This is the repository for our lab's network model of cardiac fibroblast signal transduction. Includes reaction topology, ODE model, and accompanying analysis scripts.
- Reaction topology: located in
cytoscape/snm_1_1_rev4.cysas a Cytoscape Session File (requires Cytoscape 3.1.0 or later) along with XGMML and SIF files. - ODE Model: located in
data/snm_1_1_rev4.xlsx, and can be directly used in Netflux package for MATLAB. We have also included Python version of the ODE model with accompanying Python parameter and run files. - Analysis Scripts: located in
utils/folder- ModelValidation: qualitative validation against independent literature set
- MCInteractionAnalysis: analysis of mechano-chemo interactions based on biochemical dose-response behavior
- PerturbationAnalysis: analysis of node sensitivity/influence with knockdowns under multiple tension contexts
- DrugCaseStudies: comparison of model-predicted responses to drug treatments with experimental studies
- DrugScreen: comprehensive screening of drug treatments for mechano-adaptive behavior
Required software: MATLAB 2017a or later (Parallel Computing Toolbox required for select analyses)