• Backward incompatible: old connection to CTD is removed and replaced with new Data-API interface that closely check license compliance
  • Backward incompatible: old connection to DrugBank is removed and replaced with new Data-API interface that closely check license compliance
  • Backward incompatible: some custom fields (like transparency zoom level) are not exported to CellDesigner file (#1071)
  • Backward incompatible: truncation/association/dissociation points are represented as a dot in all new images/uploaded maps (#1265)
  • Backward incompatible: and/split points are represented as a dot in all new images/uploaded maps (#1253)
  • Backward incompatible: reaction will be on top of elements in maps uploaded from formats that does not contain z-index (#1251)
  • Backward incompatible: when uploading complex map with submap there is no possibility to change submap name (#947)
  • Improvement: logs provided for validation data model are structured (#325)
  • Improvement: import/export of GPML implemented
  • Improvement: API allows to merge files (#1208)
  • Improvement: export to SBGN/SBML/GPML format provides popup with list of warnings occurred in the translation process (#713)
  • Improvement: support for rendering colors in SBGNML added (#1009)
  • Small improvement: compartments in not layouted SBML file are more scattered (#326)
  • Small improvement: when downloading a map results in too big file (>1MB) the content is compressed and returned as a zip file (#348)
  • Small improvement: confirmation dialog when removing "general view" overlays contain proper warning (#809)
  • Small improvement: CellDesigner text area object can have "BorderColor" property defined (#806)
  • Small improvement: list of submaps is sorted alphabetically (#962)
  • Small improvement: notification about new releases of minerva added in admin panel (#961)
  • Small improvement: font awesome upgraded to 5.1 (new icon styles)
  • Small improvement: header contains login/logout button and access admin panel button (#982)
  • Small improvement: autocomplete for chemical searches is enabled (#841)
  • Small improvement: "bqbiol:occursIn" and "bqmodel:isDerivedFrom" and handled in annotations (#1190),
  • Small improvement: 3DMET, Evidence Code Ontology, Kegg Glycan, LipidBank, Chemical Component Dictionary annotations are supported (#1190)
  • Small improvement: SWISS-model annotations are supported (#1249),
  • Small Improvement: SBO annotation support added (#1194)
  • Small improvement: support for annotations added: ChemIDplus, EcoGene, FlyBase, GeneDB, Intact, Kegg Drug, KNApSAcK, LIPID MAPS, NCBI Protein, PATO, RGD, SPIKE, TTD Drug, ZFIN BioEntity
  • Small Improvement: additional annotation uri qualifiers added: hasProperty, isPropertyOf (#1193)
  • Small improvement: small css improvement in info tab (#1104)
  • 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)
  • Small improvement: when typing drug, list of autocomplete drugs should be available limited to the drugs that target 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)
  • Small improvement: sort order of tables in admin panel is preserved among sessions (#836)
  • Small improvement: simple molecules in SBGN compliant view are drawn as ellipses not circles (#796)
  • Small improvement: uploaded map is automatically cached (#983)
  • Small improvement: molart updated to version 1.5.0: Ability to show unobserved structure regions in the sequence view.
  • Small improvement: list of genomes is automatically refreshed during genome upload (#820)
  • Small improvement: items in context menu are reorganized (#787)
  • Small improvement: CellDesigner files from version 2.5 should be parseable
  • Small improvement: plugins in admin panel can be revalidated to update info about the plugins (name, version)
  • Small improvement: there is possibility to define default plugins loaded with every opening of a map (#967)
  • Bug fix: pathways are visualized in image converter (#1266)
  • Bug fix: conversion of file containing BOM did not work (#1264)
  • Bug fix: proper color is parsed from CellDesigner species marked as 'brief'
  • Bug fix: upload of SBGN files didn't process unicode characters properly when server was running with encoding different than UTF-8 (#1142)
  • Bug fix: kinetic equation in reaction that referenced complex (instead of target species) crashed CellDesigner upload (#1212)
  • Bug fix: kinetic equation in SBML that used speciesReference id crashed upload (#1190)
  • Bug fix: layout reaction with duplicated reaction element crashed SBML upload (#1190)
  • Bug fix: conversion from SBML to CellDesigner escaped "<" twice (#1228)
  • Bug fix: Select annotation dialog width is at least 840px (#1210)
  • Bug fix: modifiers joined by operator were exported to SBML without line corresponding to the operator (#1199)
  • Bug fix: first state variable that does not match modification residue is translated to structural state when importing from SBGNML (#1088)
  • Bug fix: exported SBML was not compliant with the standard when element name was empty (#1147)
  • Bug fix: invalid data overlays in uploaded zip file created "valid" project that could not be opened (#1086)
  • 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
  • Bug fix: newt use incorrect attributes when exporting render information that could not be parsed by minerva (#1127)
  • Bug fix: catalysis to protein was not parsed from SBGN file (#1116)
  • Bug fix: antisenseRNA shape is inferred 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: more than one authors in CellDesigner file were not parsed properly (#1156)
  • Bug fix: SBGN reaction with no reactants crashed map upload (#1148)
  • 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 instead of Ellipse which was not SBGN-compliant (#1095)
  • Bug fix: import from CellDesigner rounded alias dimension to integer
  • Bug fix: compartments limited by corner (left-top corner compartment, etc) are parsed properly from CellDesigner files
  • Bug fix: structural states of proteins are imported properly from SBGNML PD (#995)
  • Bug fix: export to CellDesigner names with new line is properly handled (#930)
  • Bug fix: layout of the exported reactome pathways is fixed when reactome exporter violates SBGN specification (#707)
  • Bug fix: unknown catalysis boolean gate modifiers in CellDesigner are visualized with proper line type across all included modifiers (#957)
  • Bug fix: dimension of the modifications is the same as in minerva when exporting to SBGNML-PD (#554)
  • Bug fix: position of structural state is preserved on upload CellDesigner file (#671)
  • Bug fix: problematic notes doesn't crash CellDesigner upload (#968)