Source code for simulations of collective chemotaxis using the cellular Potts Model (CPM) as the computational implementation. In these simulations biological cells sense a chemical gradient in the environment using intercellular communication and attempt to migrate in the direction of increasing chemical concentration based on their measurements.
The resulting migratory behavior of cell clusters of various sizes has been studied and the results are described in this paper [preprint]. You can view a video of the simulations on YouTube.
To compile the code you need a FORTRAN compiler like gfrotran. The following command will compile the code and output the executable a.out used to run simulations.
$ gfortran -c mod1* mod2* mod3*;rm *.o;gfortran cpm_main.f90 mod*
The file cpm_main.f90 is the main program file which simulates the time evolution of the cell cluster and outputs simulation results. The various module files (all module filnames start with the string mod) contain functions and subroutines which are called by the main program file.
Functions and subroutines within the module files are annotated in order to explain their use. Module files are organized in the following manner.
mod1util.f90: Initialization functions and commonly used functions.mod2sense.f90: All functions relevant to creating the chemical concentration profile and measuring the chemical gradient.mod3goal.f90: All functions pertaining to the evaluation of the energy term for the CPM.mod3polar.f90: All functions relevant to cell polarization and evaluation of the bias for the CPM.mod3sc.f90: Functions pertaining to the CPM implementation.mod3wrt.f90: Functions that print out simulation information to various output files.
Required input filenames: input.txt, polarInput.txt
In order for the executable to run, it requires two additional text files in order to initialize certain parameter values. Lines 40-60 in cpm_main.f90 further explain the purpose of each parameter value.
Below are two examples.
Sample file:
7 7
2 2
40 60
40
151
1
50.0
The different rows in input.txt correspond to the following parameter values:
r0(1), r0(2)
rCell(1), rCell(2)
x1, x2
rSim(2)
tmax
runTotal
df
Sample file:
1.00
0.20
The different rows in polarInput.txt correspond to the following parameter values:
plrP
plrR
Files that are modules need to be compiled first by themselves before being used in compilation of the main program file. All module files start with the string mod in their filenames.
Module files can be individually compiled using the following command:
$ gfortran -c my_module.f90
Once all modules are compiled, proceed to compile the main program using the following command.
$ gfortran -o a.out main.f90 my_module_1.f90 my_module_2.f90
For debugging, the following flags are helpful.