ComputationalColonicCrypts is a modification and extension of the existing Chaste implementation on colonic crypt modeling for modeling Lynch syndrome carcinogenesis.
ComputationalColonicCrypts aims to be an implementation of the computational model presented in Haupt et al (2020), in preparation for the evolution of colonic crypts in Lynch syndrome carcinogenesis. The implementation is based on the Chaste software, release 2019_1. It can be included in the existing Chaste implementation by replacing some of the existing files and by adding some additional files, all available here in this repository.
For the Chaste documentation, please read https://chaste.cs.ox.ac.uk/trac/wiki/ChasteGuides.
For running the numerical simulations with Chaste, the following existing files of Chaste have to be replaced:
- crypt/src/cell/cycle/SimpleWntCellCycleModel.cpp
- cell_based/src/cell/cycle/AbstractPhaseBasedCellCycleModel.cpp
- cell_based/src/population/forces/GeneralisedLinearSpringForce.cpp
- cell_based/src/simulation/numerical_methods/ForwardEulerNumericalMethod.cpp
- cell_based/src/population/AbstractCellPopulation.cpp
- cell_based/src/population/AbstractCentreBasedCellPopulation.cpp
The following .cpp and .hpp files (if not stated otherwise) have to be added to the existing Chaste code:
- all mutations except wild-type in cell_based/src/cell/properties/mutations
- cell_based/src/population/killers/CryptFissionCellKiller
- cell_based/src/population/killers/HomeostaticCellKiller
- crypt/test/cell/TestColonicCryptSimulation.hpp
The main file is crypt/test/cell/TestColonicCryptSimulation.hpp
To compile the code, go to the build folder and
make TestColonicCryptSimulation
Run the code on one processor with
ctest -V -R TestColonicCryptSimulation
or on multiple processor to simulate multiple crypts in parallel with
mpirun -n 4 ./run
This will run the code on 4 processors.
The following parameter settings can be altered in crypt/test/cell/TestColonicCryptSimulation.hpp:
- the length of the simulation, measured in multiples of the stem cell cycle
- the number of crypts to be simulated sequentially
- the MLH1/MSH2 mutation status
- initial conditions, such as number of cells and possible stem cell mutations
- stem cell mutation rates, exchange rate, death rate
- the number of stem cells
- the crypt fission rate
In crypt/src/cell/cycle/SimpleWntCellCycleModel.cpp, we can change
- the MLH1/MSH2 mutation status (this has to be in concordance with the main file)
- effect of mutations on cell differentiation
- mutation rate for TA cells
For hardware requirements, we refer to https://chaste.cs.ox.ac.uk/trac/wiki/GettingStarted#SupportedOperatingSystems.
For running the simulations, you need to install Chaste, release 2019_1 available on https://www.cs.ox.ac.uk/chaste/download.html.
For OS requirements, we refer to https://chaste.cs.ox.ac.uk/chaste/tutorials/release_2019.1/.
The Installation Guide for Chaste is available online https://chaste.cs.ox.ac.uk/chaste/tutorials/release_2019.1/InstallGuides/InstallGuide.html.
Further, the modified and the additional files have to be included in the Chaste folders as listed above.
Chaste source is released under 3-clause BSD license.
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