{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,7]],"date-time":"2026-06-07T07:18:44Z","timestamp":1780816724021,"version":"3.54.1"},"reference-count":76,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2022,6,7]],"date-time":"2022-06-07T00:00:00Z","timestamp":1654560000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100004339","name":"sanofi-aventis","doi-asserted-by":"publisher","award":["ANR-17-CE40-0036"],"award-info":[{"award-number":["ANR-17-CE40-0036"]}],"id":[{"id":"10.13039\/100004339","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100004339","name":"sanofi-aventis","doi-asserted-by":"publisher","award":["DFG-391322026"],"award-info":[{"award-number":["DFG-391322026"]}],"id":[{"id":"10.13039\/100004339","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100004339","name":"sanofi-aventis","doi-asserted-by":"publisher","award":["2020\/0766"],"award-info":[{"award-number":["2020\/0766"]}],"id":[{"id":"10.13039\/100004339","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R35GM119770"],"award-info":[{"award-number":["R35GM119770"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["NSF188553"],"award-info":[{"award-number":["NSF188553"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["NSF1720625"],"award-info":[{"award-number":["NSF1720625"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["U24 EB028887"],"award-info":[{"award-number":["U24 EB028887"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01 GM122424"],"award-info":[{"award-number":["R01 GM122424"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Inserm Cancer"},{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","award":["251654672"],"award-info":[{"award-number":["251654672"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","award":["2117-422037984"],"award-info":[{"award-number":["2117-422037984"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100010767","name":"Innovative Medicines Initiative","doi-asserted-by":"publisher","award":["116030"],"award-info":[{"award-number":["116030"]}],"id":[{"id":"10.13039\/501100010767","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100010767","name":"Innovative Medicines Initiative","doi-asserted-by":"publisher","award":["BB\/N019482\/1"],"award-info":[{"award-number":["BB\/N019482\/1"]}],"id":[{"id":"10.13039\/501100010767","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100010767","name":"Innovative Medicines Initiative","doi-asserted-by":"publisher","award":["BB\/N019474\/1"],"award-info":[{"award-number":["BB\/N019474\/1"]}],"id":[{"id":"10.13039\/501100010767","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000070","name":"National Institute for Biomedical Imaging and Bioengineering","doi-asserted-by":"crossref","award":["P41EB023912"],"award-info":[{"award-number":["P41EB023912"]}],"id":[{"id":"10.13039\/100000070","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,7,18]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Computational models are often employed in systems biology to study the dynamic behaviours of complex systems. With the rise in the number of computational models, finding ways to improve the reusability of these models and their ability to reproduce virtual experiments becomes critical. Correct and effective model annotation in community-supported and standardised formats is necessary for this improvement. Here, we present recent efforts toward a common framework for annotated, accessible, reproducible and interoperable computational models in biology, and discuss key challenges of the field.