the Kegg Drug database. A molecular weight field was added, as well as the display of sequence information for peptides
	icarus/db/ldrug.i icarus/db/ldrug.is web/WEB-INF/jsp/views/ldrugentry/ldrugentry.jsp
2011/08/16: kegg	Update for the kegg species mapping file we use. Note that if you use SRS Prisma, the updated file will be generated for you by Prisma each time the kegg databases are updated
	icarus/db/kegg_species.i
2011/08/15: dssp	Change to allow for that fact that DSSP is now provided as .gz files, and no longer as .Z files
	icarus/db/dssp.i
2011/08/15: prisma	Fix for a problems where prisma would time-out on or misinterpret symbolic links on remote download sites
	icarus/lion/prisma/remoteConnection.i
2011/08/15: srscheck prisma	Made some changes to the building of links for virtual databases, so a few unnecessay files are no longer build
	icarus/workflows/linkPhase.i
2011/08/12: kegg	Changed the command for the removal of obsolete pathway files to allow for different behaviour of find on some systems
	icarus/db/pathwaytar.it
2011/08/12: embl genbank refseq ddbj imgt system	Reduced memory usage for EMBL/GenBank/Refseq/DDBJ entries with very large feature tables. Also introduced a mechanism to limit the number of sequence variant features which are processed for RefSeq (default limit is 10000 - this can be customized by editing a parameter in SRSSITE/standard.is). Note that the new version of standard.is needs to be merged with your copy in SRSSITE
	icarus/db/embl.is icarus/db/gbemblcommon.i icarus/db/gbemblcommon.is icarus/db/genbank.is icarus/db/genbankcommon.i icarus/db/standard.is
2011/08/12: srscheck prisma	Some changes so srscheck knows abou database depedencies. This means that databases which share data files (like emblnewfiles/emblnew, refseqfiles/refseqnew or uniseq/uniest) can be indexed in the same srsheck/srsdo run
	icarus/workflows/moveData.i icarus/workflows/moveIndicesPhase.i icarus/workflows/srsCheckMain.i
2011/08/11: prisma	Fixes for some problems in prisma, where it would loose track of index files created, or datafiles to be installed, occuring within database dependencies when prisma is used to re-index databases locally. Also a few other minor corrections
	icarus/lion/prisma/checkDependentDbs.i icarus/lion/prisma/localcopyPhase.i icarus/lion/prisma/movePrismaData.i icarus/lion/prisma/pretransPhase.i icarus/lion/prisma/prismaCheckClasses.i icarus/lion/prisma/reformatPhase.i icarus/lion/prisma/remoteConnection.i
2011/08/08: prosite	Change so prosite patterns can be used to launch the EMBOSS patmatdb program
	icarus/db/prosite.i
2011/08/08: srscheck prisma	Fixes for several issues with srscheck (and also prisma), which in some circomstances could result in srscheck not detecting valid on-line data files, warnings for duplicate targets when running srsdo or prisma, and some wrong link dependencies when multiple links exist between libraries
	icarus/workflows/buildPhase.i icarus/workflows/coreCheckClasses.i icarus/workflows/linkPhase.i
2011/08/08: system	LibLoc and data-tool related changes for EMBOSS 6.4. Please note that the changes need to be merged with your copies of these files in SRSSITE
	icarus/db/srsdb.i icarus/db/srsgen.i
2011/08/08: clustalw	Updated our support for ClustalW to version 2.1
	icarus/db/clustalw.i icarus/db/clustalw.is icarus/db/clustalw.it icarus/db/clustalwcommon.i icarus/db/nclustalw.i icarus/db/nclustalw.it
2011/08/08: emboss	Upgraded emboss support to emboss 6.4.0. For your convenience we make this upgrade also available as a separate tarball: EMBOSS6.4.0.tar.gz. Before applying this update make sure you read README.EMBOSS6.4.0
	EMBOSS6.4.0.tar.gz
2011/08/08: blast fasta	Upgraded our support for the Fasta programs to release 3.6. Main change for the user is that the output can now contain additional alignments for a hit (like blast HSPs). Note that we still provide an integration for TfastA, although this program no longer automatically is compiled if you install FastaA, and the author recommends to use TFastX
	icarus/db/blastgraphicdatamodel.i icarus/db/fasta.i icarus/db/fastacommon.i icarus/db/fastx.i icarus/db/fasty.i icarus/db/nfasta.i icarus/db/ssearch.i icarus/db/tfasta.i icarus/db/tfastx.i icarus/db/tfasty.i
2011/08/08: fasta	Upgraded our support for the Fasta programs to release 3.6. Main change for the user is that the output can now contain additional alignments for a hit (like blast HSPs). We also added support for the GLSearch and GGSearch programs, and for searching with peptides/oligos using FastS/M/F. Note that we still provide an integration for TfastA, although this program no longer automatically is compiled if you install FastaA, and the author recommends to use TFastX
	icarus/db/fasta.is
2011/08/05: genecards	Added support for the new DrugBank, HMDB and I2D data in the latest version of GeneCards
	icarus/db/genecards.i icarus/db/genecards.is web/WEB-INF/jsp/views/genecardsentry/genecardsentry.jsp
2011/08/05: cath	Update to allow for some changes on the CATH download site
	icarus/db/cath.it
2011/08/04: ccds	Some changes to work around some problems when downloading ccds fron the ncbi ftp site
	icarus/db/ccds.i icarus/db/ccds.is icarus/db/ccdsnuc.it
2011/08/04: reactome	Updates for some schema changes in Reactome 36
	icarus/db/reactome_schema.i
2011/08/03: kegg	Change to prevent parser crashes for the latest version of pathway
	icarus/db/pathway.is
2011/08/03: srscheck prisma	Fix for a problem where srscheck might not find valid online files
	icarus/workflows/coreCheckClasses.i
2011/07/19: ensembl_mysql	Some minor schema changes for release ensembl release 63
	icarus/db/ensemblRDB.i icarus/db/ensembl_funcgen_schema.i icarus/db/ensemblcore_schema.i
2011/07/18: blast fasta	Fix for an issue when linking to the matched results after refining the original blast result
	web/WEB-INF/jsp/views/blastentry/blastgraphic.jsp
2011/07/07: kegg	Switch to use the pathway kgml files to provide the KEGG pathway database, as KEGG no longer provides the html files we used for this. See comments in pathway.i for details
	icarus/db/pathway.i icarus/db/pathway.is icarus/db/pathwaykgml.i icarus/db/pathwaytar.it icarus/db/pathwayxml.il
2011/07/07: kegg	Updates for several KEGG databases: removed some obsolete fields (structure from lenzyme, compound and binding from lglycan, compound and glycan from lreaction. Added new Mass fields to lcompound, and changed the way these databases are linked to the pathway database
	icarus/db/lcommon.is icarus/db/lcompound.i icarus/db/lcompound.is icarus/db/lenzyme.i icarus/db/lglycan.i icarus/db/lglycan.is icarus/db/lreaction.i icarus/db/lreaction.is web/WEB-INF/jsp/views/lcompoundentry/lcompgeneral.jsp web/WEB-INF/jsp/views/lenzymeentry/lenzymeentry.jsp web/WEB-INF/jsp/views/lglycanentry/lglycangeneral.jsp web/WEB-INF/jsp/views/lreactionentry/lreactgeneral.jsp
2011/06/07:	Conversion information needed for old usage objects after extending usage recording in prisma
	icarus/util/classAttic/Class_PrismaLibResourceUsage_2429876272.i icarus/util/classAttic/Class_PrismaResourceUsage_1123318200.i
2011/06/01: pfam	Change to allow for the new WK (wikipedia) line in Pfam
	icarus/db/pfam.i icarus/db/pfam.is web/WEB-INF/jsp/views/pfamentry/pfamentry.jsp
2011/06/01: kegg	Fix for a parsing error occuring with the latest version of the Kegg Genome database
	icarus/db/kegggenome.is
2011/06/01: transfac	Fixes for some parser errors occurring with the latest data
	icarus/db/tffactor.is icarus/db/tffragment.is
2011/06/01: ensembl_mysql	Update to allow for some minor scheme changes in EnsEMBL 62
	icarus/db/ensemblRDB.i icarus/db/ensembl_compara_schema.i icarus/db/ensemblcore_schema.i
2011/05/19: prisma	Change so the main dates on the prisma reports refer to the date a prisma run was started, and no longer to the date the report was generated (but we still mention the generation date)
	icarus/lion/prisma/decisionReport.i icarus/lion/prisma/dumpTarget.i icarus/lion/prisma/generateLinkReports.i icarus/lion/prisma/printBuildPages.i icarus/lion/prisma/printDownloadPages.i icarus/lion/prisma/printLinkPages.i icarus/lion/prisma/printMainPage.i icarus/lion/prisma/printMovePages.i icarus/lion/prisma/printPretransPages.i icarus/lion/prisma/printReformatPages.i
2011/05/19: prisma	Change to include the display of cpu/walltime and dowload size and time in the prisma usage reports
	icarus/lion/prisma/cpuslots.il icarus/lion/prisma/printUsageReport.i icarus/lion/prisma/prismaCheckClasses.i icarus/lion/prisma/prismatime.i icarus/lion/prisma/setReportPhase.i
2011/05/19: prisma	Change to reduce the amount of STDOUT when downloading large files, and a change to allow for a odd behaviour of the ls command on SELinux systems
	icarus/lion/prisma/remoteConnection.i
2011/05/19: prisma	Fix for a problem with sending reports by Email in some configurations
	etc/runPrisma icarus/lion/prisma/printMainPage.i
2011/05/11: uniprot	Fix for a problem with the indexing of teh xml version of UniProt. If you have enabled the uniprot xml databases in SRS, and they contain 0 entries, you should re-index uniprot_swissprotxml and uniprot_tremblxml
	icarus/db/uniprotxml.is
2011/05/11: transfac	Removed sorting for the ElementDomination field in tfsite, as it soes not provide a single value per entry
	icarus/db/tfsite.i
2011/04/20: srscheck prisma	Fix for a problem where srscheck or prisma might not detect valid online datafiles
	icarus/workflows/coreCheckClasses.i
2011/04/11: blast fasta system	Improved the blast/fasta graphical view by displaying the alignments on the same page as the image, with selectionboxes to select results for further analysis. Note that the new version of loader.i needs to be merged with your copy of this file in SRSSITE
	icarus/db/blastgraphicdatamodel.i icarus/db/loader.i web/WEB-INF/jsp/views/blastentry/blastgraphic.jsp
2011/04/08: srscheck prisma	Fix for a problem where srscheck and prisma might not find the current datafiles if the indices are missing
	icarus/workflows/coreCheckClasses.i
2011/04/08: prisma	Fix for an email problem if reporting is invoked using the reportPrisma command
	icarus/lion/prisma/printMainPage.i
2011/04/06: genecards	Adjusted codes to get better behaviour when using getz -f for the display of fields. Note that for GeneCards we would recomment to use getz -vf for field retrieval, as for some fields where the data has to be collected from differnt parts of the data the -f option will not work.
	icarus/db/genecards.i
2011/04/06: genecards	Changed Genecards so IDs are now case-sensitive (this is needed to avoid duplicate ID proplems. After applying this update you will have to re-index the GeneCards ID field
	icarus/db/genecards.i
2011/04/04: system	Fix for a tallying problem when creating weekly/monthly usage reports
	logs/logcount.is
2011/03/30: ensembl_mysql	Fix for a problem with the ExonSequence view for Ensembl transcripts
	icarus/db/ensemblRDB.i
2011/03/30: omim	Removed debug code which was displaying the SRS internal XML reoresentation of the entry within the omim entry view
	web/WEB-INF/jsp/views/omimentry/omimentry.jsp
2011/03/29: prisma	Fix for a problem where fasta/blast file generation result in duplicates if a fasta file generated by a previous Prisma run is still present in an offline location when a new Prisma run is started
	icarus/lion/prisma/reformatPhase.i
2011/03/29: genbank refseq ddbj	Removed a srs83 specific construction which allows for the transparent construction of contig sequences
	icarus/db/genbank.is
2011/03/28: prisma	Fix for a problem where fasta data generated during the Prisma Reformat phase could end up in the STDOUT of a command instead of in a datafile
	icarus/lion/prisma/reformatPhase.i
2011/03/25: pfam	Change to allwo once again for the download of swisspfam (it was not available for a while), and fix for a prsing problem with the latest version of teh swisspfam data
	icarus/db/swisspfam.is icarus/db/swisspfam.it
2011/03/25: genbank embl refseq ddbj imgt	Fix for some parsing errors in IMGT
	icarus/db/gbemblcommon.is
2011/03/25: blast fasta	Modified a step which removes version numbers from EMBL/GenBank/RefSeq identifiers to be more specific, so it does not strip numbers from other identifiers
	icarus/db/blast.is icarus/db/fasta.is
2011/03/23: srscheck prisma	Change so srscheck and Prisma will keep the file order for multiple files of the original indexing job in cases where only a few fields are (re-)indexed.
