wiki du projet insyght

[improvement] : added a filter functionality to search more effectively for genomes on the search page → featured genome list

[improvement] added a functionality to compute summary statistics with regard to conservation in compared genomes for a given reference CDS: number of compared organism with orthologs, synteny, average percentage identity for alignment, alignment coverage, median evalue, and pourcentage GC.

[improvement] : export summary conservation stat for a list of reference CDS : comparison with featured organisms and main organisms list (number of compared organism with orthologs, synteny, avg %id for alignment, alignment coverage, median evalue)

[improvement] : allow searching organism by accession number in the taxonomic browser

[improvement] : migrated forge from svn migale to git sourcesup

[bug] : taxonomic level (species, phylum, etc.) are not correct in the taxonomy browser : Firmicutes is class but should be phylum, Streptococus is species but should be Genus. Got rid of taxonomic levels in the browser, the depth is not related to taxonomic levels

[bug] : display error in Firefox when zoom 50%, in the search tab the button “select reference gene set” was disappearing

[Bug] fixed bug manage list compared organism was having duplicated data after onDetach

[bug] For some CDS, the gene name was not displayed correctly, only the locus tag was displayed

[bug] disable sorting by Abundance of orthologs' annotations for now as it is not yet fully implemented

[bug] : fixed bug java.lang.Exception: Error in QueriesTableAlignments getHMalignmentId2AlignmentParamIdAndPairs_WithSetAlignmentParamId ; alPostiveAlignmentParamIdSent=[XXX] ; convertSetLongToSortedRangeItem_allowGapWithinRange=true ; shouldBePresentInTable=true: java.lang.Exception: shouldBePresentInTable is true && hmToReturn.isEmpty() at fr.inra.jouy.server.queriesTable.QueriesTableAlignments.getHMalignmentId2AlignmentParamIdAndPairs_WithSetAlignmentParamId(QueriesTableAlignments.java:426) : some database like origami_cg still have some alignment_para_id that do not have any row in the table alignments

[improvement] allow to filter genes by genomic location with thousand comma separator

[bug] fixed bug when exporting sequences for a large number of CDS, error URI is too large >16386 badMessage: 414 ; changed method from GET to POST

[improvement] download of protein and nucleic sequences of CDSs as a local file instead of displaying the data in new browser tab

[bug] : getStatSummaryRefCDS : no calculation for the main list, only the featured list. Calculation on the main genome list was causing problem for the private genomes

[improvement] : modified method QueriesTableGenes getAlGenesIdsWithElementId_optionalPbStartAndPbStop_optionalListGeneIdsToExclude to add option orderCDSByStartAsc

[Improvement] : speed up initial request to list organisms and load taxo tree : initialy took ~10-12 seconds for 5000 genomes, now down to 5-6 seconds (2X improvement)

[Feature] : new script PrevalenceCDSsInOrthologsSynteny.java -byPairwiseComparisons : Prevalence CDSs In Orthologs and Synteny ; distribution of the number of pairwise comparison by the % of CDS in genome in ortho BDBH or synteny relationship

[Bug] : fixed bug missing data when displaying genomes with 2 elements somtimes : the lower bound pair was not inserted into getCumulatedLongWithinRangesAsIndividual as it should in the method convertSetLongToSortedRange_PositiveSingletonAsIndividualThenPositiveRangeAsPairThenNegativeSingletonAsIndividualThenNegativeRangeAsPair

[Bug] : fixed bug calculating pb distance between features when a CDS start had a start of 0pb relative to ORI

[Bug] : the use of the methodUtilitiesMethodsServer.excecuteCommandAndParseMultipleRowRS could cause “limit overhead problems” if the number of elements parsed was big. Bypass of this method.

[Improvement] : core / disp genome functionality : increase the limit for the maximum number of genomes in group plus minus combined to 300

[Bug] : fixed bug display was hung : on the genomic organisation tab when searching for a CDS within a synteny, the display could hung because the mask would stay forever and do not detect that the multiple request came back from the server

[Improvement] : revamped search tab : easier navigation, management of compared organisms, functionality for core genome improved

[Improvement] : suppport for organisms with a lot of contigs by speeding up display in the ortholog table view or the genomic context view. For a genome with ~500 contigs, it now takes ~1.5 seconds (it previsouly took ~5 minutes, a 85X improvement). Remark : transfering a large number of parameters (~300000) to postgresql was causing a 5 minutes long delay whereas the query itself just took a few miliseconds.

