Repository for methods of control of multistate networks.

Author: Luis Sordo Vieira, sordovieira@uchc.edu

This repository includes control methods that use the Polynomial Dynamical System representation of signaling/regulatory networks for finding controls. The BiorXiv preprint can be found here.

These are the scripts to find controls from two models:

1. A Modeling Approach to Explain Mutually Exclusive and Co-Occurring Genetic Alterations in Bladder Tumorigenesis. PMID:26238783

2. Activated oncogenic pathway modifies Iron network in breast epithelial cells: a dynamic modeling perspective. PMID 28166223.

The script

parsing.py

is a helper script to pull out generators that only contain "us" from Macaulay2 output.

Directory Structure

├── iron_cancer_network_PMID_28166223
├── E2Fnetwork_PMID_26238783_booleanized
├── E2Fnetwork_PMID_26238783
├── FVScontrol
├── LICENSE
├── README.md
├── .gitkeep
├── .gitignore
├── parsing.py

1. The iron_cancer_network_PMID_28166223 contains the control scripts for the iron network.
2. The E2Fnetwork_PMID_26238783_booleanized contains the control scripts for the E2F network in the boolean format originally presented in PMID 26238783.
3. The E2Fnetwork_PMID_26238783 contains the control scripts for the E2F network and the scripts for convert it into a polynomial dynamical system over GF(3).
4. The FVScontrol contains the scripts used to find the feedback vertex set of the E2F network. It uses the code from yanggangthu/FVS_cython to find the Feedback Vertex Set of the wiring diagram presented in PMID 26238783. See the script FVScontrol/FVSsrc/find_fvs.py