	icarus/workflows/buildPhase.i icarus/workflows/coreCheckClasses.i
2011/03/23:	Fixed an issue with the selection of groups of databases in complex nested blast databse selection setups
	web/WEB-INF/jsp/toollaunch/checkboxHelper.jsp
2011/03/23: kegg	Updated Kegg species mapping file. Note that if you use SRS Prisma you do not need to update this file as Prisma will generate it automatically
	icarus/db/kegg_species.i
2011/03/22: medline	Added a new field which contains PubMed Ids for references which are cited by an article. We use this to create an internal link within the medline databases, which allows us not only to display in the entry viewthe references wich are cited, but also to display a list of articles which are refering to the article you are viewing. It should be noted that this list will be incomplete, as currently only about 7% of medline entries contain citation information. After applying this update you should fully re-index all medline databases is SRS
	icarus/db/medline.i icarus/db/medline.is icarus/db/medlinecommon.i icarus/db/medlinenew.i icarus/db/medlinerelease.i web/WEB-INF/jsp/views/medlineentry/medlineentry.jsp
2011/03/22: system kegg	Added hypertext links to LigandBox, LipidBank, LipidMap, pdb ligands, 3DMet, NikkaJi (the Japan Chemical Substance Dictionary) and KnapSack to the Kegg Drug and Compound databases. Please note that the new href.i file needs to be merged with your copy of that file in SRSSITE
	icarus/db/href.i icarus/db/lcommon.is icarus/db/ldrug.is
2011/03/22: kegg	Change for the way the keyword field in Kegg Genome is indexed, as the keywords are no longer separated by a ; but by a ,
	icarus/db/kegggenome.i icarus/db/kegggenome.is
2011/03/22: dbsts embl genbank refseq ddbj interpro omim pdb pfam prosite rebase system uniprot ipi	Harmonized the way author names and journal abbreviations are indexed for various databases, so they match the way these are indexed for medline - which is without "." between initials and abbreviation terms. Previously we were including "." in this for the major sequence databases. If you anticipate that this change might confuse your users, the new standard.is file (to be merged with your copy in SRSSITE) contains a mechanism to retain the old behaviour, or to have both the old and new way of indexing the author and journal fields
	icarus/db/dbsts.is icarus/db/embl.is icarus/db/genbank.is icarus/db/interpro.is icarus/db/omim.is icarus/db/pdb.is icarus/db/pfam.is icarus/db/prositedoc.is icarus/db/rebase.is icarus/db/standard.is icarus/db/swissprot.is
2011/03/22: dbsts interpro omim pdb pfam prosite rebase system uniprot medline embl genbank ddbj	Harmonized the way literature references are displayed for different databases, sticking to a format which resembles the Vancouver style for citations, which is also used by the NLM. See also http://www.nlm.nih.gov/bsd/uniform_requirements.html
	icarus/db/dbsts.i icarus/db/interpro.i icarus/db/omim.i icarus/db/pdb.i icarus/db/pfam.i icarus/db/prositedoc.i icarus/db/rebase.i icarus/db/srsgen.i icarus/db/swisscommon.i web/WEB-INF/jsp/views/interproentry/interproentry.jsp web/WEB-INF/jsp/views/medlineentry/medlineresults.jsp web/WEB-INF/jsp/views/omimentry/omimentry.jsp web/WEB-INF/jsp/views/pdbentry/pdbentry.jsp web/WEB-INF/jsp/views/pfamentry/pfamentry.jsp web/WEB-INF/jsp/views/prositedocentry/prositedocentry.jsp web/WEB-INF/jsp/views/rebaseentry/rebaseentry.jsp web/WEB-INF/tags/referencetable.tag
2011/03/22: refseq	Reduced partsize for inedxing to prevent memory problems with some RefSeq datafiles
	icarus/db/refseqrelease.i
2011/03/21: prisma	Removed a debug print statement
	icarus/lion/prisma/prismastatus.is
2011/03/18: uniprot	Added a (non-indexed) field which allows for the retrieval of the coordinates of a sequence feature
	icarus/db/swisscommon.i
2011/03/17: genecards system	Updates for release 3.05 of GeneCards. Note that the name of the download server has changed, so if you do not use prisma you may have to change your own update procedure. As usual, the new href.i will need to be merged with your copy of this file in SRSSITE
	icarus/db/genecards.i icarus/db/genecards.is icarus/db/genecards_datamodel.i icarus/db/genecardstar.it icarus/db/href.i web/WEB-INF/jsp/views/genecardsentry/genecardsentry.jsp
2011/03/16: chebi	Fix for a problem with the display of comments in ChEBI
	web/WEB-INF/jsp/views/chebientry/chebientry.jsp
2011/03/14: ccds	Fix needed to handle empty fields in CCDS
	icarus/db/ccds.is
2011/03/03: ensembl_mysql	Fix for a display problem for some Pufferfish ensembl gene entries
	icarus/db/ensemblgenemodel.i
2011/03/01: prisma	Change so one cannot activate on obsolete feature image generation feature which we had in provious version of SRS/Prisma
	icarus/lion/prisma/configurePrisma.i
2011/03/01: prisma	Fix for a potential crash during the generation of the usage report image if all commands timed during a prisma run have take very little time to complete
	icarus/lion/prisma/cpuslots.il
2011/03/01: prisma	Fix for a problem with sending Emails during reporting and monitoring of a prisma run
	icarus/lion/prisma/printMainPage.i icarus/lion/prisma/prismaRunWatcher.i
2011/03/01: prisma srscheck	We added the collection of timing information to the various checking steps in prisma, so the usage report can show how much time is spend in these stages. Added more timestamps in the debug output, which should help troubleshooting. Removed some duplication of tasks which was occuring between update rounds in prisma.
	etc/runPrisma icarus/lion/prisma/dumpTarget.i icarus/lion/prisma/inspectClasses.i icarus/lion/prisma/prismaCheckMain.i icarus/lion/prisma/prismadata.i icarus/lion/prisma/reformatPhase.i icarus/workflows/coreCheckClasses.i
2011/03/01: prisma srscheck	We implemented a new mechanism for staging the index merge steps for large databases, which should greatly reduce the number of partial index files which accumulates in the offline index directory. This can be controlled via a new -mergeThreads command line option available to both srscheck and runPrisma. For a full explanation see README.mergethreads
	icarus/lion/prisma/checkRemoteFiles.i icarus/lion/prisma/remoteConnection.i icarus/workflows/buildPhase.i icarus/workflows/srsCheckClasses.i icarus/workflows/srsCheckMain.i
2011/03/01: prisma	We made some changes to the prisma status database to prevent duplicate ID errors occuring during a prisma run
	icarus/lion/prisma/prismaCheckClasses.i icarus/lion/prisma/prismaInvalidate.i icarus/lion/prisma/prismastatus.i icarus/lion/prisma/prismastatus.is icarus/lion/prisma/prismaview.i
2011/02/11: system	Added support for the new GeneTree and NextProt hypertext links in UniProtKB. Please note that the new href.i and dbxref.i need to be merged with your copies of these files in SRSSITE
	icarus/db/dbxref.i icarus/db/href.i
2011/02/10: reactome	Removed a debug print statement
	web/WEB-INF/jsp/views/reactomeentry/go.jsp
2011/02/09: ensembl_mysql	Modifications to allow for some schema changes in ensembl 61
	icarus/db/ensemblRDB.i icarus/db/ensembl_compara_schema.i icarus/db/ensembl_funcgen_schema.i icarus/db/ensemblcore_schema.i
2011/02/03: ipi	Change in the way prisma looks for ipi file updates, as the previous method had to follow some symbolic links, which on some platforms could cause the wgetPrisma program to crash
	icarus/db/ipi.it
2011/01/24: blast	Fix for a problem with linking to uniseq data
	icarus/db/blast.is
2011/01/21: system	Added support for the new Allergome link in UniProt. Please note that the new versions of href.i and dbxref.i need to be merged with your copies of those files in SRSSITE
	icarus/db/dbxref.i icarus/db/href.i
2011/01/19: system	Removed a unnecessary bracket which was causing problems with srssection
	icarus/db/rdbaccess.i
2011/01/19: system	removed some srs83 specific acceptPattern attributes
	icarus/db/localApplicationOptions.i
2011/01/18: blast	Change so blast indexing will not stop at entry IDs which contain characters which have a special meaning in regular expressions
	icarus/db/blast.is
2011/01/05: entrezgene	removed debug statement that writes output to terminal window
	icarus/db/entrezgene_dm.i
2010/12/23: entrezgene	Change so the entryview does not crash if there is a failure when trying to retrieve information needed for drawing teh genomic context cartoon
	icarus/db/entrezgene_dm.i
2010/12/22: kegg	Added support for the new drug target field in the kegg gene databases
	icarus/db/kegggenes.i icarus/db/kegggenes.is icarus/db/kegggenes_aa.i icarus/db/kegggenes_na.i web/WEB-INF/jsp/views/kegggenesentry/kegggenesentry.jsp
2010/12/21: blast	Change so psiblast uses the the same set of protein sequence databases which is available for the other blast programs
	icarus/db/psiblast.i
2010/12/21: reactome	Updates for Reactome version 35. Note that there are fairly major schema changes in this release, so you should apply this update at the same time when you load Reactome 35 into mysql.
	icarus/db/reactome.i icarus/db/reactome_schema.i web/WEB-INF/jsp/views/reactomeentry/go.jsp
2010/12/15: pdb	Change so we can export all models in PDB files which contains multiple structures (usually NMR derived)
	icarus/db/pdb.is
2010/12/13: kegg	Change to deal with stricter session management in SRS 8.3.0.5
	icarus/db/pathwayxml.is
2010/12/08: entrezgene	Fix for a coding error which could couse entrezgene indexing to crash
	icarus/db/entrezgene.is
2010/12/08: kegg	Fix for the conversion script which builds data for chemical structure searching for the Kegg databases, needed to deal with session management changes in SRS 8.3.0.5
	icarus/db/lcommon.is
2010/12/06: entrezgene	We have added a genomic context image, showing neighbouring genenes on the chromosome, to the entry display for entrezgene. Note that this update requires two new fields: chrll and chrlr - and that the entrydisplay will fail until these fields have been indexed. If you have a seperate test installation we would recommend that you index these new fields first on that installation, and then apply the update to your production installation with the new indices. If that is not possible, first update the entrezgene.i and entrezgene.is files, then build the new indices, and then apply the updates entrezgene_dm.i and entrezgeneentry.jsp files.
	icarus/db/entrezgene.i icarus/db/entrezgene.is icarus/db/entrezgene_dm.i web/WEB-INF/jsp/views/entrezgeneentry/entrezgeneentry.jsp
2010/12/02: kegg	Change to ensure that the Kegg Drug data is downloaded and unpacked, as the tar archive containing this data sometime only changes its timestamp, but not its size
	icarus/db/kegg_images.i
2010/12/01: fasta	Another small fix needed for correct html linking in fasta results
	icarus/db/fasta.is
2010/11/29: taxonomy	Fix for a problem which would stop prisma from downloading the taxonomy data file due to an issue with a symbolic link in the taxonomy download directory
	icarus/db/taxonomy.it
2010/11/29: fasta	Some corrections to handle linking from fasta results
	icarus/db/fasta.is
2010/11/29: ensembl_mysql	Updates for release ensembl release 60. The main change is that the table containing ontology references has been renamed
	icarus/db/ensemblRDB.i icarus/db/ensembl_compara_schema.i icarus/db/ensembl_funcgen_schema.i icarus/db/ensemblcommon.i icarus/db/ensemblcore_schema.i icarus/db/ensembldatamodel.i
2010/11/25: fasta	Fix for linking when multiple databases have been selected for a fasta search and ensure fasta hits have hypertext links in the graphical results view
	icarus/db/fasta.is
2010/11/05: blast	Added an option to switch off sequence filtering for bl2seq
	icarus/db/bl2seq.i
2010/11/01: prisma	Extend the method for estimating the uncompressed file size for remote data by using existing local data as a guide to zip archives
	icarus/lion/prisma/checkRemoteFiles.i
2010/11/01: prisma	Fix so the inspection part of prisma will not crash if a tool is not part of a group
	icarus/lion/prisma/inspectReport.i
2010/10/26: prisma	Fix for a problem with dependent databases which are updated by mirroring, where SRS/Prisma might try to index the data before the downloading of the data has finished.
