SABRE: A tool for the stochastic analysis of biochemical reaction networks Conference Paper


Author(s): Didier, Frédéric; Henzinger, Thomas A; Mateescu, Maria; Wolf, Verena
Title: SABRE: A tool for the stochastic analysis of biochemical reaction networks
Affiliation IST Austria
Abstract: The importance of stochasticity within biological systems has been shown repeatedly during the last years and has raised the need for efficient stochastic tools. We present SABRE, a tool for stochastic analysis of biochemical reaction networks. SABRE implements fast adaptive uniformization (FAU), a direct numerical approximation algorithm for computing transient solutions of biochemical reaction networks. Biochemical reactions networks represent biological systems studied at a molecular level and these reactions can be modeled as transitions of a Markov chain. SABRE accepts as input the formalism of guarded commands, which it interprets either as continuous-time or as discrete-time Markov chains. Besides operating in a stochastic mode, SABRE may also perform a deterministic analysis by directly computing a mean-field approximation of the system under study. We illustrate the different functionalities of SABRE by means of biological case studies.
Conference Title: QEST: Quantitative Evaluation of Systems
Conference Dates: September 15-18, 2010
Conference Location: Williamsburg, VA, USA
Publisher: IEEE  
Date Published: 2010-10-14
Start Page: 193
End Page: 194
Sponsor: This research has been partially funded by the Swiss National Science Foundation under grant 205321-111840 and by the Cluster of Excellence on Multimodal Computing and Interaction at Saarland University.
URL:
DOI: 10.1109/QEST.2010.33
Open access: yes (repository)
IST Austria Authors
  1. Thomas A. Henzinger
    415 Henzinger
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