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.

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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.

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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.

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