Metabolic viewer - SBML/JSON

TO DO:

• input function: To convert a SBML file to JSON to be visualized.

• updating sbml2json to parse all kind of SBML files (managing errors and stuff).

• Add different options for the user: Updating the physarum file or visualizing their own file.

• improving the layout.

JSON file structure:

Example of the different part needed to construct the network and the information needed.

[
  {
    "group": "nodes", 
    "data": {
      "id": "M_13dpg_c", 
      "name": "M_13dpg_c"
    }
  }, 
  {
    "group": "nodes", 
    "classes": "rxn", 
    "data": {
      "id": "R_ACKr", 
      "name": "R_acetate_kinase"
    }
  }, 
  {
    "group": "edges", 
    "classes": "reactant", 
    "data": {
      "source": "M_atp_c", 
      "id": "M_atp_c_R_ACKr", 
      "target": "R_ACKr"
    }
  }, 
   {
    "group": "edges", 
    "classes": "product", 
    "data": {
      "source": "R_ACKr", 
      "id": "M_adp_c_R_ACKr", 
      "target": "M_adp_c"
    }
  }
]

SBML2JSON:

Can convert a SBML level 2 version 4 to our json structure.

Does not take into account the and tags.

Need to be tested on other SBML files from Biomodels and others to manage the errors and the different levels.

(Does not use libSBML)

Credits:

Inspired by https://github.com/funasoul/visualizeSBML

Using Cytoscapejs