	icarus/lion/prisma/pretransPhase.i
2010/10/18: system	Changed some single quotes in blast database selection examples to double quotes - as they involved variable substition, and added some database mapping values for refseq
	icarus/db/localApplicationOptions.i
2010/10/18: genecards	Corrected some database names used in linking from GeneCards to RefSeq
	icarus/db/genecards.i
2010/10/18: homologene	Removed PubMed links/fields from HomoloGene, as the data no longer contains PubMed references
	icarus/db/homologene.i icarus/db/homologene_datamodel.i web/WEB-INF/jsp/views/homologeneentry/homologeneentry.jsp
2010/10/13: cath	Change to allow for new file names on the cath download site. Since the new filenames still have a date stamp well in the past, you may to do a "runPrisma -force cath -nomove" to force a new download
	icarus/db/cath.i icarus/db/cath.it
2010/10/13: ccds	Fix for a display problem for ccds (dna and protein) caused by a loader mismatch
	icarus/db/ccds.i
2010/10/13: go_xml	Fix for a wget stability problem when trying to accecc the go ftp site
	icarus/db/go.it
2010/10/13: blast	Removed a SRS8.3 specific attribute from various tooloptions which were changed when we recently upgraded our blast implementation to blastplus
	icarus/db/blastcommon.i icarus/db/blastn.i icarus/db/blastp.i
2010/10/11: system uniprot ipi	Change so our hypertext links to ensembl can use the new simplified unique ID method of accessing the ensembl website (which is needed as uniprot no longer provides the species name in the ensembl reference line), while retaining the hypertext links to an internal SRS installation of ensembl. Note that the new version of href.i needs to be merged with your copy of that file in SRSSITE
	icarus/db/href.i icarus/db/swissprot.is
2010/10/07: taxonomy	Small change in the way the species field is indexed - mainly to prevent virusses ending up with the name of their target as their species name
	icarus/db/taxonomy.is
2010/10/07: intact	We have split the indexing of the intact interactions library in parts as indixing it in one run was starting to take too much time
	icarus/db/intactinteraction.i
2010/10/05: pdb	Fix for a parsing error caused by a missing journal name in a PDB entry
	icarus/db/pdb.is
2010/09/28: blast	Updated our implementation of blast to use blastplus - the latest revamp of the ncbi blast suite. Please check README.blastplus for some notes and further details
	icarus/db/bl2seq.i icarus/db/bl2seq.is icarus/db/blast.is icarus/db/blastcommon.i icarus/db/blastn.i icarus/db/blastp.i icarus/db/blastx.i icarus/db/psiblast.i icarus/db/tblastn.i icarus/db/tblastx.i
2010/09/28: kegg	latest kegg species mapping file. Note that if you use prisma, prisma will generate this file automatically with each kegg update
	icarus/db/kegg_species.i
2010/09/27: genbank refseq ddbj	Moved the protein id, taxonomy id and gene name fields from the feature subentry to the main entry of refseqp, as they only occur in the CDS feature, of which there is only in in refseqp. After applying this update you will have to reindex the ge,prd and txi fields for refseqprelease and refseqpnew - and it may be better to remove the existing indices, as otherwise srscheck or prisma will not detect that re-indexing is required
	icarus/db/genbankcommon.i
2010/09/23: system	Change to the way blast/fasta searchable databases are displayed when "guiType:multi" is set - instead of a html multiselect box, a nested menu with checkboxes is presented to the user. Please have a look at the notes/example in the new localApplicationOptions.i file to see how to configure this
	web/WEB-INF/jsp/toollaunch/index.jsp web/WEB-INF/jsp/toollaunch/main.jsp
2010/09/23: system	Update localApplicationOptions.i to include parameters for blastplus and added example databases for remote blast. Added examples and comments on how to provide menu nesting, and changed the default guiType setting for blast/fasta databases from menu (single database selection) to multi (multi database selection)
	icarus/db/localApplicationOptions.i
2010/09/23:	Updated our implementation of blast to use blastplus - the latest revamp of the ncbi blast suite. Please check README.blastplus for some notes and further details
	web/javascript/tools/blast.js
2010/09/23: system	updated quickSearchOptions.i so the database names provided for blast quicksearches match those in the new localApplicationOptions.i file - note that both quickSearchOptions.i and localApplicationOptions.i are meant to be costomized, with the active copy located in SRSSITE
	icarus/db/quickSearchOptions.i
2010/09/22: prisma	Change so prisma will print out a warning during the checking phase if a subdirectory cannot be accessed while traversing a directory tree
	icarus/lion/prisma/remoteConnection.i
2010/09/21: kegg	Change needed as reaction pair field has been removed, and glycan fields is now located in the comments line, and drug references have been added
	icarus/db/lcommon.is icarus/db/lcompound.i icarus/db/lcompound.is icarus/db/ldrug.i web/WEB-INF/jsp/views/lcompoundentry/lcompoundlinks.jsp
2010/09/21: embl	Change so we will not automatically include the expanded contigs in emblnew - SRS will then use the contigs from the release, and build the relevant sequences on the fly. If you prefer to have the expanded contigs (this takes significant diskspace), comment in the relevant section in emblnewfiles.it
	icarus/db/emblnewfiles.it
2010/09/21: embl	Change so we will not automatically include the expanded contigs in emblnew - SRS will then use the contigs from the release. If you prefer to have the expanded contigs (this takes significant diskspace), comment in the relevant section in emblnewfiles.it
	icarus/db/emblnewfiles.it
2010/09/21: prisma	Change to allow for somewhat more flexibility in specifying non-standard fasta and blast converters
	icarus/lion/prisma/reformatPhase.i
2010/09/21: kegg	Change to suppress a parsing error (caused by a fault in the data) during indexing
	icarus/db/pathway.is
2010/09/21: hssp	Increased the number of parts used for indexing hssp
	icarus/db/hssp.i
2010/09/20: prisma	Change which allows the use of database dependencies for libraries which are updateded by mirroring, so they can be scheduled later in the update cycle
	icarus/lion/prisma/checkDependentDbs.i icarus/lion/prisma/localcopyPhase.i icarus/lion/prisma/prismaCheckClasses.i
2010/09/10: kegg	Support added to KEGGGENOME for KEYWORDS field
	icarus/db/kegggenome.i icarus/db/kegggenome.is web/WEB-INF/jsp/views/kegggenomeentry/kegggenomeentry.jsp
2010/08/13: system	Change to allow for the new ProteinModelPortal link in uniprot. Please note that the new versions of href.i and dbxref.i need to be merged with your copies of these files in SRSSITE
	icarus/db/dbxref.i icarus/db/href.i
2010/08/13: dbest	Change to be more tolerant for non-standard characters in est names
	icarus/db/dbest.is
2010/08/12: genecards	Workaround for a data production problem in genecards 3.03 which left the PDB references in the ENSEMBL lines empty. We now collect the PDB references from the SWISSPROT line in the genecards files
	icarus/db/genecards.i icarus/db/genecards.is
2010/08/11: genecards system	Update for genecards release 3.03. Please note that after unpacking the genecards tar archive, the data is now located in a subdirectory called old_website. We have modified the unpackcommand used by prisma to create symlinks to the directories in the old_website subdirectory, but if you are not using prisma, or if prisma has already downloaded and unpacked the file, you may have to create the relevant symlinks manually. Also not that the new copy of href.i needs to be merged with your copy of that file in SRSSITE
	icarus/db/genecards.i icarus/db/genecards.is icarus/db/genecardstar.it icarus/db/href.i web/WEB-INF/jsp/views/genecardsentry/genecardsentry.jsp
2010/08/09: ensembl_mysql	Updates for ensembl release 59
	icarus/db/ensemblRDB.i icarus/db/ensembl_compara_schema.i icarus/db/ensembl_funcgen_schema.i icarus/db/ensemblcore_schema.i
2010/08/05: imgt	Change to allow for longer entrynames, as found in the latest release of imgt
	icarus/db/imgt.i
2010/08/04: chebi	Update for some minor schema changes in release 71 of ChEBI
	icarus/db/chebi.i icarus/db/chebi_schema.i icarus/db/chebi_schema_mysql.i
2010/07/26: chebi	Fix for a case-sensitive name assignement problems slipped in with the recent changes we made to make chebi work with mysql
	web/WEB-INF/jsp/views/chebientry/chebientry.jsp
2010/07/21: prisma	Change to allow for a %d placeholder in an updateCheckCommand
	icarus/lion/prisma/checkRemoteFiles.i
2010/07/21: prisma	Fix so prisma will not stop an update if a subdirectory is inaccessible during a recursive download
	icarus/lion/prisma/remoteConnection.i
2010/07/21: system	LibLoc and data-tool relation changes for EMBOSS 6.3. Please note that the changes need to be merged with your copy of these files in SRSSITE
	icarus/db/srsdb.i icarus/db/srsgen.i
2010/07/21: emboss	Upgraded emboss support to emboss 6.3.0. For your convenience we make this upgrade also available as a separate tarball: EMBOSS6.3.0.tar.gz. Before applying this update make sure you read README.EMBOSS6.3.0
	EMBOSS6.3.0.tar.gz
2010/07/20: chebi system	Modified our implementation of ChEBI so it can also work with mysql in addition to oracle. Please see the comments in chebi.i on how to select the database system. The new chebi.i file also contains some instructions on how to increase speed for entry display. Note that the new versions of srsdb.i and rdbaccess.i need to be merged with your copies of these files in SRSSITE
	icarus/db/chebi.i icarus/db/chebi_schema.i icarus/db/chebidatamodel.i icarus/db/rdbaccess.i icarus/db/srsdb.i
2010/07/19: system	Fix for a problem which would prevent the tools/export slider to be visible in Internet Explorer 8
	web/javascript/slider.js
2010/07/13: geneseq	Fix for a problem where data compression is used with geneseq files
	icarus/db/geneseq.is
2010/07/13: reactome	update for release 33 of Reactome (Note that without this update the reactome entrview will crash)
	icarus/db/reactome.i icarus/db/reactome_schema.i
2010/06/25: embl	Correction for the indexing of the length of sequence features in databases in EMBL format
	icarus/db/emblcommon.i
2010/06/24: kegg	Fix for a display error for chemical structures in lcompound and ldrug when using the Marvin applet
	icarus/db/lcommon.is
2010/06/18: system	Added support for several new ensembl hypertext links in uniprot. Please note that the new version of href.i and dbxref.i will need to be merged with your copies of these files in SRSSITE
	icarus/db/dbxref.i icarus/db/href.i
2010/06/01: uniref	Change so we build the link between uniref50 and uniref90 in parts, in order to reduce memory usage
	icarus/db/uniref90.i
2010/06/01: blast	Fix for a bug when using external links in blast results
	icarus/db/blast.is
2010/06/01: ensembl_mysql	Updates for ensembl release 58
	icarus/db/ensemblRDB.i icarus/db/ensembl_compara_schema.i icarus/db/ensembl_funcgen_schema.i
2010/05/28: system entrezgene go_mysql	Added some new concepts (Gene, Small Molecule), which should make it easier for your users to find certain databases. Also added new cocepts to some databases. Note that the new concepts.i file should be merged with your copy of this file in SRSSITE.