<\/jats:p>","DOI":"10.1093\/bib\/bbac212","type":"journal-article","created":{"date-parts":[[2022,6,7]],"date-time":"2022-06-07T21:05:27Z","timestamp":1654635927000},"source":"Crossref","is-referenced-by-count":33,"title":["Addressing <i>barriers in comprehensiveness, accessibility, reusability, interoperability and reproducibility of computational models in systems biology<\/i>"],"prefix":"10.1093","volume":"23","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-9687-7426","authenticated-orcid":false,"given":"Anna","family":"Niarakis","sequence":"first","affiliation":[{"name":"Universit\u00e9 Paris-Saclay, Laboratoire Europ\u00e9en de Recherche pour la Polyarthrite rhumato\u00efde - Genhotel , Univ Evry, Evry, France"},{"name":"Lifeware Group, Inria, Saclay-\u00eele de France , 91120 Palaiseau, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5886-5563","authenticated-orcid":false,"given":"Dagmar","family":"Waltemath","sequence":"additional","affiliation":[{"name":"Department of Medical Informatics, University Medicine Greifswald , Greifswald, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"James","family":"Glazier","sequence":"additional","affiliation":[{"name":"Biocomplexity Institute and Department of Intelligent Systems Engineering, Indiana University , Bloomington, IN, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Falk","family":"Schreiber","sequence":"additional","affiliation":[{"name":"Department of Computer and Information Science, University of Konstanz , Konstanz, Germany"},{"name":"Faculty of Information Technology, Monash University , Clayton, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sarah M","family":"Keating","sequence":"additional","affiliation":[{"name":"University College London , London, United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David","family":"Nickerson","sequence":"additional","affiliation":[{"name":"Auckland Bioengineering Institute, University of Auckland , Auckland, New Zealand"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2350-0756","authenticated-orcid":false,"given":"Claudine","family":"Chaouiya","sequence":"additional","affiliation":[{"name":"Aix Marseille Univ, CNRS , I2M, Marseille, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6542-1568","authenticated-orcid":false,"given":"Anne","family":"Siegel","sequence":"additional","affiliation":[{"name":"Univ Rennes, CNRS, Inria - IRISA lab. Rennes"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vincent","family":"No\u00ebl","sequence":"additional","affiliation":[{"name":"Institut Curie, PSL Research University , Paris, France"},{"name":"INSERM , U900, Paris, France"},{"name":"MINES ParisTech, PSL Research University, CBIO-Centre for Computational Biology , Paris, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8479-0262","authenticated-orcid":false,"given":"Henning","family":"Hermjakob","sequence":"additional","affiliation":[{"name":"EMBL-European Bioinformatics Institute, Wellcome Genome Campus , Cambridge, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3653-1906","authenticated-orcid":false,"given":"Tom\u00e1\u0161","family":"Helikar","sequence":"additional","affiliation":[{"name":"Department of Biochemistry, University of Nebraska-Lincoln , Lincoln, NE, 68588, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5525-7418","authenticated-orcid":false,"given":"Sylvain","family":"Soliman","sequence":"additional","affiliation":[{"name":"Lifeware Group, Inria, Saclay-\u00eele de France , 91120 Palaiseau, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7835-1148","authenticated-orcid":false,"given":"Laurence","family":"Calzone","sequence":"additional","affiliation":[{"name":"Institut Curie, PSL Research University , Paris, France"},{"name":"INSERM , U900, Paris, France"},{"name":"MINES ParisTech, PSL Research University, CBIO-Centre for Computational Biology , Paris, France"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2022,6,8]]},"reference":[{"issue":"2","key":"2024051308554518000_ref1","doi-asserted-by":"crossref","first-page":"1848","DOI":"10.1093\/bib\/bbaa046","article-title":"Setting the basis of best practices and standards for curation and annotation of logical