SABRE: A tool for stochastic analysis of biochemical reaction networks. 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.
Keywords for this software
References in zbMATH (referenced in 6 articles )
Showing results 1 to 6 of 6.
- Barbot, Beno^ıt; Kwiatkowska, Marta: On quantitative modelling and verification of DNA walker circuits using stochastic Petri nets (2015)
- Dannenberg, Frits; Hahn, Ernst Moritz; Kwiatkowska, Marta: Computing cumulative rewards using fast adaptive uniformization (2015)
- Brim, Luboš; Češka, Milan; Šafránek, David: Model checking of biological systems (2013)
- Heiner, Monika; Rohr, Christian; Schwarick, Martin: MARCIE -- model checking and reachability analysis done efficiently (2013)
- Didier, Frédéric; Henzinger, Thomas A.; Mateescu, Maria; Wolf, Verena: Approximation of event probabilities in noisy cellular processes (2011)
- Didier, Frédéric; Henzinger, Thomas A.; Mateescu, Maria; Wolf, Verena: SABRE: A tool for stochastic analysis of biochemical reaction networks (2010) ioport