Signal2RGraph is a biological tool, that helps to calculate all EFM (elementary flux modes) in a given metabolic pathway.

For detailed explanation please refer to the article

In short:

1. Each activation reaction produces 3 reactions
2. Each inhibition reaction produces 2 reactions
3. Reactions are then placed into stoichiometric matrix
4. Based on the matrix calculate EFMs

pip install -r requirements.txt
git clone git@github.com:stashkov/Signal2RGraph.git
cd Signal2RGraph
python main.py edge_list.csv

Suppose GRK2 is activated by cAMP and GEF1 is inhibited by GRK2.

This means we have cAMP -> GRK2 -| GEF1. We can represent these edges as follows:

cAMP, GRK2, ACTIVATION
GRK2, GEF1, INHIBITION

Note: The use of "" is only necessary when you have a comma inside the name of a node (e.g. "Complex II, III, IV").

Example file can be found in examples folder

Results can be found in result folder. It contains:

• EFM in human readable format (node names from input file)
• EFM with numbers instead of node names
• Original imported graph from edge list and node names as GraphML
• Expanded graph as GraphML