Matlab code for the in-silico simulation of the effects of mutations and targeted therapies in a chemical reaction network modeling the G1-S transition phase of a colorectal cancer cell.
We also provide the implementation of the NLPC (non-linearly projected combined) method, a fast and globally convergent combined Newton and gradient descent method for computing equilibrium points of chemical reaction networks.
The code allows to reproduce the results shown in
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Sommariva, S., Caviglia, G., Ravera, S., Frassoni, F., Benvenuto, F., Tortolina, L., Castagnino, N., Parodi, S., Piana, M. (2021) Computational quantification of global effects induced by mutations and drugs in signaling networks of colorectal cancer cells. Scientific reports 11(1), 1-13
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Berra, S., La Torraca, A., Benvenuto, F., Sommariva, S., A fast and convergent combined Newton and gradient descent method for computing steady states of chemical reaction networks, submitted.
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Sommariva, S., Berra, S., Biddau, G., Caviglia, G., Benvenuto, F., Piana, M., In-silico modelling of the mitogen-activated protein kinase (MAPK) pathway in colorectal cancer: mutations and targeted therapy, submitted.
Code is written in Matlab R2015b. Results of the simulations are provided in the folder './results'.
Run script_fig_*.m to reproduce the figures of the paper. Run main_script_*.m to reproduce the results of the paper.
Code is written in Matlab R2017b. Results of the simulations are provided in the folder './test_NLPC/results_paper'.
The implementation of the NLPC methods can be found in './funcs/f_NLPC_restart.m'
To reproduce the figures of the paper, run ./test_NLPC/script_figure_*.m . To reproduce the analysis of the paper, run:
- ./test_NLPC/main_extract_x0.m to sample the initial points for NLPC.
- ./test_NLPC/main_NLPC.m and ./test_NLPC/main_NLPC_orthogonal.m to run NLPC with the proposed non linear projector and the classical orthogonal projector, respectively
- ./test_NLPC/main_dyn.m to compute the steady states with a classical ODEs solver.
To reproduce the analysis in the Online resource, run ./test_NLPC/test_*.m
Code is written in Matlab R2017b. Results of the simulations are provided in the folder './test_MAPK/results_paper'.
To reproduce the figures of the paper, run ./test_MAPK/script_figure_*.m . To reproduce the analysis of the paper, run the m-files ./test_MAPK/main_*.m .The scope of each script is extensively described therein.
Our code makes use of the following external graphical tools:
- Robert (2021). symlog (https://github.com/raaperrotta/symlog), GitHub. Retrieved January 15, 2021.
- Povilas Karvelis (2022). daboxplot (https://github.com/frank-pk/DataViz), GitHub. Retrieved December 28, 2022.