Wiki source code of Overview
author | version | line-number | content |
---|---|---|---|
6.1 | 1 | = Overview = | |
1.1 | 2 | ||
4.1 | 3 | {{msbionet/}} is a simulation 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. | |
1.1 | 4 | ||
5 | On top of the framework, a logic-oriented specification language is used to flexibly specify simulation scenarios: on the one side it tightly focusses on biochemistry, by providing constructs to directly express biochemical reactions, compartments, compartment link topology, and reactions involving selective transfer through membranes; on the other side it relies on logic-based goal resolution and unification, achieving the expressiveness needed to easily handle size and complexity of the biochemical network. | ||
6 | |||
7.1 | 7 | Behind the hood, such a specification is turned into an intermediate language (a sort of bytecode) that feeds a simulation engine implemented by adapting the optimised version of Gillespie's algorithm ([[Gibson and Bruck's paper>>Publication.StochasticsimulationJphyschema104]]) to the computational model of biochemical cell networks. | |
5.1 | 8 | ||
9 | {{include reference="Environment" excludeFirstHeading="true"/}} |