[Improvement] : suppport for organisms with a lot of contigs by allowing and speeding up searching for CDS in multiple contigs ; querying CDSs that match a specific genomic locations or qualifier (product, molecular fonction, lenght protein, etc…) filter when searching within ~500 contigs now takes ~300-450 milliseconds (it previsouly took ~4-5 seconds, a ~10-15X improvement) ; querying CDSs that match a specific presence / absence homologs filter when searching within ~500 contigs now takes ~2.4 seconds (it previsouly took 50 seconds, a ~20X improvement)

[Improvement] : Added management of result organisms (such as featuring, sorting, etc…) directly in the results tab, option “Result quick Navigation”

[Improvement] : To save disk space, tables related to syntenies and orthologs (alignment_params, alignments, alignment_pairs) have non redundant / mirror data.

[Improvement] :updated home page to display the links to the multiple Insyght public website available

[Bug] : gene name was not displayed properly on canvas

[Feature] : improved search for organisms and taxons : return a close best match if no exact match are found

[Improvement] : web app is now compatible with database schema v3 (see release notes on database schema for more details)

[Improvement] : migration to GWT 2.8.2 → GWT2.8 + junit.jar + validation-api-1.0.0.GA.jar in war/WEB-INF ; fixed Error at compile time The template code generator cannot guarantee HTML-safety of the template

[Bug] : fixed bug : the full list of organism didn't come back after (1) searching for a particular organism, (2) adding it to the featured list, (3) closing the ManageListComparedOrganisms, (4) re-opening ManageListComparedOrganisms and adding the full list of organisms again by clearing the filter

[Improvement] : the web app doesn't display organisms if their computation process (comparison with all other species) is not finished

[Improvement] : update link to Ensemblgenome : http://ensemblgenomes.org/id/

[Bug] : fixed bug in handling taxonomic node when restricting list of compared organisms

[Improvement] : automatic display of selected gene set when adding genes to it from core/disp genome browser

[Bug] : fixed bug in moving compared organisms up and down when managing those lists

[Bug] : fixed bug when navigating orthologs table to see the last compared organisms using the next result button : IndexOutOfBoundsException due to scrollQuickNavToEnsureVisible

[Bug] : fixed bug in managing list compared organism : main list was not listing all the non features compared organisms if a filter by the user on a taxonomic node was still active

[Bug] : fixed bug not able to display genomic location if organisms had no strain information

[Improvement] : new functionality to set compared organism as reference (mirror view) directly from context specific menu while browsing results

[Improvement] : new functionality to export list of CDS sequence from compared organism as fasta

[Improvement] : url Api &listReferenceOrigamiGeneSetIds= empty if dealing with whole organism

[Improvement] : Search for organism or taxonomic group in the taxonomix browser for the functionality core / dispensable set of CDSs for reference node

[Bug] : fixed bug wrong processing of encapsulated CDSs when opening synteny in mirror view (negative alignment_id)

[Bug] : Synteny info about query subject start and stop were mixed up

[Bug] : bug automatic setting of score scope to whole genome if the gene set size was 1

[Bug] : fixed bug when contextual menu → selected symbol → list reference genes : error unrecognized case if the synteny number was negative

[Bug] : fixed Bug Export sequence from search tab → Reference CDSs → Build your reference gene set : All compared CDSs in the selected gene set was sometimes available

[Bug] : fixed bug selected ref organisms or nodes was not taken into account when clicking on the menu Reference CDSs

[Bug] : fixed bug when listing gene from core genome and searching them using filters, nothing was happening

[Improvement] : SharedAppParams MAX_NUMBER_IN_GENE_SET_ALLOWED is now 20000 instead of 200 ; MAX_NUMBER_FEATURED_ORGA_ALLOWED is now 20000 instead of 300 ; public static final int MAX_NUMBER_EXCLUDED_ORGA_ALLOWED is now 20000 instead of 1000

[Improvement] : prevent interacting with dispplay when data takes a long time loading

[Bug] : fixed bug transitioning from “Build your reference gene set” to “Whole proteome or Core / dispensable set of CDSs” showed the wrong display

[Bug] : fixed bug not to allow searching for Presence orthologs in group + and absence in group - while browsing core/disp genome : This functionality is disabled, it needs at least 1 organism in group + that is not the reference or 1 organism in group -

[Improvement] : set a compared organism as the reference organism (mirror view) from the ortholog table view or the genomic context view

[Improvement] : modified method getGeneNameLocusTagStrandWithGeneId to take advantage of newer database schema with direct access to the locus tag field (UtilitiesMethodsServer.isDatabaseGenesElementsGenomeAssemblyConvenience(conn))

[Bug] : fixed problem displaying appropriate message when no organism are available in the database

