Tags give the ability to mark specific points in history as being important
  • v14.0.12
    Release v14.0.12
    • Bug fix: comments on submaps were not visible (#1230)
    • Bug fix: removing comment from submap did not work
    • Bug fix: reaction name containing "<" character was exported inproperly to CellDesigner (#1227)
    • Bug fix: doi annotation was inproperly parsed from CellDesigner file and resulted in not clickable link (#1231)
    • Bug fix: when plugin data was too big 500 error was returned (#1232)
    • Bug fix: removing plugin in admin panel removes it from server permanently (#1211)
  • v15.0.0-beta.3
    Release v15.0.0-beta.3
      * Improvement: API allows to merge files (#1208)
      * Bug fix: exported SBML was not compliant with the standard when element
        name was empty (#1147)
      * Bug fix: flybase and pato annotations from CellDesigner were not picked
        (#1113)
      * Bug fix: invalid data overlays in uploaded zip file created "valid" project
        that could not be opened (#1086)
      * Bug fix: export to GPML preserves font color of compartments (#1111)
      * Bug fix: export to GPML preserves information about hypotetical complexes
        (#1111)
      * Bug fix: export to GPML preserves complex name (#1111)
      * Bug fix: export to GPML preserves reaction color (#1111)
      * Bug fix: modification residues are exported to gpml (#1111)
      * Bug fix: information about reaction reversibility is exported to gpml
        (#1111)
      * Bug fix: cardinality in SBGN-like view is drawn in separate unit (#1157)
      * Bug fix: notes from SBML are parsed with all html tags (#1196)
      * Bug fix: converter API append conversion warnings to generated output notes
  • v15.0.0-beta.2
    Release v15.0.0-beta.2
    • Small Improvement: SBO annotation support added (#1194)
    • Small Improvement: additional annotation uri qualifiers added: hasProperty, isPropertyOf (#1193)
    • Small Improvement: default color of complexes imported from gpml changed to the one used by wikipathways (#1107)
    • Bug fix: newt use incorrect attributes when exporting render information that could not be parsed by minevra (#1127)
    • Bug fix: catalysis to protein was not parsed from SBGN file (#1116)
    • Bug fix: upload logs for SBGN parser were not translated properly to new structured log form
    • Bug fix: antisenseRNA shape is infered from SBGN when antisenseRNA text is present in glyph label (#1114)
    • Bug fix: export to SBGN sometimes crashed due to concurrency issues (#1126)
    • Bug fix: CellDesigner models where start and end point of reaction was the same were not handled properly (#1131)
    • Bug fix: exporting map to CellDesigner from GPML file created not-editable compartments (#1146)
    • Bug fix: some CellDesigner 2.5 files could not be parsed (#1125)
    • Bug fix: more than one authors in CellDesigner file were not parsed properly (#1156)
    • Bug fix: pathways imported from gpml persist fill color (#1107)
    • Bug fix: some reversible reactions in gpml were not imported as reversible (#1107)
    • Bug fix: colors of reactants/products/modifiers were not imported from gpml (#1107)
    • Bug fix: border color of species imported from gpml is preserved (#1107)
    • Bug fix: coordinates of complex name from GPML file is preserved (#1107)
    • Bug fix: element name for general shapes imported from GPML does not contain ShapeType if feasible (#1107)
    • Bug fix: z-index of rectangles and some complexes imported from GPML was not assigned properly (#1107)
    • Bug fix: new line in label text does not split he text into name and desciption (#1107)
    • Bug fix: label omim href with "www" prefix are parsed properly
    • Bug fix: modification position imported from GPML file is preserved (#1107)
    • Bug fix: SBGN reaction with no reactants crashed map upload (#1148)
  • v14.0.11
    Release v14.0.11
    • Bug fix: complex with no border was inproperly imported from CellDesigner (#1198)
    • Bug fix: export to CellDesigner deal with CellDesigner issue that does not allow complex species alias to be shorter than 2 characters (#1204)
    • Bug fix: kinetic parameters with INFINITY values could not be uploaded to minerva (#1202)
    • Bug fix: infinity value in kinetic parameter could not be parsed from CellDesigner file minerva (#1203)
    • Bug fix: author list inproperly presented author data when some fields were missing (#1201)
    • Bug fix: refreshing minerva page with more than one plugin opened might led to an error due to race condition (#1197)
  • v14.0.10
    Release v14.0.10
    • Bug fix: reaction without ports in SBGN crashed upload (#1065)
    • Bug fix: annotations using newer identifiers.org uri schema were truncated by one character (#1191)
    • Bug fix: long annotation string broke listing of annotations (#1155)
  • v15.0.0-beta.1
    Release v15.0.0-beta.1
    • Bug fix: conflict on libraries caused some features to stop working in production (like parsing text notes of species, regresion in 15.0.0~alpha.1, #1139)