models in biology-highlights of the [BC]2 2019 CoLoMoTo\/SysMod Workshop","volume":"22","author":"Niarakis","year":"2021","journal-title":"Brief Bioinformat"},{"issue":"D1","key":"2024051308554518000_ref2","first-page":"D407","article-title":"BioModels-15 years of sharing computational models in life science","volume":"48","author":"Malik-Sheriff","year":"2020","journal-title":"Nucleic Acids Res"},{"issue":"3","key":"2024051308554518000_ref3","first-page":"19","article-title":"Promoting coordinated development of community-based information standards for modeling in biology: the COMBINE initiative","volume":"24","author":"Hucka","year":"2015","journal-title":"Front Bioeng Biotechnol"},{"issue":"7","key":"2024051308554518000_ref4","doi-asserted-by":"crossref","first-page":"1154","DOI":"10.1093\/bioinformatics\/btv013","article-title":"Cooperative development of logical modelling standards and tools with CoLoMoTo","volume":"31","author":"Naldi","year":"2015","journal-title":"Bioinformatics"},{"issue":"21","key":"2024051308554518000_ref5","doi-asserted-by":"crossref","first-page":"3702","DOI":"10.1093\/bioinformatics\/btab229","article-title":"SysMod: the ISCB community for data-driven computational modelling and multi-scale analysis of biological systems","volume":"37","author":"Dr\u00e4ger","year":"2021","journal-title":"Bioinformatics"},{"issue":"8","key":"2024051308554518000_ref6","doi-asserted-by":"crossref","first-page":"735","DOI":"10.1038\/nbt.1558","article-title":"The systems biology graphical notation","volume":"27","author":"Le Nov\u00e8re","year":"2009","journal-title":"Nat Biotechnol"},{"issue":"8","key":"2024051308554518000_ref7","doi-asserted-by":"crossref","first-page":"e9110","DOI":"10.15252\/msb.20199110","article-title":"SBML Level 3: an extensible format for the exchange and reuse of biological models","volume":"16","author":"Keating","year":"2020","journal-title":"Mol Syst Biol"},{"issue":"5","key":"2024051308554518000_ref8","doi-asserted-by":"crossref","first-page":"198","DOI":"10.1186\/1752-0509-5-198","article-title":"Reproducible computational biology experiments with SED-ML--the simulation experiment description markup language","volume":"15","author":"Waltemath","year":"2011","journal-title":"BMC Syst Biol"},{"issue":"2","key":"2024051308554518000_ref9","doi-asserted-by":"crossref","first-page":"540","DOI":"10.1093\/bib\/bby087","article-title":"Harmonizing semantic annotations for computational models in biology","volume":"20","author":"Neal","year":"2019","journal-title":"Brief Bioinformat."},{"issue":"1","key":"2024051308554518000_ref10","doi-asserted-by":"crossref","first-page":"43","DOI":"10.1186\/1478-811X-11-43","article-title":"Modeling approaches for qualitative and semi-quantitative analysis of cellular signaling networks","volume":"11","author":"Samaga","year":"2013","journal-title":"Cell Commun Signal"},{"issue":"1","key":"2024051308554518000_ref11","doi-asserted-by":"crossref","first-page":"45","DOI":"10.1186\/2191-0855-1-45","article-title":"Modeling formalisms in systems biology","volume":"5","author":"Machado","year":"2011","journal-title":"AMB Express"},{"issue":"4","key":"2024051308554518000_ref12","doi-asserted-by":"crossref","first-page":"943","DOI":"10.1109\/TCBB.2010.117","article-title":"A survey on methods for modeling and analyzing integrated biological networks","volume":"8","author":"Tenazinha","year":"2011","journal-title":"IEEE\/ACM Trans Comput Biol Bioinform"},{"issue":"2","key":"2024051308554518000_ref13","doi-asserted-by":"crossref","first-page":"659","DOI":"10.1093\/bib\/bby024","article-title":"Community-driven roadmap for integrated disease maps","volume":"20","author":"Ostaszewski","year":"2019","journal-title":"Brief