{"date_updated":"2021-01-12T07:52:37Z","status":"public","abstract":[{"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.","lang":"eng"}],"day":"14","quality_controlled":"1","pubrep_id":"63","has_accepted_license":"1","date_created":"2018-12-11T12:05:29Z","year":"2010","file":[{"date_updated":"2020-07-14T12:46:17Z","content_type":"application/pdf","date_created":"2018-12-12T10:09:03Z","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","access_level":"open_access","file_id":"4726","checksum":"38707b149d2174f01be406e794ffa849","creator":"system"}],"ddc":["004"],"date_published":"2010-10-14T00:00:00Z","language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:46:17Z","author":[{"first_name":"Frédéric","full_name":"Didier, Frédéric","last_name":"Didier"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","first_name":"Thomas A","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A"},{"last_name":"Mateescu","first_name":"Maria","full_name":"Mateescu, Maria"},{"first_name":"Verena","full_name":"Wolf, Verena","last_name":"Wolf"}],"publist_id":"2339","page":"193 - 194","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"ToHe"},{"_id":"CaGu"}],"oa":1,"scopus_import":1,"publisher":"IEEE","publication_status":"published","conference":{"name":"QEST: Quantitative Evaluation of Systems","end_date":"2010-09-18","location":"Williamsburg, USA","start_date":"2010-09-15"},"doi":"10.1109/QEST.2010.33","_id":"3847","title":"SABRE: A tool for the stochastic analysis of biochemical reaction networks","month":"10","oa_version":"Submitted Version","type":"conference","citation":{"short":"F. Didier, T.A. Henzinger, M. Mateescu, V. Wolf, in:, IEEE, 2010, pp. 193–194.","apa":"Didier, F., Henzinger, T. A., Mateescu, M., &#38; 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. <a href=\"https://doi.org/10.1109/QEST.2010.33\">https://doi.org/10.1109/QEST.2010.33</a>","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:<a href=\"https://doi.org/10.1109/QEST.2010.33\">10.1109/QEST.2010.33</a>","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.","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. <a href=\"https://doi.org/10.1109/QEST.2010.33\">https://doi.org/10.1109/QEST.2010.33</a>.","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.","mla":"Didier, Frédéric, et al. <i>SABRE: A Tool for the Stochastic Analysis of Biochemical Reaction Networks</i>. IEEE, 2010, pp. 193–94, doi:<a href=\"https://doi.org/10.1109/QEST.2010.33\">10.1109/QEST.2010.33</a>."}}