Examples

Several examples are included in the 'examples directory.

• prob_purebirth.c: Constant linear propensity pure birth system (1 species, 1 reaction, 1 parameter)
• prob_birthdeath.c: Birth-death system (1 species, 2 reactions, 2 parameters)
• prob_isomerization.c: Reversible isomerization system (2 species, 2 reactions, 2 parameters)
• prob_schlogl.c: Schloegl model exhibiting bistability (1 species, 4 reactions, 4 parameters)
• prob_toggle.c: Toggle switch example with nonlinear propensities that exhibits switching behavior (2 species, 4 reactions, 4 parameters)
• prob_oscillator.c: Genetic oscillator consisting of genes, mRNA, and protein species that exhibits steady oscillations at the nominal parameters (9 species, 16 reactions, 16 parameters)

Each can be made from the SPSens folder using make PROB_NAME=\<probname> ..., where \<probname> is the suffix after prob_ and before .c and the ellipses are whatever other make options/targets are desired.
For example, to make sensitivity and simulation executables for the birth-death model, one would type:
make PROB_NAME=birthdeath sim sens

Further information can be found in the source files for each example and the references therein.