{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,15]],"date-time":"2026-05-15T05:01:07Z","timestamp":1778821267365,"version":"3.51.4"},"reference-count":24,"publisher":"Oxford University Press (OUP)","issue":"9","license":[{"start":{"date-parts":[[2025,9,9]],"date-time":"2025-09-09T00:00:00Z","timestamp":1757376000000},"content-version":"vor","delay-in-days":8,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100004359","name":"Swedish Research Council","doi-asserted-by":"publisher","award":["VR2023-04319"],"award-info":[{"award-number":["VR2023-04319"]}],"id":[{"id":"10.13039\/501100004359","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001729","name":"Swedish Foundation for Strategic Research","doi-asserted-by":"publisher","award":["FFL15-0238"],"award-info":[{"award-number":["FFL15-0238"]}],"id":[{"id":"10.13039\/501100001729","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100010438","name":"Francis Crick Institute","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100010438","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000289","name":"Cancer Research UK","doi-asserted-by":"publisher","award":["CC2242"],"award-info":[{"award-number":["CC2242"]}],"id":[{"id":"10.13039\/501100000289","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000265","name":"UK Medical Research Council","doi-asserted-by":"publisher","award":["CC2242"],"award-info":[{"award-number":["CC2242"]}],"id":[{"id":"10.13039\/501100000265","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001659","name":"German Research Foundation","doi-asserted-by":"publisher","award":["432325352"],"award-info":[{"award-number":["432325352"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001659","name":"German Research Foundation","doi-asserted-by":"publisher","award":["443187771"],"award-info":[{"award-number":["443187771"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,9,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>Dynamic models represent a powerful tool for studying complex biological processes, ranging from cell signalling to cell differentiation. Building such models often requires computationally demanding modelling workflows, such as model exploration and parameter estimation. We developed two Julia-based tools: SBMLImporter.jl, an SBML importer, and PEtab.jl, an importer for parameter estimation problems in the PEtab format, designed to streamline modelling processes. These tools leverage Julia\u2019s high-performance computing capabilities, including symbolic pre-processing and advanced ODE solvers. PEtab.jl aims to be a Julia-accessible toolbox that supports the entire modelling pipeline from parameter estimation to identifiability analysis.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>SBMLImporter.jl and PEtab.jl are implemented in the Julia programming language. Both packages are available on GitHub (github.com\/sebapersson\/SBMLImporter.jl and github.com\/sebapersson\/PEtab.jl) as officially registered Julia packages, installable via the Julia package manager. Each package is continuously tested and supported on Linux, macOS, and Windows.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaf497","type":"journal-article","created":{"date-parts":[[2025,9,5]],"date-time":"2025-09-05T11:58:15Z","timestamp":1757073495000},"source":"Crossref","is-referenced-by-count":6,"title":["PEtab.jl: advancing the efficiency and utility of dynamic modelling"],"prefix":"10.1093","volume":"41","author":[{"given":"Sebastian","family":"Persson","sequence":"first","affiliation":[{"name":"Department of Mathematical Sciences, Chalmers University of Technology , Gothenburg, SE-412 96,","place":["Sweden"]},{"name":"Department of Mathematical Sciences, University of Gothenburg , Gothenburg, SE-412 96,","place":["Sweden"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Fabian","family":"Fr\u00f6hlich","sequence":"additional","affiliation":[{"name":"Dynamics of Livings Systems Laboratory, The Francis Crick Institute , London, NW1 1AT,","place":["United Kingdom"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9524-6633","authenticated-orcid":false,"given":"Stephan","family":"Grein","sequence":"additional","affiliation":[{"name":"Life and Medical Sciences (LIMES) Institute and Bonn Center for Mathematical Life Sciences, University of Bonn , Bonn, 53113,","place":["Germany"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Torkel","family":"Loman","sequence":"additional","affiliation":[{"name":"Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology , Boston, MA 02139,","place":["United States"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Damiano","family":"Ognissanti","sequence":"additional","affiliation":[{"name":"Department of Mathematical Sciences, Chalmers University of Technology , Gothenburg, SE-412 96,","place":["Sweden"]},{"name":"Department of Mathematical Sciences, University of Gothenburg , Gothenburg, SE-412 96,","place":["Sweden"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Viktor","family":"Hasselgren","sequence":"additional","affiliation":[{"name":"Department of Mathematical Sciences, Chalmers University of Technology , Gothenburg, SE-412 96,","place":["Sweden"]},{"name":"Department of Mathematical Sciences, University of Gothenburg , Gothenburg, SE-412 96,","place":["Sweden"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4935-3312","authenticated-orcid":false,"given":"Jan","family":"Hasenauer","sequence":"additional","affiliation":[{"name":"Life and Medical Sciences (LIMES) Institute and Bonn Center for Mathematical Life Sciences, University of Bonn , Bonn, 53113,","place":["Germany"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5142-5100","authenticated-orcid":false,"given":"Marija","family":"Cvijovic","sequence":"additional","affiliation":[{"name":"Department of Mathematical Sciences, Chalmers University of Technology , Gothenburg, SE-412 96,","place":["Sweden"]},{"name":"Department of Mathematical Sciences, University of Gothenburg , Gothenburg, SE-412 96,","place":["Sweden"]}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2025,9,9]]},"reference":[{"key":"2025092403220579600_btaf497-B1","doi-asserted-by":"crossref","first-page":"1404","DOI":"10.1126\/science.1184913","article-title":"Covering a broad dynamic range: information processing at the erythropoietin receptor","volume":"328","author":"Becker","year":"2010","journal-title":"Science"},{"key":"2025092403220579600_btaf497-B2","doi-asserted-by":"crossref","first-page":"65","DOI":"10.1137\/141000671","article-title":"Julia: a fresh approach to numerical computing","volume":"59","author":"Bezanson","year":"2017","journal-title":"SIAM Rev"},{"key":"2025092403220579600_btaf497-B3","doi-asserted-by":"crossref","first-page":"e1005331","DOI":"10.1371\/journal.pcbi.1005331","article-title":"Scalable parameter estimation for genome-scale biochemical reaction networks","volume":"13","author":"Fr\u00f6hlich","year":"2017","journal-title":"PLoS Comput Biol"},{"key":"2025092403220579600_btaf497-B4","doi-asserted-by":"crossref","first-page":"567","DOI":"10.1016\/j.cels.2018.10.013","article-title":"Efficient parameter estimation enables the prediction of drug response using a mechanistic pan-cancer pathway model","volume":"7","author":"Fr\u00f6hlich","year":"2018","journal-title":"Cell Syst"},{"key":"2025092403220579600_btaf497-B5","doi-asserted-by":"crossref","first-page":"3676","DOI":"10.1093\/bioinformatics\/btab227","article-title":"Amici: high-performance sensitivity analysis for large ordinary differential equation models","volume":"37","author":"Fr\u00f6hlich","year":"2021","journal-title":"Bioinformatics"},{"key":"2025092403220579600_btaf497-B6","doi-asserted-by":"crossref","first-page":"e1010322","DOI":"10.1371\/journal.pcbi.1010322","article-title":"Fides: reliable trust-region optimization for parameter estimation of ordinary differential equation models","volume":"18","author":"Fr\u00f6hlich","year":"2022","journal-title":"PLoS Comput Biol"},{"key":"2025092403220579600_btaf497-B7","doi-asserted-by":"crossref","first-page":"35","DOI":"10.1146\/annurev.physchem.58.032806.104637","article-title":"Stochastic simulation of chemical kinetics","volume":"58","author":"Gillespie","year":"2007","journal-title":"Annu Rev Phys Chem"},{"key":"2025092403220579600_btaf497-B8","doi-asserted-by":"crossref","first-page":"3073","DOI":"10.1093\/bioinformatics\/btz020","article-title":"Benchmark problems for dynamic modeling of intracellular processes","volume":"35","author":"Hass","year":"2019","journal-title":"Bioinformatics"},{"key":"2025092403220579600_btaf497-B9","doi-asserted-by":"crossref","first-page":"363","DOI":"10.1145\/1089014.1089020","article-title":"Sundials: suite of nonlinear and differential\/algebraic equation solvers","volume":"31","author":"Hindmarsh","year":"2005","journal-title":"ACM Trans Math Softw"},{"key":"2025092403220579600_btaf497-B10","first-page":"1593","article-title":"The