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