--- _id: '3847' abstract: - lang: eng text: 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. author: - first_name: Frédéric full_name: Didier, Frédéric last_name: Didier - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Maria full_name: Mateescu, Maria last_name: Mateescu - first_name: Verena full_name: Wolf, Verena last_name: Wolf citation: ama: 'Didier F, Henzinger TA, Mateescu M, Wolf V. SABRE: A tool for the stochastic analysis of biochemical reaction networks. In: IEEE; 2010:193-194. doi:10.1109/QEST.2010.33' apa: 'Didier, F., Henzinger, T. A., Mateescu, M., & Wolf, V. (2010). SABRE: A tool for the stochastic analysis of biochemical reaction networks (pp. 193–194). Presented at the QEST: Quantitative Evaluation of Systems, Williamsburg, USA: IEEE. https://doi.org/10.1109/QEST.2010.33' chicago: 'Didier, Frédéric, Thomas A Henzinger, Maria Mateescu, and Verena Wolf. “SABRE: A Tool for the Stochastic Analysis of Biochemical Reaction Networks,” 193–94. IEEE, 2010. https://doi.org/10.1109/QEST.2010.33.' ieee: 'F. Didier, T. A. Henzinger, M. Mateescu, and V. Wolf, “SABRE: A tool for the stochastic analysis of biochemical reaction networks,” presented at the QEST: Quantitative Evaluation of Systems, Williamsburg, USA, 2010, pp. 193–194.' ista: 'Didier F, Henzinger TA, Mateescu M, Wolf V. 2010. SABRE: A tool for the stochastic analysis of biochemical reaction networks. QEST: Quantitative Evaluation of Systems, 193–194.' mla: 'Didier, Frédéric, et al. SABRE: A Tool for the Stochastic Analysis of Biochemical Reaction Networks. IEEE, 2010, pp. 193–94, doi:10.1109/QEST.2010.33.' short: F. Didier, T.A. Henzinger, M. Mateescu, V. Wolf, in:, IEEE, 2010, pp. 193–194. conference: end_date: 2010-09-18 location: Williamsburg, USA name: 'QEST: Quantitative Evaluation of Systems' start_date: 2010-09-15 date_created: 2018-12-11T12:05:29Z date_published: 2010-10-14T00:00:00Z date_updated: 2021-01-12T07:52:37Z day: '14' ddc: - '004' department: - _id: ToHe - _id: CaGu doi: 10.1109/QEST.2010.33 file: - access_level: open_access checksum: 38707b149d2174f01be406e794ffa849 content_type: application/pdf creator: system date_created: 2018-12-12T10:09:03Z date_updated: 2020-07-14T12:46:17Z file_id: '4726' file_name: IST-2012-63-v1+1_SABRE-A_tool_for_the_stochastic_analysis_of_biochemical_reaction_networks.pdf file_size: 433824 relation: main_file file_date_updated: 2020-07-14T12:46:17Z has_accepted_license: '1' language: - iso: eng month: '10' oa: 1 oa_version: Submitted Version page: 193 - 194 publication_status: published publisher: IEEE publist_id: '2339' pubrep_id: '63' quality_controlled: '1' scopus_import: 1 status: public title: 'SABRE: A tool for the stochastic analysis of biochemical reaction networks' type: conference user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 year: '2010' ...