'rebop' is a fast stochastic simulator for well-mixed chemical reaction networks. Click here to visit rebop
Example Topo file structure for a 4-node GRN.
Here, under 'Type', '1' represents Activation, '2' represents Inhibition. In our formalism for interpreting a GRN as a rebop reaction to be simulated, the following assumptions have been made:
1) Activation - Target node is generated at rate: r = k * {Source}, where k is a adjustable rate parameter.
2) Inhibition - Target node is consumed at rate: r = k * {Source} * {Target}, the inclusion of Target node concentration is to avoid negative populations.
The formalism is still under review, and will be updated.