- Abstract:
-
CBS is a Calculus of Biochemical Systems intended to allow the modelling of metabolic, signalling and regulatory networks in a natural and modular manner. In this paper we extend CBS with features directed towards practical, large-scale applications, thus yielding LBS: a Language for Biochemical Systems. The two main extensions are expressions for modifying large complexes in a step-wise manner and parameterised modules with a notion of subtyping; it also has nested declarations of species and compartments. The extensions are demonstrated with examples from the yeast pheromone pathway. A formal specification of LBS is then given through an abstract syntax, static semantics and a translation to a variant of coloured Petri nets. Translation to other formalisms such as ordinary differential equations and continuous time Markov chains is also possible.
- Links To Paper
- 1st Link
- Bibtex format
- @InProceedings{EDI-INF-RR-1270,
- author = {
Michael Pedersen
and Gordon Plotkin
},
- title = {A Language for Biochemical Systems},
- book title = {Computational Methods in Systems Biology},
- publisher = {Springer},
- year = 2008,
- month = {Oct},
- volume = {5307/2008},
- pages = {63-82},
- doi = {10.1007/978-3-540-88562-7_9},
- url = {http://homepages.inf.ed.ac.uk/s0677975/papers/lbs.pdf},
- }
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