Tags give the ability to mark specific points in history as being important
  • 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
    • Bug fix: Genetic data overlay uploaded prior to 14.0.0 crashed maps (#988)
  • v14.0.1
    • Bug fix: maps that were annotated using old Biocompendium annotator could not load properly (#986)
  • 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)
  • v14.0.0-beta.2
    51a91464 · Update CHANGELOG ·
  • v14.0.0-beta.1
  • v13.2.0
    • Small improvement: MolArt v1.4 is used which provide information from PredictProtein (#913)
    • Bug fix: search by drugs didn't check synonyms in chembl database
    • Bug fix: verification of overlay type added (#917)
    • Bug fix: opening edit project/user dialog returned list of users/projects to the 1st page (#909)
    • Bug fix: show element title option wasn't influencing title visibility (#910)
  • v14.0.0-beta.0
  • v13.1.3
    90fad475 · Merge branch... ·
    • Bug fix: refreshing list of projects or list of users doesn't change active page (#870)
    • Bug fix: submap list must be selected to export from every submap (#874)
    • Bug fix: export map as image properly uses bottom limit (#875)
    • Bug fix: reaction info window wasn't closed on CLEAR (#876)
    • Bug fix: name of the uploaded file is displayed when adding overlay (#849)
  • v14.0.0-alpha.1
  • v14.0.0-alpha.0
  • v13.1.2
    • Bug fix: Information about problematic zip file is more specific (#865)
    • Bug fix: Url didn't contain list of opened plugins and they weren't reload automatically on refresh (#866)
  • v13.1.1
    • Bug fix: adding gene mapping before the genome caused an error (#835)
    • Bug fix: "Terms of Use" change to "Terms of Service" in all places (#843)
    • Bug fix: upgrade to 13.1.0 crashed on machines where every element was inside compartment (#856)
    • Bug fix: searching for some drugs in chembl didn't provide any results even though that data exists, for instance 'DORLIMOMAB ARITOX' (#842)
    • Bug fix: user wasn't logged out in all tabs when the log out event appeard in only one of them (#847)
  • v13.1.0
    • Feature: annotators are more flexible - you can define set of input and outputs used by annotator (#617)
    • Feature: changes in admin panel doesn't require saving - they are saved automatically (#676)
    • Feature: elements can have custom glyphs used for visualization (#487)
    • Small improvement: model_name renamed to map_name in data overlay columns (#827)
    • Small improvement: name, type, reference_genome_type and reference_genome_version column in genetic variant data overlay are deprecated (#827)
    • Small improvement: all bio entities have z-index associated with them (#487)
    • Small improvement: validation of the organism and disease id on map upload added (#618)
    • Small improvement: added current username next to logout button in admin panel (#660)
    • Small improvement: New comment dialog does not contain content of previous comment dialog (#680)
    • Small improvement: Left logo is configurable (#731)
    • Small improvement: list of element types in choose annotator dialog is sorted (#798)
    • Small improvement: Plugin API provides list of overview images (#702)
    • Small improvement: Plugin API allows to show/hide overview images (#702)
    • Small improvement: Plugin API allows to trigger search on the map (#702)
    • Small improvement: Plugin API allows to clear search results on map (#702)
    • Small improvement: edit/remove project button is disabled until project is uploaded (#683)
    • Small improvement: warning about capslock is visible on login page when necessary (#658)
    • Small improvement: names of columns in data overlay are unified: no whitespace, "_" used as separator (#596)
    • Small improvement: list of references in drug panel contains PUBMED prefix (#666)
    • Small improvement: list of projects is auto refreshed every 5 seconds if at least one of the project is uploading/removing (#610)
    • Small improvement: passwords to email account and ldap are not sent over API (#732)
    • Small improvement: reactant/product/modifier specific colors are parsed properly from CellDesigner file (#597)
    • Small improvement: Info tab contains information about disease and organism when info is provided
    • Small improvement: Info tab provides information about model annotations and submap tabs provide information about submaps annotations if applicable (#591)
    • Small improvement: uploading sbml file should automatically discover a file type (#784)
    • Small improvement: when plugin listeners crash the system notifies user about problem with a plugin (#767)
    • Small improvement: when exporting reaction and elements there is possibility to filter by (sub)map (#615)
    • Small improvement: during first opening of a map, the zoom level is automatically computed if no default information is provided (#776)
    • Small improvement: when adding new project columns "Root map", "Mapping file" and "Map type" are merged (#700)
