{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,9,27]],"date-time":"2025-09-27T00:14:46Z","timestamp":1758932086025,"version":"3.44.0"},"reference-count":22,"publisher":"Oxford University Press (OUP)","issue":"9","license":[{"start":{"date-parts":[[2025,9,2]],"date-time":"2025-09-02T00:00:00Z","timestamp":1756771200000},"content-version":"vor","delay-in-days":1,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute"},{"name":"French Embassy in London"}],"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>Computational models in biology can increase our understanding of biological systems, be used to answer research questions, and make predictions. Accessibility and reusability of computational models is limited and often restricted to experts in programming and mathematics. This is due to the need to implement entire models and solvers from the mathematical notation models are normally presented as. Here, we present SBMLtoOdin, an R package that translates differential equation models in SBML format from the BioModels database into executable R code using the R package odin, allowing researchers to easily reuse models. We also present Menelmacar, a web-based application that provides interactive visualisations of these models by solving their differential equations in the browser. This platform allows non-experts to simulate and investigate models using an easy-to-use interface.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and Implementation<\/jats:title>\n                  <jats:p>SBMLtoOdin is published under the open source Apache 2.0 licence at https:\/\/github.com\/bacpop\/SBMLtoOdin and can be installed as an R package. The code for the Menelmacar website is published under the MIT License at https:\/\/github.com\/bacpop\/odinviewer, and the website can be found at https:\/\/biomodels.bacpop.org\/.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaf484","type":"journal-article","created":{"date-parts":[[2025,9,2]],"date-time":"2025-09-02T14:27:54Z","timestamp":1756823274000},"source":"Crossref","is-referenced-by-count":0,"title":["SBMLtoOdin and Menelmacar: interactive visualisation of systems biology models for expert and non-expert audiences"],"prefix":"10.1093","volume":"41","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-1471-5782","authenticated-orcid":false,"given":"Leonie J","family":"Lorenz","sequence":"first","affiliation":[{"name":"European Bioinformatics Institute, European Molecular Biology Laboratory, Wellcome Genome Campus , Cambridge, CB10 1SD,","place":["United Kingdom"]}]},{"given":"Antoine","family":"Andr\u00e9oletti","sequence":"additional","affiliation":[{"name":"European Bioinformatics Institute, European Molecular Biology Laboratory, Wellcome Genome Campus , Cambridge, CB10 1SD,","place":["United Kingdom"]},{"name":"Department of Computer Science, Data and Artificial Intelligence, \u00c9cole Polytechnique , Palaiseau Cedex, 91128,","place":["France"]},{"name":"Department of Health Technology, Technical University of Denmark , Kongens Lyngby, 2800,","place":["Denmark"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2876-6046","authenticated-orcid":false,"given":"Tung V N","family":"Nguyen","sequence":"additional","affiliation":[{"name":"European Bioinformatics Institute, European Molecular Biology Laboratory, Wellcome Genome Campus , Cambridge, CB10 1SD,","place":["United Kingdom"]}]},{"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, Wellcome Genome Campus , Cambridge, CB10 1SD,","place":["United Kingdom"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8888-3837","authenticated-orcid":false,"given":"Richard G","family":"FitzJohn","sequence":"additional","affiliation":[{"name":"MRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (JIDEA), School of Public Health, Imperial College London, London, W2 1PG,","place":["United Kingdom"]}]},{"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, Wellcome Genome Campus , 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