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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
Contact: Sara Montagna