13.1.0 MINERVA Release

27 June 2019

Feature enhancements:

  • Currently, the annotators are more flexible. During adding a new project, the user can define a set of parameters (inputs and outputs) used by the annotators.

  • The changes made in Admin panel are saved automatically. Previously, to save the changes, clicking Save button was necessary.

  • The elements (species, compartments, pathways) can have custom glyphs (an images provided by user) used for the visualization.

Small improvements:

  • In data overlay columns, the parameter model_name is renamed to map_name.

  • In genetic variant data overlay the following terms are deprecated: name, type, reference_genome_type and reference_genome_version.

  • All bio entities have Z-index associated with them. Z-index allows on defining the position of the element in relation to other elements (front or back to them).

  • Export from/import to SBML supports Z-index in the LAYOUT extension.

  • The validation of the organism id and disease id during the map upload is added.

  • The username is displayed next to logout button in the Admin panel.

  • A new comment dialog is empty by default. Previously, it contained the content of the previous comment dialog.

  • The logo displayed in the left bottom corner of the map is configurable.

  • The list of the element types in Select annotators dialog is sorted alphabetically.

  • Plugin API provides the list of the overview images.

  • Plugin API allows to show/hide overview images.

  • Plugin API allows to trigger search on the map.

  • Plugin API allows to clear the search results on map.

  • Edit/Remove project button is disabled until a project is uploaded.

  • The warning “Caps lock is on” is visible on the login page when necessary.

  • The names of the columns in data overlay are unified: no whitespace, instead here is the underscore _ used as the separator.

  • The list of the references in the Drug panel contains PubMed prefix.

  • The list of the projects is auto refreshed every 5 seconds in case at least one of the projects is uploading/removing.

  • The passwords to the email accounts and LDAP are not available over API.

  • The reactant/product/modifier specific colors are parsed properly from the CellDesigner file.

  • Info tab contains information about the disease and the organism, if that information is provided.

  • Info tab provides information about the model annotations and the Submap tab provides the information about submaps annotations, if applicable.

  • Uploading the SBML file automatically discover the type of file.

  • In case the plugin listeners crash, the system notifies the user about that problem with the plugin.

  • Export of the reaction and the elements can be filtered by a (sub)map.

  • During the first opening of a map, the zoom level is optimized automatically, in case there is no default zoom level provided.

  • In Add project dialog, the columns: Root map, Mapping file and Map type are merged.

  • The admin is allowed to disable the Cross-Origin Resource Sharing check.

  • TransparencyZoomLevelVisibility parameter is renamed to SemanticZoomLevelTransparency.

Bugs fixed:

  • Due to blocking of our requests from ctdbase, the auto-complete for this database is disabled.

  • The deprecated columns in the data overlay are not visible to the end user.

  • The invalid color parameters in the data overlay provides a proper feedback to the user.

  • Genetic variant overlay without the name provided caused problems.

  • TAIR locus identifiers were used improperly to get annotations - instead of id the name was used.

  • Plugin tab header was not properly resized after adding plugins that introduced second line for the tabs selection. It caused some plugin tabs were hidden.

  • The invisible layer (in CellDesigner) are not shown on the map. Previously, these layers overlapped the pathways generated by MINERVA.

  • Redirect URL from Export panel was fixed. Before, that URL directed to the default map instead of the map user was browsing.

  • Allow to re-upload the same data overlay file without closing the Add overlay dialog.

  • gene_name column is allowed only in the genetic variant data overlay.

  • The protein types are sorted alphabetically in Select valid annotations dialog.

  • If there is a description of a (sub)map, it is available in Info/Submap panel.

  • In data overlay the column type might be empty now. Previously, uploading an data overlay with type empty crashed that upload.

  • Genetic variants data overlay was ignoring the color parameter, thus the map was colored only by the default colors.

  • Asynchronous calls on showing/hiding data overlays might cause problems due to network latency.

  • The progress bar of upload the Genome mapping is refreshing properly.

  • While editing the project, disease id and organism id can be removed now.

  • The dashed line was displayed partially as continuous one in “Unknown Catalysis and Unknown Inhibition reactions.

  • The Unknown Catalysis and Unknown Inhibition reaction end is slightly separated from the targeted phenotype.

  • Currently, the order of the genomes list in Admin panel does not change after refreshing page.

  • Starting of the MolArt was crashed in case MolArt started with gene variant overlay that does not contain the amino_acid_change column.

  • Export map to CellDesigner preserves the font size.

  • The layout data was ignored for some reactions during import from SBML.

See previous MINERVA 13 release notes: