/SilicoStat

SilicoStat is a reaction simulator generates biochemical circuits with desired functions.

Primary LanguageC++

SilicoStat

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

Running the simulator

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