  • v14.0.9
    Release v14.0.9
      * Bug fix: simultanous export to SBML of more than one file could result in
        500 Internal Server Error (#1110)
      * Bug fix: refresh data overlay did not hide data overlays that were removed
        and selected (#1097)
      * Bug fix: transparent complexes are shown with wrong color (#1103)
      * Bug fix: CellDesigner sometimes marked reduced notation reaction as
        reversible even though they were not visualized so (#1109)
      * Bug fix: when data overlay was being removed user could request to remove
        overlay second time and an error was thrown (#1121)
      * Bug fix: when data overlay name in zip uploaded zip file is not present the
        name of a file is used as overlay name (#1065)
      * Bug fix: uploading empty data overlay resulted in an error (#1123)
      * Bug fix: exporting map with glyphs crashed (#1130)
      * Bug fix: transcription factor on black&white gene are drawn in black
        (#1132)
      * Bug fix: when SBGN file contained consumption starting in process minerva
        crashed (#1063)
      * Bug fix: when SBGN file contained reaction where every node started in the
        same process port minerva crashed crashed (#1063)
      * Bug fix: activity flow reaction inside SBGN PD caused upload of map to
        crash
      * Bug fix: reaction without product in SBGN crashed upload of map
      * Bug fix: when SBGN production pointed directly to process instead of
        process port upload crashed
      * Bug fix: handle properly corrupted cached chembl drug data (#1140)
  • v15.0.0-beta.0
    Release v15.0.0-beta.0
    • Feature removal: old connection to CTD is removed and replaced with new Data-API interface that closely check license compliance
    • Feature removal: some custom fields (like transparency zoom level) are not exported to CellDesigner file (#1071)
    • Improvement: export to SBGN/SBML/GPML format provides popup with list of warnings occurred in the translation process (#713)
    • Small improvement: autocomplete for chemical searches is enabled (#841)
    • Small improvement: import/export to SBML of unit of information obtained from SBGN source is supported (#1088)
    • Small improvement: rounded rectangle is used to visualize Simple chemicals in SBGN-like view according to the newest SBGN specification (#1094)
    • Small improvement: after removing project is confirmed the system enforce waiting until remove status is confirmed (#1106)
    • Bug fix: import from SBGN assigned invalid name to species that didn't have label defined (#1093)
    • Bug fix: drawing protein in SBGN-like style didn't handle properly dimension of the species for multimers bigger than 2 (#1091)
    • Bug fix: drawing of structural state in SBGN-like style uses RoundedRectangle insetad of Ellipse which was not SBGN-compliant (#1095)
    • Bug fix: export to GPML provided invalid font size and pathviosio could not open it (#1108)
  • v14.0.8
    Release v14.0.8
    • Bug fix: API didn't allow to upload pluins with local url (#1084, regression 14.0.7)
    • Bug fix: upload of data overlay with two entries having different uniprot identifier but pointing to the same gene crashed (#1083)
    • Bug fix: don't allow to remove plugin twice (#1081)
    • Bug fix: upload of SBML file with very short reaction length could produce a map that couldn't be exported to SBML anymore (#1078)
    • Bug fix: import of structural state from SBGN-ML PD that cannot be normalized to residue is changed into structural state without losing information (#1062)
    • Bug fix: import of stimulation modifiers from SBGN-ML crashed converter (#1063)
    • Bug fix: export to SBGN files created from newt source produced corrupted disconnected reactions
    • Bug fix: upload from zip file allowed empty overlay name (#1065)
    • Bug fix: genome browser slider didn't work properly in Safari on non-default Browser zoom level (#1048)
    • Bug fix: project without background overlay but with some custom data overlays crashed with an error (#1066)
    • Bug fix: when session expires updating options in configuration panel threw unhandled error (#1068)
  • v15.0.0-alpha.2
    Release v15.0.0-alpha.2
    • Feature removal: old connection to drugBank is removed and replaced with new Data-API interface that closely check license compliance
    • Small improvement: when typing drug, list of autocomplete drugs should be available limited to the drugs targetting something on the map (#641)
    • Small improvement: data not compliant with database constraints (for instance too long species identifiers) will be automatically adjust instead of crashing project upload (#1041)
    • Small improvement: reaction lines in SBML files without layout are set outside of the species (not in the center, #1023)
    • Bug fix: import from CellDesigner rounded alias dimension to integer
    • Bug fix: old project with structural state couldn't be removed (regression 15.0.0~alpha.1, #1021)