	icarus/db/concepts.i icarus/db/entrezgene.i icarus/db/gogeneproducts.i
2010/05/21: emboss	Change so the mandatory pattern option is more prominently displayed on the launch pages for fuzzpro, fuzznuc and fuzztran
	icarus/lion/emboss/fuzznuc.i icarus/lion/emboss/fuzzpro.i icarus/lion/emboss/fuzztran.i
2010/05/21: system interpro iprmatches	Updated, added and fixed various hypertext links for interpro and iprmatches. Please note that the new version of href.i needs to ne merged with your copy of that file in SRSSITE
	icarus/db/href.i icarus/db/interpro.is icarus/db/iprmatches.is
2010/05/13: genecards system	Added support for the new LSDB and EPITOMICS lines in genecards. Please note that the new version of href.i needs to be merged with your copy of this file in SRSSITE
	icarus/db/genecards.i icarus/db/genecards.is icarus/db/href.i web/WEB-INF/jsp/views/genecardsentry/genecardsentry.jsp
2010/05/07: kegg system	Added a field to search lcompound by pubchem sid. After applying this update you will have to index the new fields. Please note that the new version of srsgen.i needs to be merged with your copy of this file in SRSSITE
	icarus/db/lcompound.i icarus/db/lcompound.is icarus/db/srsgen.i
2010/05/07: system	Added a new concept for drugs. Pleae note that the new concepts.i file needs to be merged with your copy of this file in SRSSITE
	icarus/db/concepts.i
2010/05/07: kegg system	Added new views which allows for the export of references from the major sequence databases in a format suitable for reference manager software, and added a view which allows for the export of chemical structures as molfile. Please note that the new versions of views.i and loader.i need to be merged with your copy of this file in SRSSITE
	icarus/db/lcommon.is icarus/db/loader.i icarus/db/seqreferences.il icarus/db/views.i
2010/05/07: uniprot	Corrected an error with browser display of uniprot xml
	icarus/db/uniprotxml.il
2010/05/07: blast	Fix for a display issue in pdf exports
	icarus/db/blast.is
2010/05/07: embl uniprot ipi	Fix for a problem with the parsing of volume numbers for some literature references
	icarus/db/embl.is icarus/db/swissprot.is
2010/05/07:	Removed a spurious single quote from the insdseq xml output when it is displayed as a view in SRS
	icarus/db/insdseqxml.il
2010/05/07: kegg	latest version of the kegg species mapping file. Note that if you use prisma to keep your data up-to-date prisma will regenerate this file when appropriate
	icarus/db/kegg_species.i
2010/05/04: system	Added support for the new ucd-2dpage link in uniprot. Please note that you will hevato merge the new version of dbxref.i and href.i with your copies of these files in SRSSITE
	icarus/db/dbxref.i icarus/db/href.i
2010/05/04: genecards	Change so prisma will pick upda the latest version of the genecards tar archive
	icarus/db/genecardstar.it
2010/04/28: chebi kegg	Added support for the use of JChemPaint for the display of chemical structures. See README.applets for more information
	icarus/db/chebidatamodel.i icarus/db/lcommon.is
2010/04/09: medline system	Added a new view which allows for the display and export pf medline data in medline (text) format. Please note that the new srsgen.i file will have to be merged with your copy of that file in SRSSITE
	icarus/db/medline.i icarus/db/medline.is icarus/db/medlinecommon.i icarus/db/medlineformat.il icarus/db/medlinenew.i icarus/db/medlinerelease.i icarus/db/medlineupdates.i icarus/db/srsgen.i
2010/04/06: kegg	Added a synonym finder for drug names from the KEGG drug database
	icarus/db/ldrug.i icarus/db/ldrug.is
2010/03/29: system	Added support for the new conoserver, genolist and mint links in uniprot. Please note that the new versions of dbxref.i and href.i need to be merged with your copies of these files in SRSSITE
	icarus/db/dbxref.i icarus/db/href.i
2010/03/29: prisma	Fix for a daylight saving time problem (Dates would be one day out of sync with their day names) with the calendar in the prisma report.
	icarus/lion/prisma/generateCalendar.i
2010/03/10: ensembl_mysql	Changes for release 57 of ensembl
	icarus/db/ensemblRDB.i icarus/db/ensembl_compara_schema.i icarus/db/ensembl_funcgen_schema.i icarus/db/ensemblcore_schema.i
2010/03/05: system uniprot ipi	Added support for the new SUPFAM, ProtClustDB and EuPathDB links in uniprot. Please note that you will have to merge the new versions of href.i and dbxref.i with your copies of these files in SRSSITE
	icarus/db/dbxref.i icarus/db/href.i icarus/db/swissprot.is
2010/03/03: genpept	Change to allow for the fact that genpept is now distributed as multiple files (the single file available before has become too large to handle for the genpept ftp server)
	icarus/db/genpeptrelease.it
2010/03/01: chebi	Fix for a problem drawing the ontology image caused by a change in ID for the root element of the ontology
	icarus/db/chebidatamodel.i
2010/02/17: ccds	Change to allow for a change in filenames on the download site for CCDS
	icarus/db/ccds.is icarus/db/ccdsnuc.it
2010/02/17: system kegg	Change to allow for new fields (pathway, module, disease) in the kegg orthology database. Note that the new href.i and srsgen.i files need to be merged with your copy in SRSSITE
	icarus/db/href.i icarus/db/keggorthology.i icarus/db/keggorthology.is icarus/db/srsgen.i web/WEB-INF/jsp/views/keggorthology/keggorthologyentry.jsp
2010/02/17: srscheck prisma	Fixes for several problems with non-standard link names
	icarus/workflows/linkPhase.i icarus/workflows/moveIndicesPhase.i
2010/02/15: cath system	Moved the definition for the PDB field from cath.i to srsgen.i, so it can be shared with other databases (like hmdb)
	icarus/db/cath.i icarus/db/srsgen.i
2010/02/12: fasta	Small fix needed for correct html linking in fasty results
	icarus/db/fasta.is
2010/02/11: kegg system	Important change for the kegg genome database. Please see README.KEGGGENOME for full details. Note that the new verson of href.i needs to be merged with your copy of that file in SRSSITE
	icarus/db/genKeggSpecies.i icarus/db/href.i icarus/db/kegg_species.i icarus/db/kegggenome.i icarus/db/kegggenome.is web/WEB-INF/jsp/views/kegggenomeentry/kegggenomeentry.jsp
2010/02/10: fasta	Added a description field to the results databases for the fasta programs
	icarus/db/fasta.is icarus/db/fastacommon.i icarus/db/nfasta.i icarus/db/ssearch.i
2010/02/02: ccds	Correction for the command which extracts the release number for ccdsprot
	icarus/db/ccdsprot.it
2010/02/02: kegg	Some changes to improve display speed for lcompound entries (especially those which have low accession numbers which typically are involved in a large number of reactions). After applying this update you will have to build loaderCaches for lreaction, lenzyme and lglycan. srscheck/prsima will do this, but if you prefer to do it manually, use commands like "srsbuild -f id -ldrCache ".
	icarus/db/lcommon.is icarus/db/lenzyme.i icarus/db/lglycan.i icarus/db/lreaction.i
2010/02/01: pdb	Change to speed up the display of pdb data in pdbml format in a web browser
	icarus/db/pdbml.il
2010/01/27: go_mysql	Change for the latest version of GO (mysql version). The updated file is compatible with earlier versions. Note that the data file containing the mysql dump for this is now called go_YYYYMMDD.seqdb-data.gz and no longer go_YYYYMMDD.seqdblite-data.gz.
	icarus/db/gotermdatamodel.i
2010/01/26: system uniprot ipi	Added support for new db link in Uniprot, to eggNOG. Note that the new versions of href.i and dbxref.i need to be merged with your copies of those files in SRSSITE
	icarus/db/dbxref.i icarus/db/href.i icarus/db/swissprot.is
2010/01/26: genecards	Correction for the prisma command which sets the release number of genecards after an update
	icarus/db/genecards.it
2010/01/21: unigene	Re-introduced the exp and rexp fields for unigene, as these fields have re-appeared in the data. After applying this update you will have to index these two fields
	icarus/db/unigene.i icarus/db/unigene.is web/WEB-INF/jsp/views/unigeneentry/unigeneentry.jsp
2010/01/15: kegg	Added support for the new INTERACTION line in the kegg drug database. After applying this update, please re-index ldrug
	icarus/db/lcommon.is icarus/db/ldrug.i icarus/db/ldrug.is web/WEB-INF/jsp/views/ldrugentry/ldrugentry.jsp
2010/01/15: medline	The 2010 release of medline contains a newly structured Comments and Correction section. We have now taken advantage of this to add a Comments subentry for medline, which allows searching by pubmed id and comment type (retraction, comment, citation etc). After applying this update you will have to re-index the medline databases.
	icarus/db/medline.i icarus/db/medline.is icarus/db/medlinecommon.i icarus/db/medlinenew.i icarus/db/medlinerelease.i icarus/db/medlineupdates.i web/WEB-INF/jsp/views/medlineentry/medlineentry.jsp
2010/01/11: genecards	Change to make sure that prisma will download the correct tar archive for genecards
	icarus/db/genecardstar.it
2010/01/06: system kegg	Change to allow for the new DISEASE line in the Kegg gene databases. After applying this update please index the new disease field. Please note that the new href.i file needs to be merged with your copy of that file in SRSSITE
	icarus/db/href.i icarus/db/kegggenes.i icarus/db/kegggenes.is icarus/db/kegggenes_aa.i icarus/db/kegggenes_na.i web/WEB-INF/jsp/views/kegggenesentry/kegggenesentry.jsp
2009/12/22: system	Added support for new db link in Uniprot, to ArachnoServer. Note that the new versions of href.i and dbxref.i need to be merged with your copies of those files in SRSSITE
	icarus/db/dbxref.i icarus/db/href.i
2009/12/18: genecards system	Updates for release 2.41.1 of genecards. Please note that if you use prisma to keep your databases up to data, prisma will download the wrong tar archive if you do no apply these changes. If prisma has already downloaded the wrong tar archive, remove the Genecards.tar.gz file from the data directory to force prisma to download it again. Please note that the updated version of href.i needs to be merged with your copy of that file in SRSSITE
	icarus/db/genecards.i icarus/db/genecards.is icarus/db/genecardstar.it icarus/db/href.i web/WEB-INF/jsp/views/genecardsentry/genecardsentry.jsp
2009/12/17: system	Added support for new db link in Uniprot, to InParanoid. Note that the new versions of href.i and dbxref.i need to be merged with your copies of those files in SRSSITE
	icarus/db/dbxref.i icarus/db/href.i
2009/12/16: chebi	Allow for a small schema change in release 63 of CheBI
	icarus/db/chebi_schema.i
2009/12/15: reactome	Update for some schema changes in release 31 of Reactome
	icarus/db/reactome_schema.i
2009/12/14: kegg	To allow for the increasing size of kegggenes we changed the link index between kegggenes and taxonomy so it is build in parts
	icarus/db/kegggenes_aa.i icarus/db/kegggenes_na.i
2009/12/10: pdb system	Added two new views to allow for the export of pdb data in pdbml (xml) and mmcif format. This uses two new databases (pdbml and pdbcif, hidden from the end user) for which you will have to download and install the data (or use prisma). If you do not want to provide these export, simply do no enable these new libraries. Note that the new version of srsdb.i should be merged with your copy in SRSSITE
	icarus/db/pdb.i icarus/db/pdbcif.i icarus/db/pdbcif.il icarus/db/pdbcif.is icarus/db/pdbml.i icarus/db/pdbml.il icarus/db/pdbml.is icarus/db/srsdb.i web/WEB-INF/jsp/views/pdbentry/pdbentry.jsp
2009/12/10: prisma srscheck	Fix for a problem where SRS or prisma has problems linking/removing/installing datafiles where the file names contain non standard characters. Note that this not cover cases where the filename contains a ?, *, [, ] or single quote
	icarus/lion/prisma/localcopyPhase.i icarus/lion/prisma/movePrismaData.i icarus/workflows/coreCheckClasses.i icarus/workflows/moveData.i icarus/workflows/srsCheckMain.i
2009/12/09: kegg	Small change to prevent a parsing error with the new map07222 entry in the kegg pathway database
	icarus/db/pathway.is icarus/db/pathwayxml.is
2009/12/09: kegg	Update for the kegg species mapping file. Note that if you use prisma to maintain your databases, this file will be generated automatically by prisma
	icarus/db/kegg_species.i
2009/12/08: kegg system	Added an option for export in kgml and biopax format for the pathway database. This requires the enabling of the new pathwaykgml and pathwaybiopax databases, and download of the relevant data. If you have prisma the data download is handled by the pathwaybiopaxtar and pathwaykgmltar databases. If you do not want to provide these export options, simply do not enable these databases. Note that the new version of srsdb.i needs to be merged with your copy of this file in SRSSITE
	icarus/db/pathway.i icarus/db/pathwaybiopax.i icarus/db/pathwaykgml.i icarus/db/pathwaytar.it icarus/db/pathwayxml.il icarus/db/pathwayxml.is icarus/db/srsdb.i
2009/12/08: pfam	Change needed to build read-links for pfamc
	icarus/db/pfam.is
2009/12/08: kegg	removed a reference to a non-existing concept
	icarus/db/ldrug.i
2009/12/07: prisma	Added an extra safety in our new method of estimating uncompressed file sizes to prevent problems when files grow a lot between releases
	icarus/lion/prisma/checkRemoteFiles.i
2009/12/07: prisma	Fix for an access problem for the geneseq download site
	icarus/lion/prisma/remoteConnection.i
2009/12/07: refseq	lowered the part-size used for indexing refseqrelease in parts to allow for the large differences in content between different datafiles
	icarus/db/refseqrelease.i
2009/12/04: prisma srscheck	Fixed a problem with building links for databases with mixed case database names
	icarus/lion/prisma/moveLibs.i icarus/lion/prisma/setReportPhase.i icarus/workflows/linkPhase.i
2009/12/04: prisma	Some improvements to the usage report: we make clearer on which nodes failures occur (these node names are now in red), and we now display all failures (previously we only displayed them if they had a runtime of more than one minute). Note that short processes which failed may still be invisible as they can be hidden by subsequent successfull processes in the graph
	icarus/lion/prisma/cpuslots.il
2009/12/03: dbsts enzyme go_xml kegg omim system uniprot	Added a new "AllNAmes" group field which allows a user to use a single search for all name type fields, like names, synonyms, alternative names, symbols etc. Please merge the new version of srsgeni.i with your copy of that file in SRSSITE, and also re-index enzyme after applying this update
	icarus/db/dbsts.i icarus/db/enzyme.i icarus/db/go.i icarus/db/lcompound.i icarus/db/ldrug.i icarus/db/lenzyme.i icarus/db/lglycan.i icarus/db/omim.i icarus/db/srsgen.i icarus/db/swisscommon.i
2009/12/03: pfam	Changes for release 24 of pfam. If you have already installed that data release, please re-index all pfam databases after applying these parser updates
	icarus/db/pfam.is icarus/db/pfama.i icarus/db/pfamc.i
2009/12/03: prisma	Fix for a LONG to INT overflow which could cause wrong sizes/times to be reported in the usage reports
	icarus/lion/prisma/printUsageReport.i icarus/lion/prisma/prismaCheckClasses.i
2009/12/03: medline system	Update for some small dtd changes in the 2010 release of medline. You shoukd preferably apply this update before you index the 2010 release, which is expected to become available mid December
	icarus/db/medlinecommon.i icarus/db/pubmedarticlesxml.il icarus/db/xml.il
2009/12/01: emboss	Minor change to allow colour postscript output for EMBOSS tools that produce colour graphics
	icarus/lion/emboss/charge.i icarus/lion/emboss/dotpathn.i icarus/lion/emboss/dotpathp.i icarus/lion/emboss/epestfind.i icarus/lion/emboss/hmoment.i icarus/lion/emboss/pepinfo.i icarus/lion/emboss/pepnet.i icarus/lion/emboss/pepwheel.i icarus/lion/emboss/plotorf.i icarus/lion/emboss/prettyplotn.i icarus/lion/emboss/prettyplotp.i icarus/lion/emboss/syco.i icarus/lion/emboss/tcode.i icarus/lion/emboss/wobble.i
2009/11/27: system	Parser update to include hyperlinks to phylomeDB and orthoDB in Uniprot
	icarus/db/dbxref.i icarus/db/href.i
2009/11/23: kegg system	Added support for the new METABOLISM field in the kegg drug database. Please merge the new version of srsgen.i with your copy in SRSSITE
	icarus/db/ldrug.i icarus/db/ldrug.is icarus/db/srsgen.i web/WEB-INF/jsp/views/ldrugentry/ldrugentry.jsp
2009/11/23: interpro	fix to permit parsing of 'Abstract' fields containing html layout markup
	icarus/db/interpro.is
2009/11/19: kegg	Fix for a problem which occurs if the sequence length is missing in the data
	icarus/db/kegggenes.is
2009/11/18: chebi	Update for release 62 of chebi, including support for the new Star field
	icarus/db/chebi.i icarus/db/chebi_schema.i icarus/db/chebidatamodel.i web/WEB-INF/jsp/views/chebientry/chebientry.jsp
2009/11/17: uniprot	Following customer feedback we have changed the NCBI Taxon ID field from a numerical field to a string field, since there is really no need to search this field with numerical ranges.