Bioinformat"},{"issue":"10","key":"2024051308554518000_ref14","doi-asserted-by":"crossref","first-page":"e10387","DOI":"10.15252\/msb.202110387","article-title":"COVID19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms","volume":"17","author":"Ostaszewski","year":"2021","journal-title":"Mol Syst Biol"},{"issue":"16","key":"2024051308554518000_ref15","doi-asserted-by":"crossref","first-page":"4473","DOI":"10.1093\/bioinformatics\/btaa484","article-title":"Automated inference of Boolean models from molecular interaction maps using CaSQ","volume":"36","author":"Aghamiri","year":"2020","journal-title":"Bioinformatics"},{"issue":"7","key":"2024051308554518000_ref16","doi-asserted-by":"crossref","first-page":"135","DOI":"10.1186\/1752-0509-7-135","article-title":"SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools","volume":"10","author":"Chaouiya","year":"2013","journal-title":"BMC Syst Biol"},{"issue":"2","key":"2024051308554518000_ref17","doi-asserted-by":"crossref","first-page":"20190022","DOI":"10.1515\/jib-2019-0022","article-title":"Systems biology graphical notation: process description language level 1 version 2.0","volume":"16","author":"Rougny","year":"2019","journal-title":"J Integr Bioinform"},{"issue":"2","key":"2024051308554518000_ref18","doi-asserted-by":"crossref","first-page":"264","DOI":"10.1515\/jib-2015-264","article-title":"Systems biology graphical notation: entity relationship language level 1 version 2","volume":"12","author":"Sorokin","year":"2015","journal-title":"J Integr Bioinform"},{"issue":"2","key":"2024051308554518000_ref19","doi-asserted-by":"crossref","first-page":"265","DOI":"10.1515\/jib-2015-265","article-title":"Systems biology graphical notation: activity flow language level 1 version 1.2","volume":"12","author":"Mi","year":"2015","journal-title":"J Integr Bioinform"},{"issue":"18","key":"2024051308554518000_ref20","doi-asserted-by":"crossref","first-page":"2340","DOI":"10.1093\/bioinformatics\/btq407","article-title":"Editing, validating and translating of SBGN maps","volume":"26","author":"Czauderna","year":"2010","journal-title":"Bioinformatics"},{"issue":"14","key":"2024051308554518000_ref21","doi-asserted-by":"crossref","first-page":"250","DOI":"10.1186\/1471-2105-14-250","article-title":"Conversion of KEGG metabolic pathways to SBGN maps including automatic layout","volume":"16","author":"Czauderna","year":"2013","journal-title":"BMC Bioinformat"},{"issue":"10","key":"2024051308554518000_ref22","doi-asserted-by":"crossref","first-page":"375","DOI":"10.1186\/1471-2105-10-375","article-title":"A generic algorithm for layout of biological networks","volume":"12","author":"Schreiber","year":"2009","journal-title":"BMC Bioinformat"},{"issue":"6","key":"2024051308554518000_ref23","doi-asserted-by":"crossref","first-page":"961","DOI":"10.1109\/TVCG.2009.109","article-title":"A comparison of user-generated and automatic graph layouts","volume":"15","author":"Dwyer","year":"2009","journal-title":"IEEE Trans Vis Comput Graph"},{"issue":"6","key":"2024051308554518000_ref24","doi-asserted-by":"crossref","first-page":"1293","DOI":"10.1109\/TVCG.2008.130","article-title":"Exploration of networks using overview+detail with constraint-based cooperative layout","volume":"14","author":"Dwyer","year":"2008","journal-title":"IEEE Trans Vis Comput Graph"},{"issue":"3","key":"2024051308554518000_ref25","first-page":"252","article-title":"Visual analysis of transcriptome data in the context of anatomical structures and biological networks","volume":"15","author":"Junker","year":"2012","journal-title":"Front Plant Sci"},{"key":"2024051308554518000_ref26","doi-asserted-by":"crossref","first-page":"8.13.1","DOI":"10.1002\/0471250953.bi0813s47","article-title":"Biological network exploration with Cytoscape 3","volume":"47","author":"Su","year":"2014","journal-title":"Curr Protoc Bioinformat"},{"key":"2024051308554518000_ref27","doi-asserted-by":"crossref","first-page":"121","DOI":"10.1007\/978-1-4939-0805-9_11","article-title":"Modeling and simulation using CellDesigner","volume":"1164","author":"Matsuoka","year":"2014","journal-title":"Methods Mol Biol"},{"issue":"9","key":"2024051308554518000_ref28","doi-asserted-by":"crossref","first-page":"1600","DOI":"10.1093\/bioinformatics\/bty829","article-title":"SemGen: a tool for semantics-based annotation and composition of biosimulation models","volume":"35","author":"Neal","year":"2019","journal-title":"Bioinformatics"},{"issue":"2\u20133","key":"2024051308554518000_ref29","doi-asserted-by":"crossref","first-page":"20200021","DOI":"10.1515\/jib-2020-0021","article-title":"CellML 2.0","volume":"17","author":"Clerx","year":"2020","journal-title":"J Integr Bioinform"},{"issue":"8","key":"2024051308554518000_ref30","doi-asserted-by":"crossref","first-page":"42","DOI":"10.1186\/1752-0509-8-42","article-title":"Multistate Model Builder (MSMB): a flexible editor for compact biochemical models","volume":"4","author":"Palmisano","year":"2014","journal-title":"BMC Syst Biol"},{"key":"2024051308554518000_ref31","doi-asserted-by":"crossref","first-page":"119","DOI":"10.1007\/978-1-4939-9102-0_5","article-title":"Efficiently encoding complex biochemical models with the multistate model builder (MSMB)","volume":"1945","author":"Palmisano","year":"2019","journal-title":"Methods Mol Biol"},{"key":"2024051308554518000_ref32","doi-asserted-by":"crossref","first-page":"17","DOI":"10.1007\/978-1-59745-525-1_2","article-title":"Computational modeling of biochemical networks using COPASI","volume":"500","author":"Mendes","year":"2009","journal-title":"Methods Mol Biol"},{"key":"2024051308554518000_ref33","article-title":"Simulation and model-based design","author":"Documentation","year":"2020","journal-title":"MathWorks"},{"issue":"3","key":"2024051308554518000_ref34","doi-asserted-by":"crossref","first-page":"160018","DOI":"10.1038\/sdata.2016.18","article-title":"The FAIR Guiding Principles for scientific data management and stewardship","volume":"15","author":"Wilkinson","year":"2016","journal-title":"Sci Data"},{"issue":"D1","key":"2024051308554518000_ref35","doi-asserted-by":"crossref","first-page":"D404","DOI":"10.1093\/nar\/gkw1032","article-title":"FAIRDOMHub: a repository and collaboration environment for sharing systems biology research","volume":"45","author":"Wolstencroft","year":"2017","journal-title":"Nucleic Acids Res"},{"issue":"2","key":"2024051308554518000_ref36","doi-asserted-by":"crossref","first-page":"e22505","DOI":"10.2196\/22505","article-title":"Initiatives, concepts, and implementation practices of FAIR (findable, accessible, interoperable, and reusable) data principles in health data stewardship practice: protocol for a scoping review","volume":"10","author":"Inau","year":"2021","journal-title":"JMIR Res Protoc"},{"issue":"281","key":"2024051308554518000_ref37","first-page":"779","article-title":"Fairifying clinical studies metadata: a registry for the biomedical research","volume":"27","author":"Meloni","year":"2021","journal-title":"Stud Health Technol Inform"},{"issue":"2","key":"2024051308554518000_ref38","doi-asserted-by":"crossref","first-page":"97","DOI":"10.1089\/bio.2017.0110","article-title":"Enhancing reuse of data and biological material in medical research: from FAIR to FAIR-health","volume":"16","author":"Holub","year":"2018","journal-title":"Biopreserv Biobank"},{"issue":"S 01","key":"2024051308554518000_ref39","doi-asserted-by":"crossref","first-page":"e21","DOI":"10.1055\/s-0040-1713684","article-title":"From raw data to FAIR data: the fairification workflow for health research","volume":"59","author":"Sinaci","year":"2020","journal-title":"Methods Inf Med"},{"issue":"2","key":"2024051308554518000_ref40","doi-asserted-by":"crossref","first-page":"20150103","DOI":"10.1098\/rsfs.2015.0103","article-title":"The Human Physiome: how standards, software