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User view refers to the visualization and functionalities accessed by users of the content hosted by your MINERVA instance.

You can also see the brief summary of this page in the MINERVA Quick Reference Guide or you can follow the guide.

User login and sign up

Logged users can upload their data overlays and administer the platform and its contents, if they have admin privileges. User login is not mandatory to browse publicly available content.

Users can log in to the MINERVA platform through three distinct interfaces:

I) Overlays

II) Info tab

III) Admin login: For administrator access, please refer to the Administrator login

User Login

They can log in using either a Local ID or an ORCID account:

1) Local ID: Local IDs are for users who are manually added or have signed up themselves. The availability of either Sign Up or Request an Account depends on your MINERVA configuration (see below).

2) ORCID: Users can use their ORCID ID and password to log in.

Setting up a local ID User sign up option (if available), allows users to set up their account. Upon completing the sign-up process, users receive a notification to confirm their email address.

Sign up form Confirmation notification

After confirming their email, based on MINERVA configuration, users may either have to wait for administrator approval or they can immediately access their account.

Wait for approval No need to wait for approval


Request an Account option (if available), will redirected users to request an account via email.


Accessing the project

Your instance of MINERVA Platform can host many projects, which are uploaded by the administrators (see add project). Every project can be accessed by a dedicated web address.


Exploring the display area

The MINERVA Platform displays molecular interaction diagrams with their annotations. Click on any element in the display area - it will be marked with a color pin Pin and its details will be displayed in the left panel (see the map).

Display Area


Systems biology diagrams

The MINERVA Platform visualises diagrams using three formats: SBGN-compliant, SBML and GPML. Read more about customising the content here. Especially for SBML format, it is worthwhile to customise the file before the upload to MINERVA in order to improve its visualization.

The content is visualized using Google Maps API or Open Layers Library (chosen on the project upload), and allows for similar pan-and-zoom functionalities. The content is interactive, the user can click on an element or an interaction to examine additional details, which are displayed in the left panel (functional area). More tools are available via right click on the map.

The MINERVA Platform allows to use custom graphics (glyphs) provided by user in combination with displayed diagrams (check section glyphs).

Semantic zoom

Semantic zoom is a default view of the map. It makes the compartments and pathways cover underlying elements on higher levels of zoom. This view is generated procedurally - areas covering others are calculated based on the content assigned to appropriate zoom levels. Find out more here: procedural generation of the semantic zoom.

Note: In Overlays tab in the left panel, semantic zoom is activated via Pathways and compartments background. You can turn it off by changing the view on Network or Empty background.

Show overview

Located tn the Information bar, this button invokes a static image associated with the displayed content. It may be a graphics helping to understand the underlying map, or any other visual cue that the content curator decided to present. The initial image displayed with the Show overview button can be linked to:

  • another static image to be displayed next
  • a defined area in the displayed content
  • a set of elements or interactions

Comments

Located tn the Information bar, if this checkbox is checked, the comments provided by users with Pinned option set to Yes will become visible in the display area (see Add comment).

Legend

Located tn the Information bar, if this checkbox is checked, the legend describing element and interaction types will be displayed.

Clear

Located tn the Information bar, this button clears all search results currently shown in the display area.

Submaps tab

Shows all the submaps linked to the main map of this project hosted by your MINERVA instance. See Administrator manual - advanced upload to learn how to upload the submaps together with the main file.
The tab Submaps is visible in the left panel only if the map contains at least one submap. The tab contains: 1) names of the submaps 2) + icon to show maps’ description, if one is provided 3) anchor elements of the submaps (which user can see on the main map when selecting the Anchor icon related to that submap) and 4) magnifying glass buttons to display them. The submaps show as a pop-up window on top of the main map (image below).

Submaps

Search results and search pins will be visible in the main map and the active submaps. Also, on the main map there is an icon multi icon informing that search results hit submap (see image below).

Submaps


Info tab

The Info tab has two components, displaying Project info and User data (for registered and logged users).


Project info

Displays name, version and the details of the map.

The Data section features the links to:

  • Browse the publications supporting the map. The Publication list dialogue allows to search for articles by title, author names or year. It contains links to interactions supported by particular articles. The list of the publications can be downloaded.
  • Download the project’s source files.
  • Export the contents of the map (see below for more details).
  • Open the MINERVA manual.
  • The information about the disease type (Mesh id).
  • The information about the organism type (Taxonomy id).

The Description section contains information from the CellDesigner file from Model Notes and Model Description (if provided).


Export

The Export page contains three tabs (Elements, Network and Graphics), allowing to download the map contents in different formats.

  • ELEMENTS tab allows to download the list of elements in the map as a text file. Available filters include:
    • Type - filters elements by the element type (e.g. Protein, RNA)
    • (sub)map - filters elements by the (sub)map
    • Column - selects particular details, including:
      • Id - identifier of the element in the MINERVA system
      • Name - name of the element
      • Map id - identifier of the (sub)network containing this element
      • Type - type of element
      • Complex id - if applicable, id of the complex containing this element
      • Compartment - the smallest compartment/pathway containing the element
      • Element external id - corresponding source file e.g. CellDesigner ID
    • Annotations - filters the annotations of elements in the downloaded file; by default all annotation types are considered. Fields highlighted in green are non-empty annotation sources
    • Included/excluded compartment/pathways - filters the elements by compartments/pathways they are in; by default all compartments are considered as “included”, none as “excluded”


  • NETWORK tab allows to narrow down and download the interactions in the map. The exported network file is not a fixed-column table. As interactions are in fact hyper-edges, each line may contain different number of reactants, products and identifiers. Available filters include:
    • Element type - filters the nodes of exported interactions by the element type
    • Reaction type - filters interactions by type
    • (sub)map - filters elements by the (sub)map
    • Column - selects particular columns, including:
      • Elements - information about reactants, products and reaction modifiers
      • Reaction external id - reaction identifier from the source file e.g. CellDesigner ID
      • Map id - identifier of the (sub)network containing this element
    • Annotations - filters the annotations of elements and interactions in the downloaded file; by default all annotation types are considered. Green highlighted fields are non empty annotation sources
    • Included/excluded compartment/pathways - filters the elements by compartments they are in; by default all compartments are considered as “included”, none as “excluded”


  • GRAPHICS tab allows to download graphics of the (Sub)map in one of the Format: PNG image, PDF and SVG image. Also, user can provide size of graphics in Image size.


User data

If registered, users can login here, or request for an account from the administrators of this MINERVA instance. Platform administrators can register new users (see Administrator’s manual - USERS) and configure Request an account functionality (see Administrator’s manual - Configuration)

After login, this panel displays information about the user. After the successful login the user gains the possibility to upload custom overlays (see Overlays).