Rule-based modeling
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Rule-based modeling is a
BioNetGen[1] is a suite of software tools used to generate mathematical models consisting of ordinary differential equations without generating the equations directly. For example below is an example rule in the BioNetGen format:
Where:
- A(a,a): Represents a model species A with two free binding sites a
- B(b): Represents a model species B with one free binding site
- A(a!1).B(b!1): Represents model species where at least one binding site of A is bound to the binding site of B
With the above line of code, BioNetGen will automatically create an ODE for each model species with the correct mass balance. Additionally, an additional species will be created because the rule above implies that two B molecules can bind to a single A molecule since there are two binding sites. Therefore, the following species will be generated:
4. A(a!1,a!2).B(b!1).B(b!2): Molecule A with both binding sites occupied by two different B molecules.
For biochemical systems
Early efforts to use rule-based modeling in simulation of biochemical systems include the stochastic simulation systems StochSim[2]
A widely used tool for rule-based modeling of biochemical networks is BioNetGen
A close alternative is the Kappa language.[4] Another alternative is BioChemical Space language.[5]
References
- PMID 19399430, retrieved 2020-12-14
- ^ Morton-Firth CJ, Bray D (1998) Predicting temporal fluctuations in an intracellular signalling pathway. J Theor Biol. 1998 192(1):117-28.
- ^ BioNetGen
- ^ Kappa
- ^ Děd et al. (2016) Formal Biochemical Space with Semantics in Kappa and BNGL ENTCS 326:27-49.