	icarus/db/swisscommon.i
2009/11/13: kegg	minor fix to prevent intermittent parsing error in lglycan due to an uninitialized variable
	icarus/db/lcommon.is
2009/11/09: entrezgene go_xml homologene interpro iprmatches medline uniref	Added views to allow for data export for these databases in their native xml format, including dtd or xml schema references
	icarus/db/entrezgene.i icarus/db/go.i icarus/db/homologene.i icarus/db/interpro.i icarus/db/iprmatches.i icarus/db/medlinecommon.i icarus/db/unirefcommon.i
2009/11/04: system uniprot ipi	Added two new fields for uniprot, which allow the user to retrieve (or restrict searches to) complete proteomes by either orgainism name or ncbi taxonomy Id. Please note that the new version of general.it needs to be merged with your copy of this file in SRSSITE
	icarus/db/general.it icarus/db/swisscommon.i icarus/db/swissprot.is
2009/11/03: prisma	Fixed an issue with some proxies, and an error reporting issue which could cause a crash
	icarus/lion/prisma/remoteConnection.i
2009/10/30: kegg	Added support for the new literature references in the kegg orthology database. After applying this update, re-index keggorthology, and if you have medline, also build the link indices to medline
	icarus/db/keggorthology.i icarus/db/keggorthology.is web/WEB-INF/jsp/views/keggorthology/keggorthologyentry.jsp
2009/10/30: ccds	Change to allow for a difference in the layout of the human and mouse data for CCDS
	icarus/db/ccds.is
2009/10/30: kegg	Correction for the way authors are indexed/displayed for the kegg genome database
	icarus/db/kegggenome.is
2009/10/30: geneseq genecards	Small correction for the download directory used by prisma
	icarus/db/aageneseqtar.it icarus/db/genecardstar.it icarus/db/nageneseqtar.it
2009/10/29: kegg	fix for a problem with structure display in lcompound
	icarus/db/lcompound.i
2009/10/27: entrezgene genecards homologene system	Moved some field definitions from databases specific files to srsgen.i so they can be used by multiple databases. Please merge the new version of srsgen.i with your copy in SRSSITE
	icarus/db/entrezgene.i icarus/db/genecards.i icarus/db/homologene.i icarus/db/srsgen.i
2009/10/22: entrezgene system	Change to allow for a change in the way links to the reactome database are provided. Please note that the new href.i file needs to merged with your copy of that file in SRSSITE
	icarus/db/entrezgene.is icarus/db/href.i
2009/10/22: reactome	Schema changes for release 30 of reactome
	icarus/db/reactome_schema.i
2009/10/21: kegg	Added a mechanism so SRS can deliver kegg images and molfiles directly via a http link instead of encoding them en sending them through the web services server. To use this, all you need to do is to link the kegg_images data directory to SRSROOT/web. This will only work if your tomcat installation has direct access to your data directories
	icarus/db/lcommon.is
2009/10/21: ddbj embl genbank refseq	Changed part sizes for the major sequence databases so less parts need to be build and merged. This should be suitable for most modern hardware configurations
	icarus/db/ddbj.i icarus/db/ddbjnew.i icarus/db/ddbjnewfiles.i icarus/db/ddbjrelease.i icarus/db/ddbjwgs.i icarus/db/embl.i icarus/db/emblcommon.i icarus/db/emblcontigs.i icarus/db/emblnew.i icarus/db/emblrelease.i icarus/db/emblwgs.i icarus/db/emblwgsnew.i icarus/db/emblwgsnewfiles.i icarus/db/emblwgsrelease.i icarus/db/genbank.i icarus/db/genbankcommon.i icarus/db/genbanknew.i icarus/db/genbankrelease.i icarus/db/genbankwgs.i icarus/db/refseq.i icarus/db/refseqnew.i icarus/db/refseqp.i icarus/db/refseqpnew.i icarus/db/refseqprelease.i icarus/db/refseqrelease.i
2009/10/21: prisma	Implemented a better way of estimating the size of uncompressed datafiles, using older versions of those files (if available) as a template. This should ensure more evenly distributed part sizes when indexing large databases in parts
	icarus/lion/prisma/checkRemoteFiles.i
2009/10/21: prisma	Small change to correct a proxy setting for wgetPrisma
	icarus/lion/prisma/remoteConnection.i
2009/10/21: kegg	latest kegg species mapping file. Note that if you have prisma this file will be automatically re-generated when the kegg databases are updated
	icarus/db/kegg_species.i
2009/10/19: pfam	Allow for a new line in the pfamA data, and change the download location for the pfam databases to use ftp.sanger.ac.uk. Note that we do not yet download the hmm data for HMMER version 3, as we do not yet support that version
	icarus/db/pfam.is icarus/db/pfama.it icarus/db/pfamb.it icarus/db/pfamc.it icarus/db/pfamhmm.it icarus/db/pfamseed.it
2009/10/15: system	Added support for the new genevestigator link in uniprot. Please note that the new dbxref.i and href.i need to be merged with your copies of those files in SRSSITE
	icarus/db/dbxref.i icarus/db/href.i
2009/10/15: kegg	removed an erroneous concept defintion for the kegg drug database
	icarus/db/ldrug.i
2009/10/14: kegg	fix for a jsp coding error which would break the lcompound view
	web/WEB-INF/jsp/views/lcompoundentry/lcompgeneral.jsp
2009/10/07: chebi kegg system	Added support for the marvin chemical structure viewing applet for chebi, kegg compound and kegg drug database. See README.applets for information about marvin. Please note that the new version of srsgen.i needs to be merged with your copy of that file in SRSSITE
	icarus/db/chebi.i icarus/db/chebidatamodel.i icarus/db/lcommon.is icarus/db/lcompound.i icarus/db/ldrug.i icarus/db/srsgen.i web/WEB-INF/jsp/views/chebientry/chebientry.jsp web/WEB-INF/jsp/views/lcompoundentry/lcompgeneral.jsp web/WEB-INF/jsp/views/ldrugentry/ldrugentry.jsp
2009/10/06: ensembl_mysql system	There have been significant changes with ensembl release 56. Please see README.ensembl56 for full details
	icarus/db/ensemblRDB.i icarus/db/ensembl_compara_schema.i icarus/db/ensembl_funcgen_schema.i icarus/db/ensemblaffy.i icarus/db/ensemblaffymodel.i icarus/db/ensemblaffymosquitomodel.i icarus/db/ensemblcommon.i icarus/db/ensemblcore_schema.i icarus/db/ensembldatamodel.i icarus/db/ensemblgene.i icarus/db/ensemblgenemodel.i icarus/db/ensemblkar.i icarus/db/ensemblmarker.i icarus/db/ensemblmosquito.i icarus/db/ensemblproteinmodel.i icarus/db/ensemblseq.i icarus/db/ensembltranscript.i icarus/db/rdbaccess.i icarus/db/srsdb.i icarus/lion/packages/ensemblRDB.ip web/WEB-INF/jsp/views/ensemblaffyentry/affymosquitoentry.jsp icarus/db/ensemblRDBconfig.i icarus/db/ensemblhuman_cq.i icarus/db/ensemblmouse_cq.i icarus/db/ensemblrat_cq.i
2009/10/02: entrezgene	Added a test which checks if the entrezgene xml file is properly terminated. This will prevent prisma from moving the data online in case the conversion from ASN1 has failed, but the gene2xml program has exited cleanly
	icarus/db/entrezgene.it
2009/09/22: refseq	Change so we build the link between refseqrelease and refseqprelease in parts, as building the link in one part now requires more than 4GB of memory
	icarus/db/refseqrelease.i
2009/09/17: refseq	Change so prisma will not download the refseq wgs master record files, as these do not contain sequence information
	icarus/db/refseqrelease.it
2009/09/14: system entrezgene	Change to handle 12 digit refseq accession numbers in the transcript and products cartoon in the entrezgene entry view
	web/WEB-INF/tags/geneproductimage.tag
2009/09/14: interpro	Fix for a display problem with interpro entries which have embedded an CDATA tag in the abstract field
	icarus/db/interpro.is
2009/09/14: entrezgene	removed a spurious debug print statement from the entrezgene parser
	icarus/db/entrezgene.is
2009/09/08: kegg	Change to allow for the fact that the kegg drug database is now provided in a separate tar archive
	icarus/db/kegg_images.i
2009/09/08: blast	Small change to prevent a parsing error with some bl2seq output
	icarus/db/bl2seq.is
2009/09/04: system	Change to allow for the new STRING link in the uniprot DR lines. Please note that you wil have to merge the new dbxref.i and href.i files with your versions of these files in SRSSITE
	icarus/db/dbxref.i icarus/db/href.i
2009/08/28: genbank embl refseq ddbj imgt	Changed the way we do hypertext links to refseq for coded_by features in refseqp - this should result in better performance when following that hypertext link
	icarus/db/gbemblcommon.is
2009/08/28: system kegg	Changes needed for the latest version of the kegg pathway database. There have been significant changes in the way references to other kegg databases are provided, and without this update these will not work in SRS. Note that the new pathway.is file is not backwards compatible with previous versions of the pathway data, so you will need to ensure that no old data is left in your pathway data directories (if you have SRS prisma, prisma will do that automatically). Please note that the new href.i file needs to be merged with your copy of that file in SRSSITE. After applying this update you will have to re-index pathway, and rebuild links to other kegg databases.