no-u-turn sampler: adaptively setting path lengths in Hamiltonian Monte Carlo","volume":"15","author":"Hoffman","year":"2014","journal-title":"J. Mach. Learn. Res"},{"key":"2025092403220579600_btaf497-B11","doi-asserted-by":"crossref","first-page":"3067","DOI":"10.1093\/bioinformatics\/btl485","article-title":"Copasi\u2014a complex pathway simulator","volume":"22","author":"Hoops","year":"2006","journal-title":"Bioinformatics"},{"key":"2025092403220579600_btaf497-B12","doi-asserted-by":"crossref","first-page":"1662","DOI":"10.1126\/science.1069492","article-title":"Systems biology: a brief overview","volume":"295","author":"Kitano","year":"2002","journal-title":"Science"},{"key":"2025092403220579600_btaf497-B13","volume-title":"Systems Biology: A Textbook","author":"Klipp","year":"2016"},{"key":"2025092403220579600_btaf497-B14","doi-asserted-by":"crossref","first-page":"e1011530","DOI":"10.1371\/journal.pcbi.1011530","article-title":"Catalyst: fast and flexible modeling of reaction networks","volume":"19","author":"Loman","year":"2023","journal-title":"PLoS Comput Biol"},{"key":"2025092403220579600_btaf497-B15","author":"Rackauckas","year":"2020"},{"key":"2025092403220579600_btaf497-B16","doi-asserted-by":"crossref","first-page":"15","DOI":"10.5334\/jors.151","article-title":"DifferentialEquations.jl\u2014a performant and feature-rich ecosystem for solving differential equations in Julia","volume":"5","author":"Rackauckas","year":"2017","journal-title":"JORS"},{"key":"2025092403220579600_btaf497-B17","doi-asserted-by":"crossref","first-page":"e74335","DOI":"10.1371\/journal.pone.0074335","article-title":"Lessons learned from quantitative dynamical modeling in systems biology","volume":"8","author":"Raue","year":"2013","journal-title":"PLoS One"},{"key":"2025092403220579600_btaf497-B18","doi-asserted-by":"crossref","first-page":"3558","DOI":"10.1093\/bioinformatics\/btv405","article-title":"Data2dynamics: a modeling environment tailored to parameter estimation in dynamical systems","volume":"31","author":"Raue","year":"2015","journal-title":"Bioinformatics"},{"key":"2025092403220579600_btaf497-B19","doi-asserted-by":"crossref","first-page":"655","DOI":"10.1038\/s41592-023-01832-z","article-title":"Julia for biologists","volume":"20","author":"Roesch","year":"2023","journal-title":"Nat Methods"},{"key":"2025092403220579600_btaf497-B20","author":"Sch\u00e4lte","year":"2023"},{"key":"2025092403220579600_btaf497-B21","doi-asserted-by":"crossref","first-page":"e1008646","DOI":"10.1371\/journal.pcbi.1008646","article-title":"Petab\u2014interoperable specification of parameter estimation problems in systems biology","volume":"17","author":"Schmiester","year":"2021","journal-title":"PLoS Comput Biol"},{"key":"2025092403220579600_btaf497-B22","doi-asserted-by":"crossref","first-page":"2696","DOI":"10.1038\/s41598-021-82196-2","article-title":"Benchmarking of numerical integration methods for ode models of biological systems","volume":"11","author":"St\u00e4dter","year":"2021","journal-title":"Sci Rep"},{"key":"2025092403220579600_btaf497-B23","author":"Veltz","year":"2020"},{"key":"2025092403220579600_btaf497-B24","doi-asserted-by":"crossref","first-page":"197","DOI":"10.1038\/nmeth.2794","article-title":"Scalable inference of heterogeneous reaction kinetics from pooled single-cell recordings","volume":"11","author":"Zechner","year":"2014","journal-title":"Nat Methods"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btaf497\/64232071\/btaf497.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/41\/9\/btaf497\/64232071\/btaf497.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/41\/9\/btaf497\/64232071\/btaf497.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,9,24]],"date-time":"2025-09-24T07:22:14Z","timestamp":1758698534000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/doi\/10.1093\/bioinformatics\/btaf497\/8250100"}},"subtitle":[],"editor":[{"given":"Jonathan","family":"Wren","sequence":"additional","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2025,9,1]]},"references-count":24,"journal-issue":{"issue":"9","published-print":{"date-parts":[[2025,9,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btaf497","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2025.04.30.651378","asserted-by":"object"}]},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2025,9]]},"published":{"date-parts":[[2025,9,1]]},"article-number":"btaf497"}}