{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,11]],"date-time":"2026-03-11T23:47:47Z","timestamp":1773272867907,"version":"3.50.1"},"reference-count":12,"publisher":"Oxford University Press (OUP)","issue":"6","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2007,3,15]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Summary: We present SGNSim, \u2018Stochastic Gene Networks Simulator\u2019, a tool to model gene regulatory networks (GRN) where transcription and translation are modeled as multiple time delayed events and its dynamics is driven by a stochastic simulation algorithm (SSA) able to deal with multiple time delayed events. The delays can be drawn from several distributions and the reaction rates from complex functions or from physical parameters. SGNSim can generate ensembles of GRNs, within a set of user-defined parameters, such as topology. It can also be used to model specific GRNs and systems of chemical reactions. Perturbations, e.g. gene deletion, over-expression, copy and mutation, can be modeled as well. As examples, we present a model of a toggle switch without cooperative binding subject to perturbations, a system of reactions within a compartmentalized environment where membrane crossing is controlled by a negative feedback mechanism and a simulation based on the yeast transcriptional network.<\/jats:p><jats:p>Availability: \u00a0SGNSim program, instructions and examples available at http:\/\/www.cs.tut.fi\/~sanchesr\/SGN\/SGNSim.html.<\/jats:p><jats:p>Contact: \u00a0andre.sanchesribeiro@tut.fi<\/jats:p>","DOI":"10.1093\/bioinformatics\/btm004","type":"journal-article","created":{"date-parts":[[2007,2,3]],"date-time":"2007-02-03T01:16:30Z","timestamp":1170465390000},"page":"777-779","source":"Crossref","is-referenced-by-count":53,"title":["SGN Sim, a Stochastic Genetic Networks Simulator"],"prefix":"10.1093","volume":"23","author":[{"given":"Andre S.","family":"Ribeiro","sequence":"first","affiliation":[{"name":"1 Institute for Biocomplexity and Informatics, University of Calgary, Canada and 2Centre for Computational Physics, University of Coimbra, P-3004-516 Coimbra, Portugal"},{"name":"1 Institute for Biocomplexity and Informatics, University of Calgary, Canada and 2Centre for Computational Physics, University of Coimbra, P-3004-516 Coimbra, Portugal"}]},{"given":"Jason","family":"Lloyd-Price","sequence":"additional","affiliation":[{"name":"1 Institute for Biocomplexity and Informatics, University of Calgary, Canada and 2Centre for Computational Physics, University of Coimbra, P-3004-516 Coimbra, Portugal"}]}],"member":"286","published-online":{"date-parts":[[2007,1,31]]},"reference":[{"key":"2023041107503394400_","first-page":"14593","article-title":"Delay-induced stochastic oscillations in gene regulation.","volume-title":"PNAS","author":"Bratsun","year":"2005"},{"key":"2023041107503394400_","first-page":"335","article-title":"A synthetic oscillatory network of transcriptional regulators.","volume-title":"Nature","author":"Elowitz","year":"2005"},{"key":"2023041107503394400_","first-page":"99","article-title":"Gene expression time delays and turing pattern formation systems.","volume-title":"Bull. Math. Biol","author":"Gaffney","year":"2006"},{"key":"2023041107503394400_","first-page":"339","article-title":"Construction of a genetic toggle switch in Escherichia coli.","volume-title":"Nature","author":"Gardner","year":"2000"},{"key":"2023041107503394400_","doi-asserted-by":"crossref","first-page":"1876","DOI":"10.1021\/jp993732q","article-title":"Efficient exact stochastic simulation of chemical systems with many species and many channels.","volume":"104","author":"Gibson","year":"2000","journal-title":"J. Phys. Chem. A"},{"key":"2023041107503394400_","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1016\/0021-9991(76)90041-3","article-title":"A general method for numerically simulating the stochastic time evolution of coupled chemical reactions.","volume":"22","author":"Gillespie","year":"1976","journal-title":"J. Comput. Phys."},{"key":"2023041107503394400_","first-page":"733","article-title":"The ensemble approach to understand genetic regulatory networks.","volume-title":"Physica A","author":"Kauffman","year":"2004"},{"key":"2023041107503394400_","first-page":"3","article-title":"Mersenne Twister.","volume-title":"SACM Trans. on Modeling and Comp. Simulation","author":"Matsumoto","year":"1998"},{"key":"2023041107503394400_","first-page":"1409","article-title":"Oscillatory Expression of Hes1, p53, and NF\u03baB driven by transcriptional time delays.","volume-title":"Current Biology","author":"Monk","year":"2003"},{"key":"2023041107503394400_","first-page":"2010","article-title":"Noise in gene expression: origins, consequences, and control.","volume-title":"Science","author":"Raser","year":"2005"},{"key":"2023041107503394400_","doi-asserted-by":"crossref","first-page":"1630","DOI":"10.1089\/cmb.2006.13.1630","article-title":"General, modeling strategy for gene regulatory networks with stochastic dynamics.","volume":"13","author":"Ribeiro","year":"2006","journal-title":"J. Comp. Bio."},{"key":"2023041107503394400_","article-title":"Validation of an algorithm for delay stochastic simulation of transcription and translation in prokaryotic gene expression, (submitted)","author":"Roussel","year":"2006"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/23\/6\/777\/49821808\/bioinformatics_23_6_777.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/23\/6\/777\/49821808\/bioinformatics_23_6_777.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,5,10]],"date-time":"2023-05-10T16:00:51Z","timestamp":1683734451000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/23\/6\/777\/418352"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2007,1,31]]},"references-count":12,"journal-issue":{"issue":"6","published-print":{"date-parts":[[2007,3,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btm004","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2007,3,15]]},"published":{"date-parts":[[2007,1,31]]}}}