Literature DB >> 18463130

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

Lorenzo Dematté1, Corrado Priami, Alessandro Romanel.   

Abstract

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.

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Year:  2008        PMID： 18463130     DOI： 10.1093/bib/bbn023

Source DB:  PubMed          Journal:  Brief Bioinform        ISSN： 1467-5463            Impact factor:   11.622


  12 in total

1.  Calibration of dynamic models of biological systems with KInfer.

Authors:  Paola Lecca; Alida Palmisano; Adaoha Ihekwaba; Corrado Priami
Journal:  Eur Biophys J       Date:  2009-08-11       Impact factor: 1.733

Review 2.  Modeling for (physical) biologists: an introduction to the rule-based approach.

Authors:  Lily A Chylek; Leonard A Harris; James R Faeder; William S Hlavacek
Journal:  Phys Biol       Date:  2015-07-16       Impact factor: 2.583

3.  Computational modeling of the EGFR network elucidates control mechanisms regulating signal dynamics.

Authors:  Dennis Y Q Wang; Luca Cardelli; Andrew Phillips; Nir Piterman; Jasmin Fisher
Journal:  BMC Syst Biol       Date:  2009-12-22

Review 4.  Modeling cellular compartmentation in one-carbon metabolism.

Authors:  Marco Scotti; Lorenzo Stella; Emily J Shearer; Patrick J Stover
Journal:  Wiley Interdiscip Rev Syst Biol Med       Date:  2013-02-13

5.  A unique transformation from ordinary differential equations to reaction networks.

Authors:  Sylvain Soliman; Monika Heiner
Journal:  PLoS One       Date:  2010-12-22       Impact factor: 3.240

6.  Transcriptional regulation is a major controller of cell cycle transition dynamics.

Authors:  Alessandro Romanel; Lars Juhl Jensen; Luca Cardelli; Attila Csikász-Nagy
Journal:  PLoS One       Date:  2012-01-06       Impact factor: 3.240

7.  Elucidation of functional consequences of signalling pathway interactions.

Authors:  Adaoha E C Ihekwaba; Phuong T Nguyen; Corrado Priami
Journal:  BMC Bioinformatics       Date:  2009-11-06       Impact factor: 3.169

8.  Snazer: the simulations and networks analyzer.

Authors:  Tommaso Mazza; Gennaro Iaccarino; Corrado Priami
Journal:  BMC Syst Biol       Date:  2010-01-07

Review 9.  State of the art in silico tools for the study of signaling pathways in cancer.

Authors:  Vanessa Medina Villaamil; Guadalupe Aparicio Gallego; Isabel Santamarina Cainzos; Manuel Valladares-Ayerbes; Luis M Antón Aparicio
Journal:  Int J Mol Sci       Date:  2012-05-29       Impact factor: 6.208

10.  Narrative-based computational modelling of the Gp130/JAK/STAT signalling pathway.

Authors:  Maria Luisa Guerriero; Anna Dudka; Nicholas Underhill-Day; John K Heath; Corrado Priami
Journal:  BMC Syst Biol       Date:  2009-04-15
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