An Automatic Translation of SBML into Beta-Binders

Authors:
Federica Ciocchetta;Corrado Priami;Paola Quaglia
Affiliations:
-;-;-
Venue:
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Year:
2008

Citing 10
Cited 0

Communicating and mobile systems: the &pgr;-calculus

Communicating and mobile systems: the &pgr;-calculus
Application of a stochastic name-passing calculus to representation and simulation of molecular processes

Information Processing Letters
BioAmbients: an abstraction for biological compartments

Theoretical Computer Science - Special issue: Computational systems biology
Multiscale stochastic simulation algorithm with stochastic partial equilibrium assumption for chemically reacting systems

Journal of Computational Physics
Web-based kinetic modelling using JWS Online

Bioinformatics
Design and implementation of a tool for translating SBML into the biochemical stochastic π-calculus

Bioinformatics
Core formal molecular biology

ESOP'03 Proceedings of the 12th European conference on Programming
An implementation for mapping SBML to BioSPI

FSKD'05 Proceedings of the Second international conference on Fuzzy Systems and Knowledge Discovery - Volume Part II
Modeling kohn interaction maps with beta-binders: an example

Transactions on Computational Systems Biology III
Beta binders for biological interactions

CMSB'04 Proceedings of the 20 international conference on Computational Methods in Systems Biology

Quantified Score

Hi-index	0.00

Visualization

Abstract

A translation of SBML (Systems Biology Markup Language) into a process algebra is proposed in order to allow the formal specification, the simulation and the formal analysis of biological models. Beta-binders, a language with a quantitative stochastic extension, is chosen for the translation. The proposed translation focuses on the main components of SBML models, as species and reactions. Furthermore, it satisfies the compositional property, i.e. the translation of the whole model is obtained by composing the translation of the subcomponents. An automatic translator tool of SBML models into Beta-binders has been implemented as well. Finally, the translation of a simple model is reported.