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Structure of a MINERVA project#

MINERVA projects can include multiple files, allowing to pre-configure a number options and functionalities. The structure explained below can be either compressed into a .zip file or uploaded from a git repository. See this repository for example.

The list of project components is as follows:

• root diagram (file, mandatory)
  a systems biology diagram in one of the compatible formats: CellDesigner SBML, SBML, SBGN-ML, or GPML, see compatible formats.
• submaps (folder, optional) - see Submaps
  • any number of compatible systems biology diagrams (file(s))
• overlays (folder, optional) - see Overlays
  files with data overlays to be set as publicly visible for the project, see more in visualisation
• glyphs (folder, optional): directory with glyphs (see Glyphs)
• images (folder, optional): directory with files displayed as Browse overview images (see Overview images)
• config.json (file, optional): configuration loaded on project creation to
  • pre-define configuration options of created projects, see here
  • pre-define glyph and submap links, see here and below
• .minervaignore (file, optional): lists files and directories to exclude when the project is created. This is useful for projects built from a git repository, or from an archive created on a system that adds its own metadata files. The syntax of the file is similar to .gitignore.

Learn more about advanced upload in example 04 - The advanced file upload.

Learn more about config.json in config file structure.

Sections of the structured project#

Submaps#

The submaps subdirectory contains files that will be displayed in the Submaps tab in the functional area of the User view (see section User view - Submaps tab).

Diagram elements can be configured to act as links (anchors) to other diagrams. Any element from the root or a submap diagram can be connected to any other diagram. To set up these links, use the dedicated Edit functionality (see Projects > Customise exploration).

Overlays#

The overlays subdirectory contains files with custom colouring of the uploaded content that will be accessible to all the users. The format is identical to the format of files uploaded by registered users. See section Upload user provided overlay data for details on file format.

Overview images#

The images subdirectory contains static image files in .png format that will be displayed after pressing the Show overview button (see Browse overview images in User manual). The links between the images and i) other images or ii) the contents of the map have to be expressed in coords.json file. The file is an array of entries, one per image, each containing the following keys:

• filename (string): linked image file.

• links: an array describing a link between image in filename with imageLinkFilename, query or modelLinkFilename.

  • polygon: an array with the coordinates of the points defining the polygon which will be treated as an active area for the link. The points are defined as a set x/y absolute coordinates (double) of the pixels in the corresponding image.

  • imageLinkFilename (string): links to other image from uploaded set, provide file’s name.

  • query (string): link to the results of a search query, provide the query.

  • modelLinkFilename (string): link to the main map, or one of the submaps.

    • zoomLevel (integer): in case of linking to modelLinkFilename - this field should contain a number corresponding to the zoom levels in the display area; otherwise it should be left empty. The furthest zoom out has number 0, each zoom in increases the zoom number by one. Smaller maps will have less zoom levels than big ones. Try uploading the map without images first, and assess the coordinates and zoom levels for the version with images.

    • modelPoint: in case of linking to modelLinkFilename - this field should contain absolute coordinates of the point in the target map, otherwise it should be left empty.

coords.json example#

An example of a coords.json file (see also example 04 - The advanced file upload):

[
  {
    "filename": "overview_sub.png",
    "links": [
      {
        "polygon": [
          {
            "x": 967.0,
            "y": 700.0
          },
          {
            "x": 2067.0,
            "y": 700.0
          },
          {
            "x": 2067.0,
            "y": 1207.0
          },
          {
            "x": 967.0,
            "y": 1207.0
          }
        ],
        "query": "reaction:re3,reaction:re4"
      }
    ]
  },
  {
    "filename": "overview_main.png",
    "links": [
      {
        "polygon": [
          {
            "x": 167.0,
            "y": 607.0
          },
          {
            "x": 1267.0,
            "y": 607.0
          },
          {
            "x": 1267.0,
            "y": 1117.0
          },
          {
            "x": 167.0,
            "y": 1117.0
          }
        ],
        "imageLinkFilename": "overview_sub.png"
      },
      {
        "polygon": [
          {
            "x": 1653.0,
            "y": 453.0
          },
          {
            "x": 2277.0,
            "y": 191.0
          },
          {
            "x": 2901.0,
            "y": 453.0
          },
          {
            "x": 2901.0,
            "y": 1500.0
          },
          {
            "x": 2277.0,
            "y": 1177.0
          },
          {
            "x": 1653.0,
            "y": 1500.0
          }
        ],
        "zoomLevel": 4,
        "modelPoint": {
          "x": 270,
          "y": 24
        },
        "modelLinkFilename": "advanced_map_example.xml"
      }
    ]
  }
]

Glyphs#

Glyphs are custom images that can be added to diagrams visualised in the MINERVA Platform, see Projects > Element glyphs. The image of any element of the diagram (species, compartment, pathways) can be replaced with such custom images.

Glyphs provided via this directory become automatically available for selection via a dropdown menu, without the need of their upload. They can be automatically assigned to specific elements on upload using config.json file.

Find more details about glyphs in the example 6 - Map with glyphs.

Alias vs identifier in CellDesigner files#

CellDesigner has a single species identifier for all copies of a certain element (e.g. SNCA protein) in a file. If you open your CellDesigner file in any text editor you can find it in species tag, parameter id:
<species metaid="s1" id="s1" name="SNCA" compartment="default">

Different instances of the same element (here: ‘s1’) have different species aliases, so they can be distinguished in the model, e.g. two copies of SNCA protein in different reactions You can find species alias of element if you open your CellDesigner file in any text editor, then find tag speciesAlias for particular species id (here: ‘s1’):
<celldesigner:speciesAlias id="sa1" species="s1">
<celldesigner:speciesAlias id="sa2" species="s1">

Aliases are the basis of assigning submap links and glyphs in MINERVA, see config file structure. If you have trouble locating species aliases in CellDesigner files, assign glyphs and submap links manually and use Download current project files from the Project info tab - the downloaded .zip file will contain necessary mappings in the config.json file.