Genetic Algorithm and Simulation Pack

stochastic simulation -- user needs to specify propensity and stoichiometry matrixdeterministic simulation -- user needs to specify function with differential equations

multi-cell stochastic simulation -- uses logistic equations to model cell growth, with a network inside each cell. user needs to specify propensity and stoichiometry matrix

genetic algorithm -- users needs to specify fitness, mutation, crossover functions

mass action genetic algorithm -- evolves a mass-action network; user provides fitness function

enzyme network genetic algorithm -- evolves a modified mass-action network; user provides fitness function

protein network genetic algorithm -- evolves a protein-network (enzyme kinetics); user provides fitness function

gene regulatory network genetic algorithm -- evolves a genetic network; user provides fitness function

reaction network genetic algorithm -- evolves any of the above network types; user provides fitness function

find bistability -- finds parameters to make a system bistable; user provided differential equation function

negative and positive loops -- find negative and positive loops in a square adjacency matrix such as a Jacobian