{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:34:29Z","timestamp":1772138069230,"version":"3.50.1"},"reference-count":18,"publisher":"Oxford University Press (OUP)","issue":"8","license":[{"start":{"date-parts":[[2024,7,30]],"date-time":"2024-07-30T00:00:00Z","timestamp":1722297600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100021778","name":"Agencia I+D+i","doi-asserted-by":"publisher","award":["PICT-2018-01516"],"award-info":[{"award-number":["PICT-2018-01516"]}],"id":[{"id":"10.13039\/501100021778","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100005363","name":"Universidad de Buenos Aires","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100005363","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,8,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Chemical reaction networks (CRNs) play a pivotal role in diverse fields such as systems biology, biochemistry, chemical engineering, and epidemiology. High-level definitions of CRNs enables to use various simulation approaches, including deterministic and stochastic methods, from the same model. However, existing Python tools for simulation of CRN typically wrap external C\/C++ libraries for model definition, translation into equations and\/or numerically solving them, limiting their extensibility and integration with the broader Python ecosystem.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>In response, we developed Poincar\u00e9 and SimBio, two novel Python packages for simulation of dynamical systems and CRNs. Poincar\u00e9 serves as a foundation for dynamical systems modeling, while SimBio extends this functionality to CRNs, including support for the Systems Biology Markup Language (SBML). Poincar\u00e9 and SimBio are developed as pure Python packages enabling users to easily extend their simulation capabilities by writing new or leveraging other Python packages. Moreover, this does not compromise the performance, as code can be just-in-time compiled with Numba. Our benchmark tests using curated models from the BioModels repository demonstrate that these tools may provide a potentially superior performance advantage compared to other existing tools. In addition, to ensure a user-friendly experience, our packages use standard typed modern Python syntax that provides a seamless integration with integrated development environments. Our Python-centric approach significantly enhances code analysis, error detection, and refactoring capabilities, positioning Poincar\u00e9 and SimBio as valuable tools for the modeling community.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>Poincar\u00e9 and SimBio are released under the MIT license. Their source code is available on GitHub (https:\/\/github.com\/maurosilber\/poincare and https:\/\/github.com\/hgrecco\/simbio) and can be installed from PyPI or conda-forge.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btae465","type":"journal-article","created":{"date-parts":[[2024,7,29]],"date-time":"2024-07-29T12:27:01Z","timestamp":1722256021000},"source":"Crossref","is-referenced-by-count":0,"title":["Poincar\u00e9 and SimBio: a versatile and extensible Python ecosystem for modeling systems"],"prefix":"10.1093","volume":"40","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-2402-1100","authenticated-orcid":false,"given":"Mauro","family":"Silberberg","sequence":"first","affiliation":[{"name":"Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de F\u00edsica , Buenos Aires 1426, Argentina"},{"name":"CONICET \u2013 Universidad de Buenos Aires, Instituto de F\u00edsica de Buenos Aires (IFIBA) , Buenos Aires 1426, Argentina"},{"name":"European Bioinformatics Institute, European Molecular Biology Laboratory (EMBL-EBI), Wellcome Genome Campus , Cambridge, CB10 1SD, United Kingdom"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8479-0262","authenticated-orcid":false,"given":"Henning","family":"Hermjakob","sequence":"additional","affiliation":[{"name":"European Bioinformatics Institute, European Molecular Biology Laboratory (EMBL-EBI), Wellcome Genome Campus , Cambridge, CB10 1SD, United Kingdom"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0705-9809","authenticated-orcid":false,"given":"Rahuman S","family":"Malik-Sheriff","sequence":"additional","affiliation":[{"name":"European Bioinformatics Institute, European Molecular Biology Laboratory (EMBL-EBI), Wellcome Genome Campus , Cambridge, CB10 1SD, United Kingdom"},{"name":"Department of Surgery and Cancer, Faculty of Medicine, Imperial College London , 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