MATLAB script for extracting the topology of the connectivity between molecular components in humanGEM. As a result the folowing files are produced:
| File name | Description |
|---|---|
| ihuman_rxns.txt | File listing all reaction IDs, reaction names, formulas and encoding genes (grRules) |
| ihuman_mets.txt | File listing all metabolites IDs, metabolite names, and chemical formulas |
| ihuman_subSystems.txt | File listing all metabolic subsystems (pathways) represented in humanGEM |
| ihuman_rxnGeneMatrix.txt | Incidence matrix connecting reactions in the model to the genes that encode for their enzmes |
| ihuman_genesMetMatrix.txt | Incidence matrix connecting genes in the model to the metabolites present in their corresponding reactions |
| ihuman_geneSubSystemsMatrix.txt | Incidence matrix connecting genes in the model to metabolic subsystems (presence or their corresponding reactions in a given pathway) |
| ihuman_metSubSstemsMatrix.txt | Incidence matrix connecting metabolites to metabolic subsystems in the model |
An additional text file storing the model version and the date of last results update is also saved for version control.
- MATLAB 2020 (or later)
- The RAVEN toolbox (see installation instructions here)
Clone master branch from Polster-Lab GitHub.
To update results in this repository, set the subfolder 'humanGEM_topology/code' in this repo as a working directory in MATLAB, then type ´extractModelTopology´ in the MATLAB command window. Results are stored as .txt files in the subfolder 'humanGEM_topology/results'.
Polster Lab, Division of Systems and Synthetic Biology, Chalmers University of Technology.
Last update: 29th of May 2024.