Modelling and simulation of biological processes in BlenX-Reference-Cited by-同舟云学术

Modelling and simulation of biological processes in BlenX

Published:2008-03 Issue:4 Volume:35 Page:32-39
ISSN:0163-5999
Container-title:ACM SIGMETRICS Performance Evaluation Review
language:en
Short-container-title:SIGMETRICS Perform. Eval. Rev.

Author:

Dematté Lorenzo¹,Priami Corrado¹,Romanel Alessandro¹

Affiliation:

1. Universitá di Trento

Abstract

We introduce a scalable framework built upon the BlenX language and inspired by the Beta-binders process calculus to model, simulate and analyse biological systems. We show the features of the Beta Workbench framework on a running example based on the mitogen-activated kinase pathway. We also discuss an incremental modelling process that allows us to scale up from pathway to network modelling and analysis. We finally provide a comparison with related approaches and some hints for future extensions of the framework.

Publisher

Association for Computing Machinery (ACM)

Subject

Computer Networks and Communications,Hardware and Architecture,Software

Link

https://dl.acm.org/doi/pdf/10.1145/1364644.1364653

Reference28 articles.

1. CONTINUOUS AND HYBRID PETRI NETS

2. Model-checking continuous-time Markov chains

3. Ciesinski F. and Groessner F. 2004. On probabilistic computation tree logic. In Validation of Stochastic Systems. Vol. 2925. Springer Berlin / Heidelberg 147--188. Ciesinski F. and Groessner F. 2004. On probabilistic computation tree logic. In Validation of Stochastic Systems . Vol. 2925. Springer Berlin / Heidelberg 147--188.

4. Dematté L. Priami C. and Romanel A. 2007. BetaWB: modelling and simulating biological processes. In 2007 Summer Simulation Multiconference. 777--784. Dematté L. Priami C. and Romanel A. 2007. BetaWB: modelling and simulating biological processes. In 2007 Summer Simulation Multiconference . 777--784.

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