IMFLer

This is a web-based tool called an Interactive Metabolic FLux visualiser and analysER or IMFLer.

It builds upon several technologies:

• Escher — a web-based tool for metabolic maps
  • https://github.com/zakandrewking/escher
• Adapted Pyodide 0.16.1 — Python 3.8 with many scientific packages, compiled to WebAssembly, see
  • the adapted version https://github.com/lv-csbg/pyodide
  • the original project https://github.com/iodide-project/pyodide
• cobrapy — a Python package for constraint-based modeling
  • https://github.com/opencobra/cobrapy

IMFLer allows both Flux Balance Analysis (FBA) and Flux Variability Analysis (FVA) of metabolic networks.

Usage

1. Go to https://lv-csbg.github.io/IMFLer/
2. Load an Escher map of interest from a JSON file.
   • Ctrl+O or from menu on the top Map -> Load map JSON
3. Load COBRA model corresponding to the map of interest.
   • Ctrl+M or from menu on the top Model -> Load COBRA model JSON
4. Change parameters of the model, like:
   • Flux minimum and maximum for the reactions
   • Simulate knockout of genes responsible for the reactions
5. Run FBA or FVA.
6. Analyse the visualised results.

Visualisation settings

IMFLer's basic default visualisation settings are encoded in a JSON file. It is stored as src/static/data/settings.json. You can change it in your local IMFLer version.

You can also pass it as a GET parameter settings in your URL.

Here is an example how to load a different map and a diffent model using JavaScript on Imfler's page:

var newSettings = 
{
  "model": "https://escher.github.io/1-0-0/6/models/Escherichia%20coli/iJO1366.json",
  "map": "https://escher.github.io/1-0-0/6/maps/Escherichia%20coli/iJO1366.Central%20metabolism.json"
}
var newURI = encodeURI(`${window.location.origin}${window.location.pathname}?settings=${JSON.stringify(newSettings)}`);
window.location.href = newURI;

The resulting URL in the example would be:

https://lv-csbg.github.io/IMFLer/?settings=%7B%22model%22:%22https://escher.github.io/1-0-0/6/models/Escherichia%2520coli/iJO1366.json%22,%22map%22:%22https://escher.github.io/1-0-0/6/maps/Escherichia%2520coli/iJO1366.Central%2520metabolism.json%22%7D

If you don't provide essential model and map parameters, default ones are going to be used.

You can also provide calculated FBA or FVA results, like in this settings example:

var settingsWithFBAResults = 
{
  "model": "static/data/models/e_coli_core.json",
  "fba_results": "static/data/examples/reaction_data/fba_results.json"
}

Please see the src/static/data/examples/reaction_data directory for examples of expected JSON.