Fortran code for manuscript of J Theor Biol, Patsatzis 2021, under review
The present Fortran code is used for running the simulations of the above manuscript, so that the user acquires all the CSP data for the desired simulation. The model introduced in de Pillis et al. J Theor Biol 238(4) 2006
The code includes the following external packages, which run independantly without prior installation:
- ODEPACK by LLNL for numerical integration of ODEs
- EISPACK by Netlib for solving the eigenproblem
The code runs through sh script.sh.
Before running:
- Edit Makefile to match the OS installed libraries.
- Edit defs.h to select the operations you want to perform (numerical/analytic Jacobian, use/no use of the CSP tools)
- Provide the parameter set, the initial conditions and the ending time for your simulation in paramet.i.
After running the code outputs the following:
- Solution of cell populations at Asol.dat, rhs at Arhs.dat, process rates at Arates.dat
- Timescales at ATmscl.dat, CSP amplitudes at AFi_PosNeg.dat and their absolute values at AFi_Pos.dat
- The CSP data: (i) number of exhausted CSP modes at ANofExhMod.dat, (ii) API for all modes at AAPI.dat, (iii) TPI for all modes ATPI.dat, (iv) Po for all modes APointers.dat, (v) II for all cell populations AII.dat
- The folder ADiag, which contains all the above indices API, TPI, Po and II from (ii)-(v) sorted in descedning order and devided per mode. In additions, each Mod1.dat - Mod4.dat files contain all the CSP data sorted in descedning order per mode, but printed at selected timepoints, as defined in SUB_main.f.
- The absolute error of the constraint solution with respect to the solution at ASIMAbsErr.dat
At the end of the run you can see the ending tumor cell population of the simulation at the terminal.
Please use with care and contact me for further assistance at [email protected]