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Readme.txt
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Readme:
This fold includes the codes (MATLAB and C++) used for the general mathematical framework model of heterogeneous stem cell regeneration. For details of the model, refer to bioRxiv 592139 (https://doi.org/10.1101/592139).
1. The matlab code (MATLAB2014b) include three part:
MATLAB-----1_StemCellgeneration
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|---2_Tissuegrowth
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|---3_Cancerdevelopment
1_StemCellgeneration include the codes to simulate the general process of stem cell regeneration
2_Tissuegrowth includes the codes to simulate tissue growth with time dependent differentiation rate, and the terminally differentiated cells.
3_Cancerdevelopment includes the codes to simulation cancer development with mutations to the pathways of proliferation and differentiation.
The matlab code is mainly designed to solve the differential-integral model numerically. Here, only one dimensional epigenetic state x (0<x<1) is considered.
Each folder includes following m-files:
--main.m The main function
--control.m The file to control the simulation
--parameter.m The file to define the parameters
--Initialization.m The file to initialize the system
--beta0.m, beta.m The files to define the function beta(Q,x)
--eta.m The function eta(x)
--fnu.m The function nu(x)
--kappa.m The function kappa(t,x)
--fkappa0.m The function for the time dependent parameter kappa0(t)
--mu.m The function mu(x)
--p.m The inheritance function p(x,y)
--phi.m The function phi(x)
--tau.m The delay tau(x)
--xi.m The function xi(x)
Please edit the control, initialization, and parameter files in according to your own applications.
2. The C++ code to perform single-cell-based stochastic simulation. In this code, we do not solve the differential-integral equation directly, but apply a stochastic simulation to model the growth process of a multiple cell system. A multiple cell system is represented as a collation of epigenetic states, and the single-cell-based stochastic simulation tracks the behaviors of each cell according to their own epigenetic states.
C++ --------StemCell include all source codes.
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|----Run the script to run the program
The program has been test in MacOS (10.11.6)
Usage:
In the folder StemCell, use the command sh compile.sh to generate the execute file bct_StemCell.
In the folder Run, edit the input files md.in and par.dat to change the control parameter and the parameter values, and use the command ./bct_StemCell md.in to run the program.