[Improvement] : faster intial display of browser for core / disp genome with lot of organisms as root : method setDefaultRefGenomeWithSelectedRefTaxoNode in SearchViewImpl. From ~1.6 seconds to ~120 milliseconds for ~300 orga (~ 14 times faster) ; From ~3.1 minutes to ~0.6 seconds for ~2600 orga (~ 330 times faster)

[Improvement] : getting the Reference Genes Most Represented among a set of 200 organisms took ~1.5 minutes, now take ~10 seconds (use of table aligment_params + alignments instead of homologies) ⇒ 9X faster

[Feature] : set a maximum number of genomes to be compared for presence / absence homology : 100 as above 190 can cause GC overhead limit exceeded

[Feature] : Taxonomic browser, core / dispensable genome functionality : checkbox to select multiple genomes / nodes. Keyboard support. (link to old forge https://migale.jouy.inra.fr/redmine/issues/8704).

[Bug] : Sometimes 2 references genomes are selected in the taxonomic browser (2 nodes in yellow) ; impossible to change the group for them… (link to old forge https://migale.jouy.inra.fr/redmine/issues/8705).

[Feature] : Taxonomic browser, core / dispensable genome functionality : upon header selection, select all nodes in appropriate categories (link to old forge https://migale.jouy.inra.fr/redmine/issues/8706).

[Bug] : Fixed examples taxon ids for release Archaea (link to old forge https://migale.jouy.inra.fr/redmine/issues/8707).

[Bug] : Fixed functionality to send email via smtp inra to report uncaught exception (link to old forge https://migale.jouy.inra.fr/redmine/issues/8708).

[Improvment] : Modified user interface to deal with database changes in schema: removal of elements.description (→ sequences.definition), elements.date_seq (→ sequences.date_seq), elements.version (→ sequences.version), genes.residue (→ prot_feat.proteine). (link to old forge https://migale.jouy.inra.fr/redmine/issues/8709).

[Bug]: Error when the database was empty. Redirect user to use the guide to add data or check out http://genome.jouy.inra.fr/Insyght/ to test functionalities. (link to old forge https://migale.jouy.inra.fr/redmine/issues/8710).

[Bug]: When transfering q genes from synteny to ortholog table view, s_insertion genes were transeferd as well. (link to old forge https://migale.jouy.inra.fr/redmine/issues/8711).

[Bug]: Synteny symbol not displaying correct number of pairs, it was missing gene mismatch and insertion. (link to old forge https://migale.jouy.inra.fr/redmine/issues/8712).

[Bug]: Compared organisms not sorted correctly for scope Whole organism. (link to old forge https://migale.jouy.inra.fr/redmine/issues/8713).

[Bug]: Navigation jumps when moving with » or « in ortholog table or genomic organisation. (link to old forge https://migale.jouy.inra.fr/redmine/issues/8714).

[Feature] : over-representation (P-Value Fisher's Exact test) of orthologs whithin phenotype+ organisms in comparison to phenotype-organisms. (link to old forge https://migale.jouy.inra.fr/redmine/issues/6502).

[Bug] : text above taxonomic browser search tab step 2 was not displaying properly. (link to old forge https://migale.jouy.inra.fr/redmine/issues/6501).

[Feature] : gene filter on PValue score if applicable. (link to old forge https://migale.jouy.inra.fr/redmine/issues/6503).

[Feature] : show info on PValue in ortholog table too. (link to old forge https://migale.jouy.inra.fr/redmine/issues/6504).

[Feature] : utilities to convert error report into stack trace with symbolMap file. (link to old forge https://migale.jouy.inra.fr/redmine/issues/6505).

[Bug] : max connection idle : better configuration of the context.xml config file (max total 97 SQL requests in parallel). (link to old forge https://migale.jouy.inra.fr/redmine/issues/6506).

[Feature] report 5 last history tocken in bug reporting tool. (link to old forge https://migale.jouy.inra.fr/redmine/issues/6132).

[Feature] Added support for url parameters: referenceSpecies, referenceStrain, referenceSubstrain, referenceAccnum, referenceGeneSetNames, referenceGeneSetLocusTag. (link to old forge https://migale.jouy.inra.fr/redmine/issues/6133).

[Feature] different shade of grey to represent the alignment based on its %identity (>85% identity = black, between 50 to 85% = dark grey, etc.). (link to old forge https://migale.jouy.inra.fr/redmine/issues/6134).

[Bug] : some genes have multiple qualifier protein_id (some ref to other db such as tigr, start with REF), this did pose a problem for the blast2seq link when it was the case ; exemple gene id 5727 EF0944 of E faecalis v583 (db origami_test). (link to old forge https://migale.jouy.inra.fr/redmine/issues/6135).

[Feature] : direct link to GO, UniParc, PDB in the gene info panel (if available as annotation). (link to old forge https://migale.jouy.inra.fr/redmine/issues/6136).