    • Bug fix: procseing sbgn file with render information was breaking sometimes (regresion 15.0.0~alpha.1, #1020)
  • v14.0.7
    Release v14.0.7
    • Bug fix: API allowed to provide malformed plugin url that could be used for xss attack (#1073)
  • v14.0.6
    Release v14.0.6
    • Bug fix: opening map with no background overlays and search request in url provides proper error message (#1046)
    • Bug fix: search by identifier didn't consider identifiers added by annotators (#1047)
    • Bug fix: if map has SHOW OVERVIEW, the legend/comment/clear were not displayed at all (regression 14.0.5, #1045)
    • Bug fix: when there is a problem with database during removing project, project removal doesn't hang (#1058)
    • Bug fix: coloring of the reaction wasn't applied to center of reaction (regression 14.0.0, #1057)
    • Bug fix: genetic variant overlay improperly processed elements identified by miriam identifiers, like uniprot (#1059)
    • Bug fix: invalid information was provided for genetic variants overlay when map organism was defined (#1060)
  • v14.0.5
    Release v14.0.5
    • Bug fix: copy-paste of genetic-variant data overlay into Add overlay content dialog could crash upload (#1040)
    • Bug fix: some annotators (like Cazy) were crashing on old installations (#1029)
    • Bug fix: uploading a map that breaks postgres constraints hung upload of the project (#1028)
    • Bug fix: uploading of the page with low internet connection speed could produce empty screen for several seconds/minutes - now the loading icon is present (#1025)
    • Bug fix: search for NADH drug resulted in drug with empty name (#1018)
    • Bug fix: export to SBML didn't handle properly arrows (#1015)
    • Bug fix: Font colour of text area was preserved in Empty view (#1014)
    • Bug fix: exported sbml file always contain model identifier (#1013)
    • Bug fix: typo allel reverted to allele in overlay data (regression 14.0.0, #1012)
    • Bug fix: after loading/removing too many plugins it was impossible to load new plugins (#1011)
    • Bug fix: CLEAR button disappears after legend, comment checkboxes when plugin tab used to much space (#976)
  • v15.0.0-alpha.1
  • v14.0.4
    Release v14.0.4
    • Bug fix: some SBGN files uploaded to minerva could not be exported to SBML due to problems with identifiers used by SBGN (#1006)
    • Bug fix: upload of data overlay with conflicting overlay types caused error (#998)
    • Bug fix: upload of sbml file with protein modifications inside complex crashed visualization (#966)
    • Bug fix: list of overlays for admin and curator included also other people overlays (regression 14.0.3, #1008)
    • Bug fix: refresh button did not refresh overlay list after overlay was removed over API (#997)
  • v15.0.0-alpha.0
  • v14.0.3
    Release v14.0.3
    • Bug fix: default zoom level on main map works even when x or y are undefined (#993)
    • Bug fix: sbml parser had sometimes problems with combining layout and multi packages (#966)
    • Bug fix: parsing of CellDesigner files that contained substanceUnits could crash the upload (#985)
    • Bug fix: verificatin of version length added when uploading project implemented (#978)
    • Bug fix: CLEAR button disappeard when plugin tab used to much space (#976)
    • Bug fix: removing data overlay refreshes list of overlays in info window (#974)
    • Bug fix: general overlays are always on top of data overlays in info window (#975)
    • Bug fix: refresh button in overlay panel synchronise list of general and user provided data overlays (#975)
    • Bug fix: changing order of data overlays is reflected in info window
    • Bug fix: opening map with no available background crashed (#964)
    • Bug fix: uploading SBGN file that does not pass xsd validation provides a warning, but does not fail upload (#937)
    • Bug fix: export of the map to SBML that was imported with older version (below 14.0.0) didn't produce valid SBML (#970)
    • Bug fix: fields in add project window are reinitialized after each open (#963)
    • Bug fix: filename case in uploaded zip files is preserved (#964)
    • Bug fix: +/- buttons were misaligned in genemove browser (#942)
    • Bug fix: color of links in the left panel was unintentionally changed (#990)
    • Bug fix: minerva logo in left panel is centered properly
    • Bug fix: width of search button icon was too big
  • v14.0.2
    Release v14.0.2
    • Bug fix: Genetic data overlay uploaded prior to 14.0.0 crashed maps (#988)
  • v14.0.1
    Release v14.0.1
    • Bug fix: maps that were annotated using old Biocompendium annotator could not load properly (#986)
  • v14.0.0
    Release v14.0.0
    • Feature removal: BioCompendium annotator removed (#32)
    • Feature removal: support for tomcat7 removed (#828)
    • Feature: security layer redesigned - privilege types and scope changed (#636, #624)
    • Feature: log4j is replaced with log4j2 logging mechanism (#291)