	icarus/db/href.i icarus/db/pathway.i icarus/db/pathway.is
2009/08/24: kegg	Change so we no longer try to extract gif image files from the pathway tar archive, as pathway has now fully switched to png images
	icarus/db/pathwaytar.it
2009/08/24: dbsts	Corrected a misconfigured sort parameter for the source fields in dbsts
	icarus/db/dbsts.i
2009/08/24: prisma srscheck	Implemented a new way of removing partial index files after index merging, in order to prevent performence problems due to NFS congestion
	icarus/lion/prisma/prismaCheckMain.i icarus/workflows/buildPhase.i icarus/workflows/linkPhase.i icarus/workflows/srsCheckMain.i
2009/08/17: genbank refseq ddbj	Correction for a wrongly configured setting for sorting by moleculetype in databases in GenBank format
	icarus/db/genbankcommon.i
2009/08/04: system	Added hypertext link support for the new CTD reference in uniprot. Please note that the new dbxref.i and href.i files need to be merged with your copies in SRSSITE
	icarus/db/dbxref.i icarus/db/href.i
2009/07/29: unigene uniprot	Change made to unigene, uniprot_swissprot and uniprot_trembl to fix problem with read links
	icarus/db/unigene.i icarus/db/uniprot_swissprot.i icarus/db/uniprot_trembl.i
2009/07/28: reactome	Update for release 29 of reactome
	icarus/db/reactome.i icarus/db/reactome_schema.i web/WEB-INF/jsp/views/reactomeentry/intercept.jsp web/WEB-INF/jsp/views/reactomeentry/notevent.jsp web/WEB-INF/jsp/views/reactomeentry/referenceentity.jsp
2009/07/27: ensembl_mysql	Updates for ensembl release 55
	icarus/db/ensemblRDB.i icarus/db/ensembl_compara_schema.i icarus/db/ensemblcore_schema.i
2009/07/23: homologene system	Moved the EntrezGeneId field defintion from homologene.i to to srsgen.i as it is also used for unigene. Please note that the new version of srsgen.i needs to be merged with your copy of srsgen.i in SRSSITE
	icarus/db/homologene.i icarus/db/srsgen.i
2009/07/23: unigene	Removed the link between unigene and entrezgene we recently added, as that link was already defined in entrezgene.i
	icarus/db/unigene.i
2009/07/21: system uniprot ipi	Added support for new UCSC link in Uniprot, and updated links to Gene3D, ArrayExpress, GeneCards, PDBsum. Note that the new versions of href.i and dbxref.i need to be merged with your copies of those files in SRSSITE
	icarus/db/dbxref.i icarus/db/href.i icarus/db/swissprot.is
2009/07/21: cath	update for the new download site for cath data
	icarus/db/cath.it
2009/06/29: prisma	Change to ensure internal links (ie links within a database) are moved online by prisma
	icarus/lion/prisma/moveLibs.i
2009/06/24: uniprot	Added a link for SRS 3D (visible if SRS3D is installed)
	web/WEB-INF/jsp/views/swissentry/swissentry.jsp
2009/06/23: unigene	Replaced the redundant/obsolete LocusLink field with a EntrezGeneId field, and removed some other fields which are no longer used. After applying this update you may want to rename the unigene loc indices to egid, and remove the pla, exp, rexp, gn and per indices
	icarus/db/unigene.i icarus/db/unigene.is web/WEB-INF/jsp/views/unigeneentry/unigeneentry.jsp
2009/06/18: embl genbank refseq ddbj imgt genpept system uniprot ipi	We have added two new views (TinySeqXML and INSDSeqXml) which allow for export of sequence data in XML format according to the INSD v.14 and NCBI TinySeq specifications. INSDSeqXML and TinySeqXML are available for EMBL, GenBank, DDBJ. RefSeq, RefSeqP and IMGT. TinySeqXML is further available for UniProt, GenPept and IPI. Note that the new versions of loader.i and views.i need to be merged with your copies of these files in SRSSITE
	icarus/db/embl.is icarus/db/emblcommon.i icarus/db/gbemblcommon.i icarus/db/gbemblcommon.is icarus/db/genbank.is icarus/db/genbankcommon.i icarus/db/genpept.is icarus/db/genpeptnew.i icarus/db/genpeptrelease.i icarus/db/insdseqxml.il icarus/db/loader.i icarus/db/swissprot.is icarus/db/tinyseqxml.il icarus/db/views.i
2009/06/11: hmmer	Change to handle entry IDs which contain a ":"
	icarus/db/hmmsearch.is
2009/06/10: hmmer	Change for more reliable hypertext linking with hmmsearch hits
	icarus/db/hmmsearch.is
2009/06/09: hmmer	Change to keep hmmsearch hit names short
	icarus/db/hmmsearch.is
2009/06/02: medline	Change to handle a new layout used for some EC numbers in medline
	icarus/db/medline.is
2009/06/01: system	Added support for the new PMAP-CutDB link in uniprot. Note that the new versions of href.i and dbxref.i need to be merged with your copies of those files in SRSSITE
	icarus/db/dbxref.i icarus/db/href.i
2009/05/28: kegg	Fixes for some inedxing errors for the kegg pathway database. After applying this update, please re-index pathway
	icarus/db/pathway.is
2009/05/28: system kegg pathway	Some more improvements for kegg pathway: added a field for glycan IDs, which are now also displayed and hypertext linked in the entry view. Fixed hypertext links in the new Metabolic Pathways entries. Made sure that png image files are unpacked from the pathway tar archive which prisma downloads. Please note that the new version of href.i needs to be merged with your copy in SRSSITE
	icarus/db/href.i icarus/db/pathway.i icarus/db/pathway.is icarus/db/pathwaytar.it web/WEB-INF/jsp/views/pathwayentry/pathwayentry.jsp
2009/05/21: srscheck prisma	Chanage to fix a problem with calculating partsizes if the partsize is set to very hight values
	icarus/workflows/buildPhase.i icarus/workflows/linkPhase.i
2009/05/21: srscheck prisma	Improved the removal of symlinked index (and other srs files) from the off-line index directory. They could be left in the off-line index directory after a crash, and a subsequent srscheck or prisma run could try to install them in the online index directory, resulting in self-referential links. The removal of these links at teh start of a run (during the check phase for a library) should prevent this.
	icarus/workflows/coreCheckClasses.i icarus/workflows/getSystemLibs.i icarus/workflows/srsCheckMain.i
2009/05/14: geneseq	Changes in the names used for the geneseq archives and megapatent files to ensure that both are downloaded. After applying this update it is recommended to remove all contents from the geneseq_tmp data directory, as not all files with old names will be automatically removed
	icarus/db/aageneseq.i icarus/db/aageneseqtar.it icarus/db/nageneseq.i icarus/db/nageneseqtar.it
2009/05/14: ensembl_mysql	updates for ensembl release 54
	icarus/db/ensemblRDB.i icarus/db/ensembl_compara_schema.i icarus/db/ensemblcore_schema.i
2009/05/11: prisma	Fix for a problem when detecting a time window for installing new data
	icarus/lion/prisma/checkTimeWindow.i
2009/05/08: system	Added support for the new oma hypertext link in uniprot. Please note that the new version of dbxref.i and href.i need to be merged with your copies of these files in SRSSITE
	icarus/db/dbxref.i icarus/db/href.i
2009/04/30: pdb	Change to handle a slight format change in the resolution remark line. After applying this fix, please re-index the resolution (res) field
	icarus/db/pdb.is
2009/04/30: uniprot ipi	Made sure that we do not insert a splice variant hypertext link for the actual variant which is used in the uniprot entry
	icarus/db/swissprot.is
2009/04/23: prisma	Change so we will not use a username and password for anonymous http access, as this can cause problems with some proxy servers
	icarus/lion/prisma/remoteConnection.i
2009/04/23: prisma	Fix for a problem where prisma would not run reformat commands with the -forceReformat option if there is nothing else to update
	icarus/lion/prisma/prismaCheckMain.i
2009/04/16: system	Added support for the new CAZy links in uniprot. Please note that the new dbxref.i and href.i files need to be merged with your copies of those files in SRSSITE
	icarus/db/dbxref.i icarus/db/href.i
2009/04/16: uniprot	Changes to handle changes in the structure of the description line in UNIPROTVARSPLICE. We have also added a Organism and Gene field. After applying this update, please re-index uniprotvarsplice
	icarus/db/uniprotvarsplic.i icarus/db/uniprotvarsplic.is
2009/04/08: blast system	Added a facility to provide hypertext links from a blast result to external (non-SRS) data. These need to be specified in the externalRefs list in localApplicationOptions.i, and a matching href definition should be provided in SRSSITE/href.i
	icarus/db/blast.is icarus/db/localApplicationOptions.i
2009/04/08: system uniprot	Added support for data export using uniprot xml - see the notes in uniprotxml.i for details. Note that the new version of srsdb.i needs to me merged with your copy of that file in SRSSITE
	icarus/db/srsdb.i icarus/db/uniprot_swissprot.it icarus/db/uniprot_trembl.it icarus/db/uniprotxml.i icarus/db/uniprotxml.il icarus/db/uniprotxml.is
2009/04/07: geneseq	Change for a more robust recognition of the start of an entry
	icarus/db/geneseq.is
2009/04/06: prosite	Fix to handle a situation in prositedoc where the entry contains two PDOC start lines
	icarus/db/prositedoc.is
2009/04/06: geneseq	fix for an issue with html display of gi values
	icarus/db/geneseq.is
2009/04/02: fasta	Change for better handling of fasta output without any hits found
	icarus/db/fasta.is
2009/03/23: genecards system	Added support for the new NOVUS line in genecards. Note that the new version of href.i needs to be merged with your copy of that file in SRSSITE
	icarus/db/genecards.i icarus/db/genecards.is icarus/db/href.i web/WEB-INF/jsp/views/genecardsentry/genecardsentry.jsp
2009/03/16: refseq embl genbank	Added a hypertext link the the NCBI revision history in the modification date line
	web/WEB-INF/jsp/views/dnadbentry/dnadbentry.jsp
2009/03/16: embl	implemented a slightly more robust method of identifying the start of an entry in embl
	icarus/db/embl.is
2009/03/12: clustalw	Fix for a problem with the display of sequence names in table views, fixed for a problem where wrong sequence names could be assigned, and improved htmlization of sequence names
	icarus/db/clustalw.is
2009/03/12: ensembl_mysql	update for release 53 of ensembl
	icarus/db/ensemblRDB.i icarus/db/ensembl_compara_schema.i icarus/db/ensemblcore_schema.i
2009/03/11: prints	A small parser change for release 39 of PRINTS, and added support for the latest version of Jalview
	icarus/db/prints.i icarus/db/prints.is
2009/03/11: system	some changes to improve linking back to SRS from JalView
	icarus/db/srsgen.i
2009/03/10: fasta	Fix for a parsing problem with fasta results from databases with more than 2.1 billion residues (this results in a slightly different Library line in the output)
	icarus/db/fasta.is
2009/03/09: system	Added hypertext link support for the new tcdb and pathway interaction references in uniprot. Note that you will have to merge the new copies of these files with your versions in SRSSITE
	icarus/db/dbxref.i icarus/db/href.i
2009/03/09: genbank refseq ddbj embl	Changes to allow for the new DBLINK link in GenBank. Since this line will replace the existing PROJECT line, we have merged these two, and use the GenomeProject field for its content (this to keep the differences between the EMBL and GenBank implementations in SRS to a minimum. There is no need to re-index after applying this update.