[Bug] : some genes have multiple qualifier protein_id, display them all in the info panel with correct link to external db. (link to old forge https://migale.jouy.inra.fr/redmine/issues/6137).

[Bug] : some gene have qualifier protein_id with ref to other db (EMBL) enclosed in curly braces, this did pose a problem for the blast2seq link when it was the case ; exemple gene id 41305 metS of Listeria Monocytogenes strain 08-5578 (db origami_test). (link to old forge https://migale.jouy.inra.fr/redmine/issues/6138).

[Bug] : In the search tab, the pre-made examples were not working properly. (link to old forge https://migale.jouy.inra.fr/redmine/issues/6139).

[Bug] : The compared genomes list in the tab orthologs table and genomic organisation did contains public organisms with no element ; those organisms are now hidden from the result list. (link to old forge https://migale.jouy.inra.fr/redmine/issues/6140).

[Feature] : switch to no color for symbols q_gene_insertion or s_gene_insertion in genomic orga view when expanding a q or s insertion region. (link to old forge https://migale.jouy.inra.fr/redmine/issues/6141).

[Feature] : Better management of info panel: When we click on synteny info, we want to keep this disclosure panel open as we click on other synteny. (link to old forge https://migale.jouy.inra.fr/redmine/issues/6142).

[Bug] : The presence / absence homology filter did not work correctly with multiple organisms in the box : java.lang.Exception: could not parse orga id as integer : presence. (link to old forge https://migale.jouy.inra.fr/redmine/issues/6143).

[Bug] : the functionality “browse core / dispensable” genome“ in the search tab is not longuer functioning correctly. (link to old forge https://migale.jouy.inra.fr/redmine/issues/6144).

[Bug] : FATAL: remaining connection slots are reserved for non-replication superuser connections. (link to old forge https://migale.jouy.inra.fr/redmine/issues/6145).

[Bug] : Uncaught exception: java.lang.IndexOutOfBoundsException when viewing resultq from core/ disp gene set directly in ortholog table. (link to old forge https://migale.jouy.inra.fr/redmine/issues/6146).

[Bug] : color is not displayed correctly at first within the core / dispensable genome browser of the search page, it appears right after clicking on another node. (link to old forge https://migale.jouy.inra.fr/redmine/issues/6147).

[Feature] WEB APP: migrate to GWT 2.7 and GSS. (link to old forge https://migale.jouy.inra.fr/redmine/issues/5813).

[Feature] WEB APP: locus tag and functional annotation links to EnsemblGenomes, GOA, Interpro, Unipro, KEGG, PFAM, NCBI, blast2seq alignment viewer. (link to old forge https://migale.jouy.inra.fr/redmine/issues/5814).

[Feature] WEB APP: export the ortholog table in .csv format ; simple output counting the number of orthologs per cell. (link to old forge https://migale.jouy.inra.fr/redmine/issues/5815).

[Feature] WEB APP: more distinguishable colors for synteny ; ortholog not in synteny colored in grey to make the synyeny stand out more. (link to old forge https://migale.jouy.inra.fr/redmine/issues/5816).

[Feature] WEB APP: SELECT REFERENCE → build your reference gene set among available molecules : new filter on protein lenght. (link to old forge https://migale.jouy.inra.fr/redmine/issues/5817).

[Feature] WEB APP: singleton synteny display the gene homology directly instead of a synteny of 1 to expand. (link to old forge https://migale.jouy.inra.fr/redmine/issues/5818).

[Bug] WEB APP: some special characters were not displaying correctly on some web browser, changed to more widely supported characters. (link to old forge https://migale.jouy.inra.fr/redmine/issues/5819).

[Feature] WEB APP: support of multiple organisms with identical taxo_id. (link to old forge https://migale.jouy.inra.fr/redmine/issues/5823).

[Feature] WEB APP: support of draft genomes with many contigs ; some queries regarding those genomes are still taking too much time though. (link to old forge https://migale.jouy.inra.fr/redmine/issues/5824).

[Feature] WEB APP: export sequences of genes within a genomic region. (link to old forge https://migale.jouy.inra.fr/redmine/issues/5820).

[Feature] WEB APP: taxonomic browser: automatic selection of the deeper node before branching. (link to old forge https://migale.jouy.inra.fr/redmine/issues/5821).

[Feature] WEB APP: Select reference : functionality to have a direct access to the core / dispensable gene set for reference node. (link to old forge https://migale.jouy.inra.fr/redmine/issues/5822).

[Improvement] WEB APP: Automatic and anonymous bug reporting tool. (link to old forge https://migale.jouy.inra.fr/redmine/issues/5833).