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Briefings in Bioinformatics Advance Access published online on May 7, 2008
Briefings in Bioinformatics, doi:10.1093/bib/bbn023
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© The Author 2008. Published by Oxford University Press. For Permissions, please email: journals.permissions@oxfordjournals.org

The Beta Workbench: a computational tool to study the dynamics of biological systems

Lorenzo Dematté, Corrado Priami and Alessandro Romanel

Corresponding author. Alessandro Romanel, Dipartimento di Ingegneria e Scienza dell’Informazione, The Microsoft Research, University of Trento, Centre for Computational and Systems Biology, Università di Trento, Povo, TN, Italy. Tel: +390-461-882-804; Fax: +390-461-882-814; E-mail: romanel{at}cosbi.eu

We introduce the Beta Workbench (BWB), a scalable tool built on top of the newly defined BlenX language to model, simulate and analyse biological systems. We show the features and the incremental modelling process supported by the BWB on a running example based on the mitogen-activated kinase pathway. Finally, we provide a comparison with related approaches and some hints for future extensions.

Keywords: systems biology, modelling and simulation, computational biology

Submitted: November 30, 2007. Received (in revised form): April 4, 2008.


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