{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,25]],"date-time":"2026-02-25T20:52:39Z","timestamp":1772052759776,"version":"3.50.1"},"reference-count":14,"publisher":"Oxford University Press (OUP)","issue":"11","license":[{"start":{"date-parts":[[2023,11,21]],"date-time":"2023-11-21T00:00:00Z","timestamp":1700524800000},"content-version":"vor","delay-in-days":20,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Galician Government","award":["ED431C 2022\/47"],"award-info":[{"award-number":["ED431C 2022\/47"]}]},{"name":"Galician Government","award":["ED431G 2019\/01"],"award-info":[{"award-number":["ED431G 2019\/01"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,11,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>One of the main causes hampering predictability during the model identification and automated design of gene circuits in synthetic biology is the effect of molecular noise. Stochasticity may significantly impact the dynamics and function of gene circuits, specially in bacteria and yeast due to low mRNA copy numbers. Standard stochastic simulation methods are too computationally costly in realistic scenarios to be applied to optimization-based design or parameter estimation.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>In this work, we present IDESS (Identification and automated Design of Stochastic gene circuitS), a software toolbox for optimization-based design and model identification of gene regulatory circuits in the stochastic regime. This software incorporates an efficient approximation of the Chemical Master Equation as well as a stochastic simulation algorithm\u2014both with GPU and CPU implementations\u2014combined with global optimization algorithms capable of solving Mixed Integer Nonlinear Programming problems. The toolbox efficiently addresses two types of problems relevant in systems and synthetic biology: the automated design of stochastic synthetic gene circuits, and the parameter estimation for model identification of stochastic gene regulatory networks.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>IDESS runs under the MATLAB environment and it is available under GPLv3 license at https:\/\/doi.org\/10.5281\/zenodo.7788692.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btad682","type":"journal-article","created":{"date-parts":[[2023,11,21]],"date-time":"2023-11-21T23:16:19Z","timestamp":1700608579000},"source":"Crossref","is-referenced-by-count":3,"title":["IDESS: a toolbox for identification and automated design of stochastic gene circuits"],"prefix":"10.1093","volume":"39","author":[{"given":"Carlos","family":"Sequeiros","sequence":"first","affiliation":[{"name":"Computational Biology Lab, MBG-CSIC (Spanish National Research Council) , 36143 Pontevedra, Spain"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7340-9737","authenticated-orcid":false,"given":"Manuel","family":"P\u00e1jaro","sequence":"additional","affiliation":[{"name":"Department of Mathematics, University of Vigo, Escola Superior de Enxe\u00f1ar\u00eda Inform\u00e1tica, Campus Ourense , 32004 Ourense, Spain"}]},{"given":"Carlos","family":"V\u00e1zquez","sequence":"additional","affiliation":[{"name":"Department of Mathematics and CITIC, Universidade da Coru\u00f1a, Campus Elvi\u00f1a s\/n , 15071 A Coru\u00f1a, Spain"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4245-0320","authenticated-orcid":false,"given":"Julio R","family":"Banga","sequence":"additional","affiliation":[{"name":"Computational Biology Lab, MBG-CSIC (Spanish National Research Council) , 36143 Pontevedra, Spain"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2895-997X","authenticated-orcid":false,"given":"Irene","family":"Otero-Muras","sequence":"additional","affiliation":[{"name":"Computational Synthetic Biology Group, Institute for Integrative Systems Biology (I2SysBio), CSIC-UV , 46980 Paterna, Val\u00e8ncia, Spain"}]}],"member":"286","published-online":{"date-parts":[[2023,11,21]]},"reference":[{"key":"2023112802462851700_btad682-B1","doi-asserted-by":"crossref","first-page":"55","DOI":"10.1049\/enb.2017.0004","article-title":"Biochemical complexity drives log-normal variation in genetic expression","volume":"1","author":"Beal","year":"2017","journal-title":"Eng Biol"},{"key":"2023112802462851700_btad682-B2","doi-asserted-by":"crossref","first-page":"136","DOI":"10.1186\/1471-2105-15-136","article-title":"MEIGO: