SilicoStat is a reaction simulator that evolves biochemical circuits with specified functions.
Requires: SUNDIALS ODE Solver (libsundials-serial-dev package on Ubuntu), Boost libraries, GNU Scientific Library (GSL), Open-MPI
Run sundial-config to get required linker flags.
Compile using ./compile.sh ode13
mpirun -n 8 ~/SilicoStat/a.out reactants.dat reactions.dat \
fitnessparam:10 \
fitnessparam2:0 \
runtime:75 \
popsize:20 \
generations:10 \
seed:12345678 \
randomize:1 \
fitnessavgover:1 \
extrinsicnoise:0 \
sigma:0.0 \
lognoisemax:1.2 \
mureacrate:0.3 \
maxrate:0.0017001 \
MaxRndRate:0.001 \
MinRndRate:0.00001 > testevolve.txt