and innovative service infrastructures are providing the building blocks to make it achievable","volume":"6","author":"Nickerson","year":"2016","journal-title":"Interface Focus"},{"issue":"1878","key":"2024051308554518000_ref41","first-page":"3017","article-title":"CellML and associated tools and techniques","volume":"366","author":"Garny","year":"2008","journal-title":"Philos Transact A Math Phys Eng Sci"},{"issue":"24","key":"2024051308554518000_ref42","doi-asserted-by":"crossref","first-page":"4898","DOI":"10.1093\/bioinformatics\/btab445","article-title":"libOmexMeta: Enabling semantic annotation of models to support FAIR principles","volume":"37","author":"Welsh","year":"2021","journal-title":"Bioinformatics"},{"issue":"1","key":"2024051308554518000_ref43","doi-asserted-by":"crossref","first-page":"457","DOI":"10.1186\/s12859-019-2987-y","article-title":"Model annotation and discovery with the Physiome Model Repository","volume":"20","author":"Sarwar","year":"2019","journal-title":"BMC Bioinformatics"},{"issue":"7","key":"2024051308554518000_ref44","doi-asserted-by":"crossref","first-page":"919","DOI":"10.1113\/expphysiol.2007.041871","article-title":"Using Physiome standards to couple cellular functions for rat cardiac excitation-contraction","volume":"93","author":"Terkildsen","year":"2008","journal-title":"Exp Physiol"},{"issue":"6","key":"2024051308554518000_ref45","doi-asserted-by":"crossref","first-page":"3029","DOI":"10.1016\/S0006-3495(01)75943-7","article-title":"A mathematical model of action potential heterogeneity in adult rat left ventricular myocytes","volume":"81","author":"Pandit","year":"2001","journal-title":"Biophys J"},{"issue":"6","key":"2024051308554518000_ref46","doi-asserted-by":"crossref","first-page":"3723","DOI":"10.1529\/biophysj.104.049973","article-title":"A simplified local control model of calcium-induced calcium release in cardiac ventricular myocytes","volume":"87","author":"Hinch","year":"2004","journal-title":"Biophys J"},{"issue":"5","key":"2024051308554518000_ref47","doi-asserted-by":"crossref","first-page":"1697","DOI":"10.1529\/biophysj.105.069534","article-title":"A quantitative analysis of cardiac myocyte relaxation: a simulation study","volume":"90","author":"Niederer","year":"2006","journal-title":"Biophys J"},{"key":"2024051308554518000_ref48","first-page":"69","article-title":"Computational modeling of the main signaling pathways involved in mast cell activation","volume":"382","author":"Niarakis","year":"2014","journal-title":"Curr Top Microbiol Immunol"},{"issue":"D1","key":"2024051308554518000_ref49","doi-asserted-by":"crossref","first-page":"D687","DOI":"10.1093\/nar\/gkab1028","article-title":"The reactome pathway knowledgebase 2022","volume":"50","author":"Gillespie","year":"2022","journal-title":"Nucleic Acids Res"},{"issue":"11","key":"2024051308554518000_ref50","doi-asserted-by":"crossref","first-page":"2407","DOI":"10.1158\/0008-5472.CAN-19-3147","article-title":"Hybrid epithelial-Mesenchymal phenotypes are controlled by microenvironmental factors","volume":"80","author":"Selvaggio","year":"2020","journal-title":"Cancer Res"},{"key":"2024051308554518000_ref51","doi-asserted-by":"crossref","first-page":"463","DOI":"10.1007\/978-1-61779-361-5_23","article-title":"Logical modelling of gene regulatory networks with GINsim","volume":"804","author":"Chaouiya","year":"2012","journal-title":"Methods Mol Biol"},{"key":"2024051308554518000_ref52","doi-asserted-by":"crossref","first-page":"1","DOI":"10.18637\/jss.v025.i01","article-title":"FactoMineR: an R package for multivariate analysis","volume":"25","author":"L\u00ea","year":"2008","journal-title":"J Stat Softw"},{"key":"2024051308554518000_ref53","doi-asserted-by":"crossref","first-page":"1917","DOI":"10.1093\/bioinformatics\/btn336","article-title":"Synchronous versus asynchronous modeling of gene