an open-source software suite based on metaheuristics for global optimization in systems biology and bioinformatics","volume":"15","author":"Egea","year":"2014","journal-title":"BMC Bioinformatics"},{"key":"2023112802462851700_btad682-B3","volume-title":"Encyclopedia of Systems Biology","author":"Ge","year":"2013"},{"key":"2023112802462851700_btad682-B4","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":"2023112802462851700_btad682-B5","doi-asserted-by":"crossref","first-page":"1097","DOI":"10.1038\/s41596-021-00675-2","article-title":"Genetic circuit design automation with cello 2.0","volume":"17","author":"Jones","year":"2022","journal-title":"Nat Protoc"},{"key":"2023112802462851700_btad682-B6","doi-asserted-by":"crossref","first-page":"aac7341","DOI":"10.1126\/science.aac7341","article-title":"Genetic circuit design automation","volume":"352","author":"Nielsen","year":"2016","journal-title":"Science"},{"key":"2023112802462851700_btad682-B7","doi-asserted-by":"crossref","first-page":"3360","DOI":"10.1093\/bioinformatics\/btw415","article-title":"SYNBADm: a tool for optimization-based automated design of synthetic gene circuits","volume":"32","author":"Otero-Muras","year":"2016","journal-title":"Bioinformatics"},{"key":"2023112802462851700_btad682-B8","doi-asserted-by":"crossref","first-page":"51","DOI":"10.1016\/j.jtbi.2017.03.017","article-title":"Stochastic modeling and numerical simulation of gene regulatory networks with protein bursting","volume":"421","author":"P\u00e1jaro","year":"2017","journal-title":"J Theor Biol"},{"key":"2023112802462851700_btad682-B9","doi-asserted-by":"crossref","first-page":"893","DOI":"10.1093\/bioinformatics\/btx645","article-title":"SELANSI: a toolbox for simulation of stochastic gene regulatory networks","volume":"34","author":"P\u00e1jaro","year":"2018","journal-title":"Bioinformatics"},{"key":"2023112802462851700_btad682-B10","doi-asserted-by":"crossref","first-page":"i319","DOI":"10.1093\/bioinformatics\/btx253","article-title":"Efficient simulation of intrinsic, extrinsic and external noise in biochemical systems","volume":"33","author":"Pischel","year":"2017","journal-title":"Bioinformatics"},{"key":"2023112802462851700_btad682-B11","doi-asserted-by":"crossref","first-page":"892","DOI":"10.1021\/acssynbio.2c00597","article-title":"Synbiosuite: a tool for improving the workflow for genetic design and modeling","volume":"12","author":"Sents","year":"2023","journal-title":"ACS Synth Biol"},{"key":"2023112802462851700_btad682-B12","doi-asserted-by":"crossref","first-page":"892","DOI":"10.1021\/acssynbio.3c00033","article-title":"Automated design of synthetic gene circuits in presence of molecular noise","volume":"12","author":"Sequeiros","year":"2023","journal-title":"ACS Synth Biol"},{"key":"2023112802462851700_btad682-B13","doi-asserted-by":"crossref","first-page":"1971","DOI":"10.1109\/TCBB.2022.3225675","article-title":"Global optimization approach for parameter estimation in stochastic dynamic models of biosystems","volume":"20","author":"Sequeiros","year":"2023","journal-title":"IEEE\/ACM Trans Comput Biol Bioinform"},{"key":"2023112802462851700_btad682-B14","doi-asserted-by":"crossref","first-page":"34107","DOI":"10.1038\/srep34107","article-title":"Process-based design of dynamical biological systems","volume":"6","author":"Tanevski","year":"2016","journal-title":"Sci Rep"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btad682\/53667236\/btad682.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/39\/11\/btad682\/53863033\/btad682.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/39\/11\/btad682\/53863033\/btad682.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,11,28]],"date-time":"2023-11-28T02:46:48Z","timestamp":1701139608000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/doi\/10.1093\/bioinformatics\/btad682\/7439590"}},"subtitle":[],"editor":[{"given":"Jonathan","family":"Wren","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2023,11,1]]},"references-count":14,"journal-issue":{"issue":"11","published-print":{"date-parts":[[2023,11,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btad682","relation":{},"ISSN":["1367-4811"],"issn-type":[{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2023,11,1]]},"published":{"date-parts":[[2023,11,1]]},"article-number":"btad682"}}