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.