    • Feature: database installed via debian package is done via dbconfig-commons (#469)
    • Feature: Replaced connection pool manager C3P0 with better maintained Hikari - restart of postgresql database doesn't require restart of tomcat (#564)
    • Small improvement: debian package can be installed on debian:buster (#879)
    • Small improvement: info window contains information about overlay No (#919)
    • Small improvement: sorting by columns that doesn't make sense in admin panel is disabled (#895)
    • Small improvement: version of minerva is visible in map browser panel
    • Small improvement: small info about annotator details is available in select annotators dialog (#923)
    • Small improvement: CellDesigner layers are always visualized as pathways (#813)
    • Small improvement: notification email uses minerva name and id of affected project (#926)
    • Small improvement: information about person who uploaded project is visible in list of projects (#927)
    • Small improvement: tab with list of glyphs is available when adding project with glyphs (#925)
    • Small improvement: BackgroundColor parameter should be assigned using ":" character (#929)
    • Small improvement: anonymous login is no longer required - each API query outside session is authorized with anonymous user privileges (#629)
    • Small improvement: bcrypt is used for password encryption (#387)
    • Small improvement: caching is active by default for new users when uploading project (#202)
    • Small improvement: when removing overlay in admin panel there is a confirmation dialog (#696)
    • Small improvement: overlay name is obligatory (#698)
    • Small improvement: list of projects in admin panel contains creation date (#447)
    • Small improvement: links in list of publications open in new tab (#447)
    • Small improvement: target gene in search panel contains also information about type of database that identifies the target (#66)
    • Small improvement: redundant 'references' field in gene variants data overlay is now deprecated (#850)
    • Small improvement: information about deprecated columns in data overlay is visible in overlay list (#838)
    • Small improvement: publication list is resizeable (#740)
    • Small improvement: user list on project edit dialog is sortable (#808)
    • Bug fix: exported SBML passes online validation (#831)
    • Bug fix: allow user to remove own comments (#931)
    • Bug fix: validation of project name length is provided (#950)
    • Bug fix: list of "Copy from" elements in "Select valid annotations" dialog is shortened to used bio entity types (#911)
    • Bug fix: version of the project is limited to 20 characters (#951)
    • Bug fix: export to CD could misalign reaction lines that were imported from format that didn't require reaction line to be attached to the species (#933)
    • Bug fix: problem with uploading data_overlays with type included in header (#936)
    • Bug fix: work on FF Private Window mode could cause logout or raise an error on when opening new tab with minerva (#892)
    • Bug fix: fetching list of miRnas resulted sometimes in "Internal Server Error" (#889)
    • Bug fix: edit project dialog verifies organism id (#914)
    • Bug fix: all colors in boolean reaction (from CellDesigner) are processed properly (#907)
    • Bug fix: proper line type for boolean reaction is used on the whole reaction (#908)
    • Bug fix: creating project with too long name hung upload (#916)
    • Bug fix: too long user login threw an error (#915)
    • Bug fix: when uploading generic data overlay the type was not updated in case the type was not specified in the input file (#906)
    • Bug fix: list of types when copying from annotators contains only types that are selectable in the dialog (#911)
    • Bug fix: too long name for data overlay in info window is trimmed (#919)
    • Bug fix: too long name in general overlay list is wrapped (#857)
    • Bug fix: after genome is removed list of genomes is refreshed (#922)
    • Bug fix: REST API bioEntities:search method didn't limit results to the submodel id (#860)
    • Bug fix: Empty Overlay colours were not preserved during export to CellDesigner (#714)
    • Bug fix: problem with unloading plugin is properly handled (#884)
    • Bug fix: upload of invalid plugin doesn't add it to plugin tab and list of loaded plugins (#885)
    • Bug fix: export to CellDesigner of reaction with two modifiers connected with boolean operator resulted was skipping some layout information
    • Bug fix: reaction in SBGNML file containing two products was improperly drawn
    • Bug fix: color handling in CellDesigner did not work properly for modifiers inside boolean gateway
    • Bug fix: CellDesigner file exported from minerva was not fully compliant with SBML standard (#831)
    • Bug fix: MiRNA targets are limited only to the organism associated with the map (#66)
    • Bug fix: Search drug by target element did not return values when this element was annotated automatically (#216)