We found a match
Your institution may have access to this item. Find your institution then sign in to continue.
- Title
An Intuitive Modelling Interface for Systems Biology.
- Authors
Kahramanoğullar, Ozan; Cardelli, Luca
- Abstract
We introduce a natural language interface for building stochastic π calculus models of biological systems. In this language, complex constructs describing biochemical events are built from basic primitives of association, dissociation and transformation. This language thus allows us to model biochemical systems modularly by describing their dynamics in a narrative-style language, while making amendments, refinements and extensions on the models easy. We give a formal semantics for this language and a translation algorithm into stochastic π calculus that delivers this semantics. We demonstrate the language on a model of Fcγ receptor phosphorylation during phagocytosis. We provide a tool implementation of the translation into a stochastic π calculus language, Microsoft Research's SPiM, which can be used for simulation and analysis.
- Subjects
SYSTEMS biology; COMPUTATIONAL biology; BIOINFORMATICS; BIOLOGICAL networks; COMPUTER simulation of human mechanics
- Publication
International Journal of Software & Informatics, 2013, Vol 7, Issue 4, p655
- ISSN
1673-7288
- Publication type
Article