MS-BioNET

MS-BioNET (MultiScale-Biochemical Network) is a computational framework for modelling and simulating large networks of compartments hosting a chemical solution and communicating through an enhanced model of chemical reaction addressing molecule transfer.

The framework provides:

• a logic-oriented specification language that is used to flexibly specify simulation scenarios providing constructs to directly express biochemical reactions, compartments, compartment link topology, and reactions involving selective transfer through membranes
• a simulation engine to perform stochastic simulation using the Gillespie's SSA
• a module for parameter optimisation