	icarus/db/genbank.is icarus/db/genbankcommon.i web/WEB-INF/jsp/views/dnadbentry/dnadbentry.jsp
2009/03/09: kegg	Fix for an indexing problem with mass field of lcompound. After applying this fix, please rebuild the mass index with a command like srsbuild -f mass lcompound
	icarus/db/lcompound.i
2009/03/04: rebase	Change to ensure that each entry has a single value in the prototype field, so sorting by prototype is possible
	icarus/db/rebase.is
2009/03/04: go_mysql	Fix for a display issue with the march 2009 version of go
	icarus/db/gotermdatamodel.i
2009/03/02: genbank refseq ddbj	Fix for a display issue with complete refseqp entries
	icarus/db/genbankcommon.i
2009/02/24: prisma	Two major changes in prisma reporting. We now also report the results of the remote checking in the main prisma report page (previously this was in other files, making it difficult to see if there was a problem with access to remote sites), and we now sort the entries in the report so that failures and errors are at the top of the various lists, so you no longer have to scroll through the entire report to find problems
	icarus/lion/prisma/checkRemoteFiles.i icarus/lion/prisma/dbSync.i icarus/lion/prisma/printBuildPages.i icarus/lion/prisma/printDownloadPages.i icarus/lion/prisma/printLinkPages.i icarus/lion/prisma/printMainPage.i icarus/lion/prisma/printMovePages.i icarus/lion/prisma/printPretransPages.i icarus/lion/prisma/printReformatPages.i icarus/lion/prisma/prismaCheckClasses.i icarus/lion/prisma/prismadata.i icarus/lion/prisma/prismastatus.is icarus/lion/prisma/qualityReport/indicesTest.i icarus/lion/prisma/setReportPhase.i icarus/lion/prisma/qualityReport/checkidsize.i icarus/lion/prisma/qualityReport/checkindexsize.i icarus/lion/prisma/report_resources/images/check_compErrors.gif icarus/lion/prisma/report_resources/images/check_completed.gif icarus/lion/prisma/report_resources/images/check_failed.gif icarus/lion/prisma/report_resources/images/check_white.gif icarus/lion/prisma/report_resources/images/local_copy2_compErrors.gif icarus/lion/prisma/report_resources/images/local_copy2_completed.gif icarus/lion/prisma/report_resources/images/local_copy2_failed.gif icarus/lion/prisma/report_resources/images/local_copy2_running.gif icarus/lion/prisma/report_resources/images/local_copy2_skipped.gif icarus/lion/prisma/report_resources/images/local_copy2_waiting.gif icarus/lion/prisma/report_resources/images/local_copy2_white.gif
2009/02/23: genbank	Change so prisma will no download the wgs master record files, as they do not contain sequence information
	icarus/db/genbankwgs.it
2009/02/23: entrezgene	Fix for a display issue with entrezgene entries for which there is no sequence cartoon
	icarus/db/entrezgene_dm.i
2009/02/23: dbsts	Workaround for a few parsing errors during indexing
	icarus/db/dbsts.is
2009/02/19: clustalw	Correction for a wrong setting for the input file name for nlcustalw
	icarus/db/nclustalw.i
2009/02/17: entrezgene	Fix for a problem where some transcript IDs were not displayed in the gene cartoon
	icarus/db/entrezgene_dm.i
2009/02/13: system	Change to handle some uniprot entries which have more than 4000 external library references (DR lines). No re-indexing is required, but the new version of srsgen.i needs to be merged with your copy of this file in SRSSITE
	icarus/db/srsgen.i
2009/02/12: entrezgene	Added a link to the new primary entry for obsolete entries, Extended the amount of information displayed in the refseq section, and fixed a few issues with the sequence cartoon
	icarus/db/entrezgene.i icarus/db/entrezgene.is icarus/db/entrezgene_dm.i web/WEB-INF/jsp/views/entrezgeneentry/entrezgeneentry.jsp
2009/02/11: system	Changes to allow for the new links to Bgee and IPI in uniprotKB. Note that the new dbxref.i and href.i files need to be merged with your copies of these files in SRSSITE
	icarus/db/dbxref.i icarus/db/href.i
2009/02/11: prisma	Fix for a problem where the usage history in the prisma reports would not display statistics (CPU etc) of previous prisma runs. Note that prisma will start to build up a usage history after applying this fix
	icarus/lion/prisma/printUsageReport.i
2009/02/11: prisma	fix for a spurious error thrown by rm during the archiving of prisma reports
	icarus/lion/prisma/prismaArchive.i
2009/02/10: emboss	Fix for a problem which results in situations where a 0 would be used instead of the default value for an option if the user has not set a value for that option
	icarus/lion/emboss/consn.i icarus/lion/emboss/consp.i icarus/lion/emboss/edialignn.i icarus/lion/emboss/edialignp.i icarus/lion/emboss/infoalignn.i icarus/lion/emboss/infoalignp.i icarus/lion/emboss/matchern.i icarus/lion/emboss/matcherp.i icarus/lion/emboss/mergern.i icarus/lion/emboss/mergerp.i icarus/lion/emboss/needlen.i icarus/lion/emboss/needlep.i icarus/lion/emboss/prettyplotn.i icarus/lion/emboss/prettyplotp.i icarus/lion/emboss/showalignn.i icarus/lion/emboss/showalignp.i icarus/lion/emboss/stretchern.i icarus/lion/emboss/stretcherp.i icarus/lion/emboss/supermatchern.i icarus/lion/emboss/supermatcherp.i icarus/lion/emboss/watern.i icarus/lion/emboss/waterp.i icarus/lion/emboss/wordfindern.i icarus/lion/emboss/wordfinderp.i
2009/02/09: iprmatches	Change to make sure prisma will not download an erroneous datafile from the interpro download site
	icarus/db/iprmatches.it
2009/02/04: genecards	Fix for some issues with genecards images
	icarus/db/genecards.i icarus/db/genecards.is web/WEB-INF/jsp/views/genecardsentry/genecardsexpression.jsp
2009/01/28: emboss	Added applet based tree viewer for display of output from (Emboss/Embassy) Phylip programs. Note that the applet (forester.jar) must be obtained separately from http://www.phylosoft.org/atv/, and installed in SRSROOT/web/java
	web/WEB-INF/jsp/views/emboss/embossTreeView.jsp
2009/01/28: clustalw	correction for an issue with displaying muscle output where sequence identifiers contain "_" characters
	icarus/db/clustalw.is
2009/01/27: system uniprot ipi	Changes to allow for the new reference to brenda in UniProt - note that the new href.i and dbxref.i files need to merged with your copies of these files in SRSSITE
	icarus/db/dbxref.i icarus/db/href.i icarus/db/swissprot.is
2009/01/20: blast fasta	Change to improve the way sequences are extracted from blast and fasta results for further processing, for instance in seuqnece alignment programs
	icarus/db/blast.is icarus/db/fasta.is
2009/01/20: bind	Change to reflect the fact that BIND is no longer available for download
	icarus/db/bindcomplex.it icarus/db/bindinteraction.it icarus/db/bindpathway.it
2009/01/20: pfam	Change to reflect the fact that swisspfam is no longer available for download
	icarus/db/swisspfam.it
2009/01/20: system	Changed the JalView view to use the latest version of jalview, which allows for correctly linking back of sequences in the view to the SRS installation. Note that you will need to obtain the new jalview applet from www.jalview.org, and install it in SRSROOT/web/java. Also note that the new version of srsgen.i needs to be merged with your version of this file in SRSSITE
	icarus/db/srsgen.i
2009/01/20: clustalw	Changed the way clustalw is run, so it no longer builds a list of sequences at the top of the output, but simply presents the plain clustalw output file. Increased support to version 2.0 (you will have to comment out some lines if you (want to) continue to use version 1.83, and made some changes to support the new JalView view
	icarus/db/clustalw.i icarus/db/clustalw.is icarus/db/nclustalw.i
2009/01/14: transfac	Change to eliminate some parsing errors during link-indexing of the tffactor database
	icarus/db/transfaccommon.is
2009/01/14: ensembl_mysql	Changes for ensembl release 52
	icarus/db/ensemblRDB.i icarus/db/ensembl_compara_schema.i icarus/db/ensemblcore_schema.i
2008/12/17: system	Added support for PRIDE and GeneCards hypertext links in uniprot
	icarus/db/dbxref.i icarus/db/href.i
2008/12/16: genbank embl refseq ddbj imgt	Change to allow for a PrimaryAccession (pac) index of more than 4GB. Following customer request we have also added a new TissueType field. Note that after applying this change all databases in GENBANK_FORMAT will become inaccesible and require a complete re-index, and that the TissueType field also needs to be indexed for REFSEQPRELEASE/REFSEQPNEW
	icarus/db/gbemblcommon.is icarus/db/genbankcommon.i
2008/12/09: embl genbank refseq ddbj imgt	Change to allow for a PrimaryAccession (pac) index of more than 4GB. Following customer request we have also added a new TissueType field. Note that after applying this change all databases in EMBL_FORMAT will become inaccesible and require a complete re-index.
	icarus/db/emblcommon.i icarus/db/gbemblcommon.is
2008/12/09: geneseq	Fix for a problem which was throwing a few parser errors each time aageneseq/nageneseq was indexed
	icarus/db/geneseq.is
2008/12/09: srscheck prisma	Fix for an issue where prisma sometimes would build link-indices on-line
	icarus/workflows/linkPhase.i
2008/12/09: system	removed an erroneous inclusion of ensembl_compara_48_schema.i from the ensembl compara LibLoc
	icarus/db/srsdb.i
2008/12/08: intact	Small change the to perl script for pre-processing intact data, so it wil not erroneously report that no interactions were found
	icarus/db/intactProcessData.pl
2008/12/03: embl genbank refseq ddbj imgt	Some changes to prevent memory problems when indexing large genomic entries: Smaller parts for refseq, and a more efficient parsing of the feature table, as full chromosome entries have well over a million features in the feature table
	icarus/db/embl.is icarus/db/gbemblcommon.is icarus/db/genbank.is icarus/db/refseqnew.i icarus/db/refseqrelease.i
2008/12/01: geneseq	FIx to make sure srs knows that the aageneseqtar is a helper library which should not be indexed
	icarus/db/aageneseqtar.it
2008/11/25: dbest	Change needed to handle the increasing size of dbest. The comments field (cc) is now larger than 4GB, and the author (aut) field will be in the near future. After applying this update, the existing dbest_cc and dbest_aut indices will become unreadable. We would recommand to remove the existing dbest_cc.* and dbest_aut.* files and re-index. To minimize impact for your users, you could set the ignoreMissingIndices parameter in SRSICA/parameter.i to 1
	icarus/db/dbest.i icarus/db/dbest.is
2008/11/20: prisma	Fix for a problem where in some cases a missing offline data directory could cause prisma to crash
	icarus/lion/prisma/movePrismaData.i
2008/11/20: ensembl_mysql	Update for Ensembl 51. Note that there is a small schema change which affects the way SRS displays proteins so make sure you apply this update at the same time you install the Ensembl 51 data
	icarus/db/ensemblRDB.i icarus/db/ensembl_compara_schema.i icarus/db/ensemblcommon.i icarus/db/ensemblcore_schema.i icarus/db/ensemblproteinmodel.i web/WEB-INF/jsp/views/ensemblproteinentry/proteinentry.jsp
2008/11/14: intact	Fixed a problem with the uniprot references and made data pre-processing (we prcess the data using a perl script prior to indexing) more robust
	icarus/db/intactProcessData.pl icarus/db/intactcommon.i icarus/db/intactcommon.is icarus/db/intactdata.it icarus/db/intactinteractor.i
2008/11/13: system prisma	Changes to make maintenance easier by reducing the number of changes made to these files when ensembl, prisma or emboss are installed. In order to reduce the risk of system confusion about what changes have been made by these packages, we would recommend to first uninstall these packages by running "srspackage -remove srsprisma/emboss/EnsemblRD" (whatever is appropriate in your situation), update srsgen.i and srsdb.i (in you SRSSITE directory), and then reinstalling the packages. For prisma this is done by running "srspackage -install $SRSLION/packages/srsprisma.ip" (make sure you get the latest version of this file). For ensembl this is done by running "srspackage -install $SRSLION/packages/ensembl.ip". For emboss this is done by running "srssetup -emboss" - but see also the notes on upgrading to EMBOSS 6. After applying this update all these packages do is setting the enabled:y flag for the relevant libraries in srsdb.i file, and no changes are made to srsgen.i.
