12.0 MINERVA Release

16 Jul 2018


New:

  • The kinetics of reaction is supported

  • OpenLayers map engine is available as alternative to Google Maps

  • Visualization of protein’s structures by MolArt available

  • Default user privileges for new project (manage comments, manage overlays, view project) are configurable

  • Plugin API build - a set of methods which allows to store data for plugin infrastructure

  • Support for annotations from following databases: STRING, STITCH, KEGG, CAZy, BRENDA


Feature enhancements:

  • Export map in pure SBML format, in both cases - with and without overlay extension

  • Distinction of annotation’s sources, between manually added annotation (Source: Annotated by curator) and automatically added one

  • All functionalities are provided via REST API

  • User-provided overlays in left panel are numbered and reordering them is supported

  • The overlaying results of searching for various elements (i.e. drug target, miRNA target) are indicated with different icon

  • Submap indicator added - it marks the top map and informs about the connection of searched element to the submap

  • Identical search results for the element are merged (marked with the same number on the display area and left panel)


Changed:

  • Legend is always on top of the map

  • Auto complete functionality in search field

  • The submap reference is marked in publication list for the element

  • The submap contains default centred position and zoom level to customize default view when entering map for the first time

  • Search by chemical names is supported

  • Confirmation window is shown before removing data overlay

  • Configuration options are grouped in categories

  • Handling of additional MIRIAM types from BiGG ontology

  • DOI is supported as MIRIAM data type

  • CellDesigner reactions of Modifier type (i.e. catalysis, inhibition) are supported

  • Opening data overlay switch the map’s background to Empty

  • Clicking on a highlighted element does not pop up a window, it behaves in the same way as clicking on not highlighted element

  • Data overlays color scale contains configurable default color for value = 0

  • Transparency level for data overlays is configurable

  • Column elementIdentifier added to data overlays allows to color particular element by its source identifier (Alias ID of element in CellDesigner)

  • Coloring elements in submaps by adding column model_name in data overlays to differentiate between maps

  • Column type is case insensitive in data overlays

  • Columns value and type are not mutually exclusive in data overlays

  • During loading data in search tab the “LOADING” icon occurs

  • Description of chemical panel refers to the disease connected to the map

  • Email for an account request contains configurable text

  • Notification email it compressed in case its size is too big

  • No duration of the text notification in overlay tab

  • The title of submaps list does not contain UNKNOWN tag


Fixed:

  • Auto complete of words typed in search field is case sensitive
    ⟹ now: Auto complete of words typed in search field is case insensitive

  • Adding new map with archived source file crashes if the zip file is created by Mac OS, due to the additional file .DS_Store in the archive file
    ⟹ Upload ignores file .DS_Store in the archived source file

  • Searching with two queries sometimes results in one complex instead of two queries
    ⟹ Searching for two queries results in two queries

  • Submaps do not have semantic zoom
    ⟹ Submaps are shown in semantic zoom as per main map


Developer:

  • Google Maps API 404 errors for non existing tiles are removed

  • Visualization of SBML function improved (lambda expression removed from the function definition)

  • Multiple x-frame domains are allowed

  • Size of connection to database reduced to 90 from 100 (so default connection pool to postgres is not completely filled with minerva)

  • Java Script plugin API allows to store data on server side

  • Database connection configuration (login, password, host, etc) can be modified using /etc/minerva/db.properties file