{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,2]],"date-time":"2026-06-02T23:14:27Z","timestamp":1780442067553,"version":"3.54.1"},"reference-count":17,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2022,12,10]],"date-time":"2022-12-10T00:00:00Z","timestamp":1670630400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"European Union\u2019s Horizon 2020 Research and Innovation","award":["722287"],"award-info":[{"award-number":["722287"]}]},{"name":"European Union\u2019s Horizon 2020 Research and Innovation","award":["675585"],"award-info":[{"award-number":["675585"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Large-scale kinetic models are an invaluable tool to understand the dynamic and adaptive responses of biological systems. The development and application of these models have been limited by the availability of computational tools to build and analyze large-scale models efficiently. The toolbox presented here provides the means to implement, parameterize and analyze large-scale kinetic models intuitively and efficiently.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We present a Python package (SKiMpy) bridging this gap by implementing an efficient kinetic modeling toolbox for the semiautomatic generation and analysis of large-scale kinetic models for various biological domains such as signaling, gene expression and metabolism. Furthermore, we demonstrate how this toolbox is used to parameterize kinetic models around a steady-state reference efficiently. Finally, we show how SKiMpy can implement multispecies bioreactor simulations to assess biotechnological processes.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>The software is available as a Python 3 package on GitHub: https:\/\/github.com\/EPFL-LCSB\/SKiMpy, along with adequate documentation.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Supplementary information<\/jats:title>\n                    <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btac787","type":"journal-article","created":{"date-parts":[[2022,12,10]],"date-time":"2022-12-10T07:24:25Z","timestamp":1670657065000},"source":"Crossref","is-referenced-by-count":18,"title":["Symbolic kinetic models in python (SKiMpy): intuitive modeling of large-scale biological kinetic models"],"prefix":"10.1093","volume":"39","author":[{"given":"Daniel R","family":"Weilandt","sequence":"first","affiliation":[{"name":"Laboratory of Computational Systems Biotechnology, \u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne (EPFL) , Lausanne 1015, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pierre","family":"Salvy","sequence":"additional","affiliation":[{"name":"Laboratory of Computational Systems Biotechnology, \u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne (EPFL) , Lausanne 1015, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maria","family":"Masid","sequence":"additional","affiliation":[{"name":"Laboratory of Computational Systems Biotechnology, \u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne (EPFL) , Lausanne 1015, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Georgios","family":"Fengos","sequence":"additional","affiliation":[{"name":"Laboratory of Computational Systems Biotechnology, \u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne (EPFL) , Lausanne 1015, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Robin","family":"Denhardt-Erikson","sequence":"additional","affiliation":[{"name":"Laboratory of Computational Systems Biotechnology, \u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne (EPFL) , Lausanne 1015, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhaleh","family":"Hosseini","sequence":"additional","affiliation":[{"name":"Laboratory of Computational Systems Biotechnology, \u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne (EPFL) , Lausanne 1015, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6432-4694","authenticated-orcid":false,"given":"Vassily","family":"Hatzimanikatis","sequence":"additional","affiliation":[{"name":"Laboratory of Computational Systems Biotechnology, \u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne (EPFL) , Lausanne 1015, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2022,12,10]]},"reference":[{"key":"2023010805375776200_btac787-B2","doi-asserted-by":"crossref","first-page":"1043","DOI":"10.1002\/biot.201300091","article-title":"Towards kinetic modeling of genome-scale metabolic networks without sacrificing stoichiometric, thermodynamic and physiological constraints","volume":"8","author":"Chakrabarti","year":"2013","journal-title":"Biotechnol. 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