	icarus/db/srsdb.i icarus/db/srsgen.i icarus/lion/packages/srsprisma.ip
2008/11/12: intact	Change so prisma will not accidentally remove the active datafiles during a data update
	icarus/db/intactProcessData.pl icarus/db/intactexperiment.i icarus/db/intactinteraction.i icarus/db/intactinteractor.i
2008/11/12: transpath	Corrections for some link names which might cause confusion when data is updated by prisma
	icarus/db/transpath_gene.i icarus/db/transpath_molecule.i icarus/db/transpath_pathway.i icarus/db/transpath_reaction.i icarus/db/transpath_reference.i
2008/11/12: entrezgene	Improvement in the way gene symbols are indexed - we were missing a few gene symbols which are located in an alternative location in the data
	icarus/db/entrezgene.i icarus/db/entrezgene.is
2008/11/12: emboss	Upgraded emboss support to emboss 6.0.1. For your convenience we make this upgrade available as a separate tarball: EMBOSS6.0.1.tar.gz. Before applying this update make sure you read README.EMBOSS6
	EMBOSS6.0.1.tar.gz
2008/11/12: system	update tool package versions supported by SRS
	icarus/db/packages.i
2008/11/11: prisma	Added a new feature in prisma reports: the usage report will now contain a graph showing the usage of each cpu slot during a prisma run. This can be useful in locating bottlenecks during data processing
	icarus/lion/prisma/cpuslots.il icarus/lion/prisma/printUsageReport.i icarus/lion/prisma/prismaGui.i icarus/lion/prisma/report_resources/wz_tooltip.js
2008/11/11: prisma	Added an option to runPrisma to ignore data move scheduling conditions (-ignoreMoveDataConditions), and improved verbosity indicating why prisma is waiting with moving data online
	icarus/lion/prisma/checkTimeWindow.i
2008/11/11: srscheck prisma	Change so srscheck and prisma will remove symbolic links in the offline index directory when checking on a library. This will prevent the srsbuild process from writing to these links, and will also prevent these links being moved online, which could result in these files ending up being self-referential links
	icarus/workflows/coreCheckClasses.i
2008/11/11: prisma	fixes for some minor tool testing issues in prisma reports
	icarus/lion/prisma/PrismaToolsTestDb/testdata.is icarus/lion/prisma/PrismaToolsTestDb/testdb.i icarus/lion/prisma/PrismaToolsTestDb/testdb/distmat.testdata icarus/lion/prisma/PrismaToolsTestDb/testdb/hmm.testdata icarus/lion/prisma/generateCalendar.i icarus/lion/prisma/inspectClasses.i icarus/lion/prisma/inspectReport.i icarus/lion/prisma/qualityReport/toolTests.i icarus/lion/prisma/srsinspect.i icarus/lion/prisma/toolsTestSets.i
2008/11/10: genecards	Change so genecards no longer relies on a linf/directory in SRSROOT/data to display images
	icarus/db/genecards.is
2008/11/10: uniprot	Change to ensure that the reldate.txt file is downloaded with uniprot_swissprot and uniprot_trembl
	icarus/db/uniprot_swissprot.it icarus/db/uniprot_trembl.it
2008/11/10: kegg system	Change to make sure all kegg data is in sync with eachother (when prisma is used to keep the data up-to-date) - we no longer download the individual ligand sets (lenzyme, lcompound, ldrug, lglycan and lreaction), but use the tar archive we download to obtain the images for these datasets (kegg_images). Note that for this to work the off-line data directory for these datasets in srsdb.i needs to be set to the data directory used for the keggimages dataset. We also changed the way the images are retrieved so it is no longer necessary to have a kegg_images directory linked to SRSROOT/data (unless you do not have the keggimages database enabled)
	icarus/db/kegg_images.i icarus/db/lcommon.is icarus/db/lcompound.is icarus/db/lcompound.it icarus/db/ldrug.is icarus/db/ldrug.it icarus/db/lenzyme.i icarus/db/lenzyme.it icarus/db/lglycan.is icarus/db/lglycan.it icarus/db/lreaction.is icarus/db/lreaction.it icarus/db/srsdb.i
2008/11/10: kegg	Change to make sure we can handle some hidden files which may be present in the kegggenome tar archive
	icarus/db/kegggenome.it
2008/11/10: dbest dbgss	Fix for a problem where SRS might mistake gzipped datafiles for actual datafiles, and a fix for a problem where SRS could not build the link between the dbest and taxonomy databases
	icarus/db/dbest.i icarus/db/dbest.it icarus/db/dbgss.i icarus/db/dbgss.it
2008/11/10: kegg	Latest kegg species mapping file. Note that it you have prisma, this file will be regenrated automatically when the kegggome database is updated
	icarus/db/kegg_species.i
2008/11/10: geneseq	Modification so prisma will also download the megapatent data with geneseq (comment out the relevant sections in [na]aageneseqtar.it if you do not want this), reorganised links so no more readlinks are build (the merge phase for this could cause problems on systems with filehandle restrictions). Note that with the addition of the megapatent data, we needed to change the structure of nageneseq indices. This will mean that after applying the updated icarus files, you will have to re-index nageneseq (preferably after first removing the old nageneseq indices
	icarus/db/aageneseq.i icarus/db/aageneseqtar.it icarus/db/geneseq.is icarus/db/nageneseq.i icarus/db/nageneseqtar.it
2008/11/10: intact	Removed a field defintion which clashed with a defintion in srsgen.i. If you have enabled any intact databases, then after applying this update, go to SRSINX and rename all *_fte.i* files to *_ften.i*
	icarus/db/intactcommon.i
2008/11/10: hmmer fasta userdna userprotein	Some changes so prisma tool testing will not faile on these tools
	icarus/db/hmmpfam.it icarus/db/hmmsearch.it icarus/db/ssearch.it icarus/db/userdna.i icarus/db/userdna.it icarus/db/userprotein.i icarus/db/userprotein.it
2008/11/10: entrezgene	added an alternative unpackcommand which strips out the xml indentation for entrezgene - this will save about 35% on diskspace, but will make the raw xml less readable. Edit the file to comment in/out the command you would like to use
	icarus/db/entrezgene.it
2008/11/06: system	Added support for nextbio and xenbase hypertext links in uniprot - note that the new versions of href.i and dbxref.i need to be merged with your copies of these files in SRSSITE
	icarus/db/dbxref.i icarus/db/href.i
2008/11/04: genecards system	Changes for release 2.39 of GeneCards. Note that the new version of href.i needs to merged with your copy in SRSSITE
	icarus/db/genecards.i icarus/db/genecards.is icarus/db/href.i web/WEB-INF/jsp/views/genecardsentry/genecardsentry.jsp
2008/11/03: chebi	Changes for release 29 of Chebi
	icarus/db/chebidatamodel.i
2008/10/27: genbank embl refseq ddbj imgt	Re-added production which was lost in a previous update
	icarus/db/gbemblcommon.is
2008/10/16: uniprot ipi	Fix for a problem with displaying subentry IDs
	icarus/db/swissprot.is
2008/10/10: go_xml	Small change to work around a dodgy data problem in the 20081005 release of go
	icarus/db/go.is
2008/10/08: fasta	Change to handle a small data output change between fasta3.5.3 and fasta3.5.4
	icarus/db/fasta.is
2008/10/06: embl	Fix so we do not download the tpa cumulative file ( we use the relevant sections instead ) . Note that for emblnew without emblnewfiles enabled, this also fixes a problem where the tpa/cumulative file was taking precendence over the main new/cumulative file, resulting in missing entries
	icarus/db/emblnew.it icarus/db/emblnewfiles.it
2008/10/02: system	Added views for vectorNTI export to the distribution. Note that to enable export to vectorNTI functionality, you will have to comment in the relevant parts in web/WEB-INF/config/srs/srs-export.xml. The new versions of loader.i and views.i need to be merged with your versions of these files in SRSSITE
	icarus/db/loader.i icarus/db/views.i icarus/lion/vectorNTI/genbankstyle.il icarus/lion/vectorNTI/vectorNTI_AAGENESEQ.il icarus/lion/vectorNTI/vectorNTI_DBEST.il icarus/lion/vectorNTI/vectorNTI_EMBL.il icarus/lion/vectorNTI/vectorNTI_FASTAGEN.il icarus/lion/vectorNTI/vectorNTI_GENBANK.il icarus/lion/vectorNTI/vectorNTI_GENPEPT.il icarus/lion/vectorNTI/vectorNTI_NAGENESEQ.il icarus/lion/vectorNTI/vectorNTI_PIR.il icarus/lion/vectorNTI/vectorNTI_REFSEQP.il icarus/lion/vectorNTI/vectorNTI_UNIEST.il icarus/lion/vectorNTI/vectorNTI_UNIPROT.il icarus/lion/vectorNTI/vectorNTI_UNISEQ.il
2008/10/02: prisma	change so the prisma test databases no longer show up in the web interface
	icarus/lion/prisma/PrismaToolsTestDb/testdb.i
2008/09/24: system kegg	Added internal hypertext links to the kegg orthology database from pathway entries. Note that the new href.i file needs to be merged with your copy in SRSSITE
	icarus/db/href.i icarus/db/pathway.is
2008/09/23: blast fasta	Added a direct hypertext link from the blast graphical view to the hit entry
	icarus/db/blastgraphicdatamodel.i
2008/09/22: system	Change to make sure that the ID field is part of the AllIds group field
	icarus/db/srsgen.i
2008/09/19: system embl genbank ddbj uniprot	Added display of comment and consortium with references in the main sequence databases
	web/WEB-INF/tags/referencetable.tag
2008/09/19: kegg	Various changes for lenzyme - removed the no longer present motif and disease fields, and allow for better processing and display of the now highly structured reference field(s) - note that after this update you will have to re-index lenzyme
	icarus/db/lenzyme.i icarus/db/lenzyme.is web/WEB-INF/jsp/views/lenzymeentry/lenzymeentry.jsp
2008/09/15: embl	Change to allow for the TSA (Transcriptome Shotgun Assembly) section
	icarus/db/embl.is
2008/09/15: chebi ensembl_mysql genecards go_mysql system	Replaced hardcoded external hypertext links by proper Hlink references. Note that you will have to merge the new version of href.i with your copy of that file in SRSSITE
	icarus/db/chebidatamodel.i icarus/db/ensembldatamodel.i icarus/db/genecards.is icarus/db/gogenproddatam.i icarus/db/href.i
2008/09/11: prints prosite rebase	Change to suppress irrelevant output to STDERR when processing datafiles for emboss usage
	icarus/db/prints.it icarus/db/prosite.it icarus/db/rebase.it
2008/09/11: embl	Corrections for the annotated contig location and filenames used for deleted entries
	icarus/db/emblnew.it icarus/db/emblnewfiles.it
2008/09/10: kegg	Changes to allow for the new PRDUCTS field in the kegg drug database
	icarus/db/ldrug.i icarus/db/ldrug.is web/WEB-INF/jsp/views/ldrugentry/ldrugentry.jsp
2008/09/08: emboss	Fix for an image display problem for the dan emboss tool
	icarus/lion/emboss/dan.is
2008/09/04: prisma	Fix for a problem where prisma would not honour all timewindows for data installation
	icarus/lion/prisma/checkTimeWindow.i
2008/08/22: emboss	Fix so showalign and remap will correctly use the colors specified by the user to color sequence regions
	icarus/lion/emboss/remap.i icarus/lion/emboss/showalignn.i icarus/lion/emboss/showalignp.i
2008/08/22: system genbank embl refseq ddbj imgt	some minor parser improvements
	icarus/db/ftseq.is icarus/db/gbemblcommon.is icarus/db/genbank.is
2008/08/19: chebi	Fix for a problem where SRS would not always retrieve the matching structure image from lcompound to be displayed with a chebi entry
	icarus/db/chebidatamodel.i
2008/08/18: reactome	Changes for release 25 of the reactome database. Note that we have changed the database name as used in the interaction with mysql to Reactome
	icarus/db/reactome.i icarus/db/reactome_schema.i
2008/08/13: pdb	added a new field providing chain Ids (combining entry name and chain designation)
	icarus/db/pdb.i icarus/db/pdb.is
2008/08/12: uniprot	Change to allow for a change in the header line in uniprot splice variant data (uniprotvarsplice)
	icarus/db/uniprotvarsplic.is
2008/08/08: prisma	Fix for a problem where prisma would not pick up an update scheduled to run on Sundays
	icarus/lion/prisma/prismaCheckClasses.i
2008/08/07: system uniprot ipi	Changes to handle the new format of the DE lines in uniprot. We have added new fields: Name, AltName,Contains, Includes and Flag, but have kept the old Description field in order to query the entire contents of the DE lines. We also added a new synonym finder which uses the Name and AltName fields. Note that the new srsgen.i file needs to be merged with your copy of that file in SRSSITE
	icarus/db/srsgen.i icarus/db/swisscommon.i icarus/db/swissprot.is icarus/db/uniprot.i web/WEB-INF/jsp/views/swissentry/swissentry.jsp
2008/08/04: enzyme	removed the disease (reference to omim) field, as it is no longer used
	icarus/db/enzyme.i icarus/db/enzyme.is icarus/db/enzyme.it web/WEB-INF/jsp/views/enzymeentry/enzymeentry.jsp