16.0.0 MINERVA Release#

29 Oct 2021#

Backward incompatibility:#

• Debian package cannot be upgraded from version prior to 12.1.0.

• layout parameter in MINERVA url is not supported anymore.

• The comment does not contain name anymore.

• Publication pagination API has been slightly changed.

• Elements in data overlay are returned differently when using data overlay API.

• Deprecated columns in data overlay table are no longer supported: reverseReaction, reaction_identifier, reactionIdentifier, reference_genome_type, reference_genome_version, allel_frequency, lineWidth, elementIdentifier, references, model_name.

• Information about old search queries are removed from database (it can be still accessed using proper log managing).

Improvement:#

• The map is available immediately after tomcat starts.

• MINERVA does not require huge amounts of memory anymore.

• Data overlay allows for multiple hits per element.

Small improvement:#

• Backgrounds are separated from general overlays.

• The layout of pin popup window is slightly improved.

• Search results are grouped by submap with hits in the left panel.

• Artificial source and sink are created separately for each incomplete reaction.

• Homomultimer information is provided in API.

• There is warning about missing information for species for SBML parsing.

• Information about dimer in SBGN is provided only once if the information is duplicated in SBGN data.

• Glyphs quality is improved.

• Search results are group by diagram.

• “Failed to fetch” errors are reported in a way that suggest retrying before submitting error report.

• Reverse search pop-up layout is redesigned.

• “dbSNP”, “IMGT HLA”, “PMC”, “Complex Portal” identifiers are supported.

• Information about perfect match search is stored in the url.

• Context menu exporting map is more precise about its scope.

• Styling of GENERIC search tab title is improved.

• SBML render contains information about species shapes.

• SBML render contains information about modification residues.

• SBML render contains information about structural states.

• SBML render contains process rectangle for reactions.

Fixed:#

• Show genetic data overlays in overlay window even when no data is available.

• Gene mapping with empty url caused issues when opening info window.

• Clear button does not show warning about missing disease ID anymore.

• Two genomics data overlays with two different reference genomes caused issue.

• Search results were limited to 10 elements.

• Currently Chrome auto fill is disabled for “Search:” in Admin panel tables.

• Search tab becomes active when drug/chemical/mirna result are available.

• Arrows without a “process” box had an irregular empty space in their lines

• When selecting drug in the species window, in left panel the Content tab is switched to Drug, and the text is search bar is updated with the drug name.

• Zoom slider was not updated when clicking on +/- in the genome browser.

• Refreshing page after removing last project on the page redirect to the proper page.

• Removing plugin that does not exist anymore does not raise an error.

• md5 hash function of plugin was not computed properly.

• Exported GPML for every compartment contained the list of species name in the comment section.