regulatory networks","volume":"24","author":"Garg","year":"2008","journal-title":"Bioinformatics"},{"key":"2024051308554518000_ref54","volume-title":"IFAC Proceedings Volumes"},{"issue":"14","key":"2024051308554518000_ref55","doi-asserted-by":"crossref","first-page":"2226","DOI":"10.1093\/bioinformatics\/btx123","article-title":"MaBoSS 2.0: an environment for stochastic Boolean modeling","volume":"33","author":"Stoll","year":"2017  15","journal-title":"Bioinformatics"},{"issue":"9","key":"2024051308554518000_ref56","doi-asserted-by":"crossref","first-page":"680","DOI":"10.3389\/fphys.2018.00680","article-title":"The colomoto interactive notebook: accessible and reproducible computational analyses for qualitative biological networks","volume":"19","author":"Naldi","year":"2018","journal-title":"Front Physiol"},{"issue":"4","key":"2024051308554518000_ref57","doi-asserted-by":"crossref","first-page":"bbaa390","DOI":"10.1093\/bib\/bbaa390","article-title":"The status of causality in biological databases: data resources and data retrieval possibilities to support logical modeling","volume":"20","author":"Tour\u00e9","year":"2021","journal-title":"Brief Bioinformatics"},{"key":"2024051308554518000_ref58","first-page":"100386","article-title":"Data integration in logic-based models of biological mechanisms, Current Opinion in Systems Biology","author":"Hall","year":"2021"},{"issue":"12","key":"2024051308554518000_ref59","doi-asserted-by":"crossref","first-page":"693735","DOI":"10.3389\/fphys.2021.693735","article-title":"The SPARC DRC: building a resource for the autonomic nervous system community","volume":"24","author":"Osanlouy","year":"2021","journal-title":"Front Physiol"},{"key":"2024051308554518000_ref60","doi-asserted-by":"crossref","DOI":"10.1093\/nar\/gkac331","article-title":"BioSimulators: a central registry of simulation engines and services for recommending specific tools","volume-title":"Nucleic Acids Research","author":"Shaikh"},{"issue":"6","key":"2024051308554518000_ref61","doi-asserted-by":"crossref","first-page":"96","DOI":"10.1186\/1752-0509-6-96","article-title":"The cell collective: toward an open and collaborative approach to systems biology","volume":"7","author":"Helikar","year":"2012","journal-title":"BMC Syst Biol"},{"issue":"8","key":"2024051308554518000_ref62","doi-asserted-by":"crossref","first-page":"754444","DOI":"10.3389\/fmolb.2021.754444","article-title":"Webmaboss: a web interface for simulating boolean models stochastically","volume":"15","author":"No\u00ebl","year":"2021","journal-title":"Front Mol Biosci"},{"issue":"10","key":"2024051308554518000_ref63","doi-asserted-by":"crossref","first-page":"1378","DOI":"10.1093\/bioinformatics\/btq124","article-title":"BoolNet--an R package for generation, reconstruction and analysis of Boolean networks","volume":"26","author":"M\u00fcssel","year":"2010","journal-title":"Bioinformatics"},{"issue":"5","key":"2024051308554518000_ref64","doi-asserted-by":"crossref","first-page":"e1006146","DOI":"10.1371\/journal.pcbi.1006146","article-title":"Traceability, reproducibility and wiki-exploration for \u201c\u00e0-la-carte\u201d reconstructions of genome-scale metabolic models","volume":"14","author":"Aite","year":"2018","journal-title":"PLoS Comput Biol"},{"key":"2024051308554518000_ref65","first-page":"9","article-title":"Metage2Metabo, microbiota-scale metabolic complementarity for the identification of key species","volume":"29","author":"Belcour","year":"2020","journal-title":"Elife"},{"key":"2024051308554518000_ref66","doi-asserted-by":"crossref","first-page":"325","DOI":"10.1016\/B978-0-12-388403-9.00013-8","article-title":"Multi-scale modeling of tissues using CompuCell3D","volume":"110","author":"Swat","year":"2012","journal-title":"Methods Cell Biol"},{"issue":"2","key":"2024051308554518000_ref67","doi-asserted-by":"crossref","first-page":"e1005991","DOI":"10.1371\/journal.pcbi.1005991","article-title":"PhysiCell: an open source physics-based cell simulator for 3-D multicellular systems","volume":"14","author":"Ghaffarizadeh","year":"2018","journal-title":"PLoS Comput Biol"},{"issue":"3","key":"2024051308554518000_ref68","doi-asserted-by":"crossref","first-page":"e1002970","DOI":"10.1371\/journal.pcbi.1002970","article-title":"Chaste: an open source C++ library for computational physiology and biology","volume":"9","author":"Mirams","year":"2013","journal-title":"PLoS Comput Biol"},{"issue":"20","key":"2024051308554518000_ref69","doi-asserted-by":"crossref","first-page":"2641","DOI":"10.1093\/bioinformatics\/btq437","article-title":"A cell-based simulation software for multi-cellular systems","volume":"26","author":"Hoehme","year":"2010","journal-title":"Bioinformatics"},{"issue":"2","key":"2024051308554518000_ref70","doi-asserted-by":"crossref","first-page":"e9982","DOI":"10.15252\/msb.20209982","article-title":"Reproducibility in systems biology modelling","volume":"17","author":"Tiwari","year":"2021","journal-title":"Mol Syst Biol"},{"issue":"1","key":"2024051308554518000_ref71","doi-asserted-by":"crossref","first-page":"369","DOI":"10.1186\/s12967-020-02540-4","article-title":"Credible practice of modeling and simulation in healthcare: ten rules from a multidisciplinary perspective","volume":"18","author":"Erdemir","year":"2020","journal-title":"J Transl Med"},{"issue":"1","key":"2024051308554518000_ref72","doi-asserted-by":"crossref","first-page":"369","DOI":"10.1186\/s12859-014-0369-z","article-title":"COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project","volume":"15","author":"Bergmann","year":"2014","journal-title":"BMC Bioinformatics"},{"issue":"16","key":"2024051308554518000_ref73","doi-asserted-by":"crossref","first-page":"2367","DOI":"10.1093\/bioinformatics\/btu210","article-title":"The cell behavior ontology: describing the intrinsic biological behaviors of real and model cells seen as active agents","volume":"30","author":"Sluka","year":"2014","journal-title":"Bioinformatics"},{"key":"2024051308554518000_ref74","doi-asserted-by":"crossref","first-page":"136","DOI":"10.1038\/s41597-020-0477-8","article-title":"COVID-19 Disease Map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms","volume":"7","author":"Ostaszewski","year":"2020","journal-title":"Sci Data"},{"issue":"12","key":"2024051308554518000_ref75","doi-asserted-by":"crossref","first-page":"1781","DOI":"10.1093\/bioinformatics\/btaa864","article-title":"Identifiers.org: Compact Identifier services in the cloud","volume":"37","author":"Bernal-Llinares","year":"2021","journal-title":"Bioinformatics"},{"key":"2024051308554518000_ref76","article-title":"COVIDGraph: Connecting biomedical COVID-19 resources and computational biology models","author":"G\u00fctebier","year":"2021","journal-title":"2nd Workshop on Search, Exploration, and Analysis in \u2026"}],"container-title":["Briefings in Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bib\/article-pdf\/23\/4\/bbac212\/57554122\/bbac212.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bib\/article-pdf\/23\/4\/bbac212\/57554122\/bbac212.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,5,13]],"date-time":"2024-05-13T09:24:17Z","timestamp":1715592257000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bib\/article\/doi\/10.1093\/bib\/bbac212\/6603929"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,6,8]]},"references-count":76,"journal-issue":{"issue":"4","published-print":{"date-parts":[[2022,7,18]]}},"URL":"https:\/\/doi.org\/10.1093\/bib\/bbac212","relation":{},"ISSN":["1467-5463","1477-4054"],"issn-type":[{"value":"1467-5463","type":"print"},{"value":"1477-4054","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2022,7]]},"published":{"date-parts":[[2022,6,8]]},"article-number":"bbac212"}}