    • Small improvement: allow admin to disable CORS check (#802)
    • Small improvement: TransparencyZoomLevelVisibility parameter renamed to SemanticZoomLevelTransparency (#801)
    • Small improvement: export/import from SBML support z-index in LAYOUT extension
    • Bug fix: due to blocking of our requests from ctdbase the autocomplete for this database is disabled
    • Bug fix: deprecated columns in data overlay are not visible to the end user (#827)
    • Bug fix: invalid color in data overlay provides proper feedback to the user (#822)
    • Bug fix: genetic variant overlay without name caused problems (#832)
    • Bug fix: tair locus identifiers were used improperly - instead of id the name was used
    • Bug fix: plugin tab header wasn't properly resized after adding plugins that introduced second line for tab selection (#758)
    • Bug fix: invisible layer shouldn't be shown on the map (#813)
    • Bug fix: list of availbale annotators is sorted alphabetically (#815)
    • Bug fix: redirect url from export panel is fixed (#819)
    • Bug fix: allow to reupload the same file without closing add overlay dialog (#833)
    • Bug fix: gene_name column is allowed only in the genetic variant data overlay
    • Bug fix: protein types are sorted properly in "Select valid annotations" dialog (#815)
    • Bug fix: if there is a description of (sub)map then it is available in info/submap panel (#824)
    • Bug fix: empty type for data overlay is allowed (#827)
    • Bug fix: genetic variants data overlay was ignoring color parameter (#827)
    • Bug fix: asynchronous calls on showing/hiding data overlays might cause problems due to network latency (#830)
    • Bug fix: progress bar of gene genome mapping upload is refreshing properly (#728)
    • Bug fix: when editing project Disease and Organism could not be removed (#616)
    • Bug fix: dashed line partially wasn't dashed in "Unknown Catalysis" and "Unknown Inhibition" reactions (#664)
    • Bug fix: "Unknown Catalysis" and "Unknown Inhibition" reaction end is slightly separated from target phenotype (#664)
    • Bug fix: order of genomes in admin panel doesn't change after refreshing list of genomes (#761)
    • Bug fix: fixing situation when Molart started with variation overlay not having the aa change information
    • Bug fix: plugin contect element width is adjusted when link to tabs are wrapped in more than one line (#758)
    • Bug fix: export to CellDesigner preserve font size (#798)
    • Bug fix: layout data was ignored for some reactions when importing from SBML (#812)
  • v13.1.0-beta.1
    41feac00 · Update CHANGELOG ·
  • v13.1.0-beta.0
  • v13.0.0
    • Bug fix: Since Oracle Java cannot be installed as debian dependency we use openjdk-8. Due to this dependency minerva can be no longer installed on Ubuntu-14 (#223)
  • v12.2.3
    • Bug fix: sorting of entries in "Edit project->overlays" dialog fixed (#790)
    • Bug fix: searching of chemicals stopped working due to expired SSL certificate on https://ctdbase.org/
    • Bug fix: remove button is disabled after starting removing of the data overlay (#791)
    • Bug fix: search autocomplete hint could be initially hidden (#793)
    • Bug fix: updating terms of use could crash when list of users was removed in separate tab or by another user (#797)
    • Bug fix: name of the checkbox in ADD PROJECT window adjusted (#799)
    • Bug fix: when user didn't have privileges to remove comments the button was active on pages other than page 1 (#792)
    • Bug fix: export of reaction to SBML didn't work when lines on the map were too short (#805)
  • v12.2.2
    • Bug fix: downloading overlays didn't work from admin panel when project with different id than default map was accessed
    • Bug fix: change of owner of the data overlay in admin panel incorrectly ordered overlays (#777)
    • Bug fix: chemical search didn't use updated disease identifier, original disease id from project upload was used instead (#779)
    • Bug fix: user login with special characters (like '@') could cause problems in admin panel (#780)
    • Bug fix: removing project without full control in the system (but with enough privileges to remove project) caused "Not enough privileges" error (#778)
    • Bug fix: export of custom properties (like synonyms) are properly encoded in CellDesigner xml (#785)
    • Bug fix: notification about not supported version in IE 11 fixed (#783)
  • v12.2.1
    • Bug fix: export of reaction colorsi in SBML is properly encoded (COPASI can read colors properly) (#744)
    • Bug fix: removing active plugin didn't switch plugin tab to the next loaded plugin (#757)
    • Bug fix: closed submap will not be reopened after page refresh (#763)
    • Bug fix: comment remove button is disabled for users without proper privileges (#766)
    • Bug fix: invalid pubmed identifier could break clicking on element containing it (#764, #765, #769)
    • Bug fix: cache for API queries is explicitly disabled - some queries could be mistakenly cached and the system behaviour might get unstable (#771)