Welcome to Dinghy

DINGHY: Dynamic Interactive Navigator for General Hypergraphs in Biology

Two input formats are possible:

Biological data

Two data loading modes are available: either by loading a file or writing directly into the appropriate box in the UPLOAD section and the python script can be download here ExtractJSON script

2 files are required in addition to the extractJSON script, and 2 more are optional:

  • System SBML (.xml)
  • List of reactions of interest (.txt)
  • List of highlighted nodes (.bn)
  • List of cofactors (.txt)
  • The preprocessing script can be run with the following command. It will output a .json file which can be uploaded in the section below.
    extractJSON.py [System SBML.xml] [list of reaction.txt] --bn [list of measured nodes.bn] --cofactors [list of cofactors.txt]

    Generic hypergraph

    a + b -> c
    b + c -> d + e