ReviewMolecular systems biology2020
SBML Level 3: an extensible format for the exchange and reuse of biological models.
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Review in Molecular systems biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 163 papers.
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163citing papers in PubMed
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Who cites it
163 citing papers in PubMed.
- Antimony 3: Extending human-readable model definitions for SBML Level 3 Core and Packages.PLoS computational biology · 2026Article
- Process bigraphs and the architecture of compositional systems biology.PLoS computational biology · 2026Article
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- From prior knowledge to data-informed models: a review of Boolean network inference.Briefings in bioinformatics · 2026Review
- Quantitative Modeling of TLR Signaling Reveals Missing Negative Feedback Guiding Identification of TANK-IKKε Checkpoint.bioRxiv : the preprint server for biology · 2026Article
- Article
- EHMN2026Metabolites · 2026Article
- Virtual twins and the future of human developmental biology.NPJ systems biology and applications · 2026Review
- How far can you go? Extrapolating values of catalytic activity from known protein landscapes in natural and directed evolution.Chemical Society reviews · 2026Review
- TabularQual: A spreadsheet-based format for annotating and curating logical models in SBML-qual.bioRxiv : the preprint server for biology · 2026Article
- Antimony 3: Extending human-readable model definitions for SBML Level 3 Core and Packages.bioRxiv : the preprint server for biology · 2026Article
- A Guide to Bayesian Optimization in Bioprocess Engineering.Biotechnology and bioengineering · 2026Review
- EHMN 2026: A Thermodynamically Refined, SBML-Standardised Human Metabolic Network for Genome-Scale Analysis and QSP Integration.Metabolites · 2026Article
- From FAIR to CURE: guidelines for computational models of biological systems.NPJ systems biology and applications · 2026Review
- PEtab-GUI: a graphical user interface to create, edit, and inspect PEtab parameter estimation problems.Bioinformatics (Oxford, England) · 2026Article
- A Physiologically Based Pharmacokinetic and Pharmacodynamic (PBPK/PD) Model of Dapagliflozin in Type 2 Diabetes Mellitus: The Effect of Dosing, Hepatorenal Impairment, and Food.Pharmaceutics · 2026Article
- A Digital Twin of the Angiotensin II Receptor Blocker Losartan: Physiologically Based Modeling of Blood Pressure Regulation.Pharmaceutics · 2026Article
- MCC: automated mass and charge curation at the genome scale applied toMicrobiology spectrum · 2026Article
- BioModelsRAG: A Biological Modeling Assistant Using RAG (Retrieval Augmented Generation).ArXiv · 2026Article
- Synthetic Biology of Plants and Microbes for Agriculture, Environment, and Future Applications.Chemical reviews · 2026Review
103 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
53 authors.
Sarah M Keating *Computing and Mathematical Sciences, California Institute of Technology, Pasadena, CA, USA.ORCID 0000-0002-3356-3542
Dagmar Waltemath *Medical Informatics, Institute for Community Health, University Medicine Greifswald, Greifswald, Germany.ORCID 0000-0002-5886-5563
Matthias KönigInstitute for Theoretical Biology, Humboldt-University Berlin, Berlin, Germany.ORCID 0000-0003-1725-179X
Fengkai ZhangLaboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.ORCID 0000-0001-7112-9328
Andreas DrägerComputational Systems Biology of Infection and Antimicrobial-Resistant Pathogens, Institute for Biomedical Informatics (IBMI), University of Tübingen, Tübingen, Germany.ORCID 0000-0002-1240-5553
Claudine ChaouiyaAix-Marseille Université, CNRS, Centrale Marseille, Marseille, France.ORCID 0000-0003-2350-0756
Frank T BergmannBioQuant/COS, Heidelberg University, Heidelberg, Germany.ORCID 0000-0001-5553-4702
Andrew FinneyANSYS UK Ltd, Milton Park, Oxfordshire, UK.
Colin S GillespieSchool of Mathematics, Statistics and Physics, Newcastle University, Newcastle upon Tyne, UK.ORCID 0000-0003-1787-0275
Tomáš HelikarDepartment of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, USA.ORCID 0000-0003-3653-1906
Stefan HoopsBiocomplexity Institute & Initiative, University of Virginia, Charlottesville, VA, USA.ORCID 0000-0001-8503-8371
Rahuman S Malik-SheriffEuropean Bioinformatics Institute, European Molecular Biology Laboratory (EMBL-EBI), Hinxton, UK.ORCID 0000-0003-0705-9809
Stuart L MoodieEight Pillars Ltd, Edinburgh, UK.ORCID 0000-0001-6191-5595
Ion I MoraruCenter for Cell Analysis and Modeling, UConn Health, Farmington, CT, USA.ORCID 0000-0002-3746-9676
Chris J MyersDepartment of Electrical and Computer Engineering, University of Utah, Salt Lake City, UT, USA.ORCID 0000-0002-8762-8444
Aurélien NaldiInstitut de Biologie de l'ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France.ORCID 0000-0002-6495-2655
Brett G OlivierComputing and Mathematical Sciences, California Institute of Technology, Pasadena, CA, USA.ORCID 0000-0002-5293-5321
Sven SahleBioQuant/COS, Heidelberg University, Heidelberg, Germany.
James C SchaffApplied BioMath, LLC, Concord, MA, USA.ORCID 0000-0003-3286-7736
Lucian P SmithComputing and Mathematical Sciences, California Institute of Technology, Pasadena, CA, USA.ORCID 0000-0001-7002-6386
Maciej J SwatSimcyp (a Certara company), Sheffield, South Yorkshire, UK.
Denis ThieffryInstitut de Biologie de l'ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France.ORCID 0000-0003-0271-1757
Leandro WatanabeDepartment of Electrical and Computer Engineering, University of Utah, Salt Lake City, UT, USA.ORCID 0000-0001-7030-8690
Darren J WilkinsonSchool of Mathematics, Statistics and Physics, Newcastle University, Newcastle upon Tyne, UK.ORCID 0000-0003-0736-802X
Michael L BlinovCenter for Cell Analysis and Modeling, UConn Health, Farmington, CT, USA.ORCID 0000-0002-9363-9705
Kimberly BegleyCalifornia Institute of Technology, Pasadena, CA, USA.ORCID 0000-0002-1642-7493
James R FaederDepartment of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA.ORCID 0000-0001-8127-609X
Harold F GómezDepartment of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland.
Thomas M HammComputational Systems Biology of Infection and Antimicrobial-Resistant Pathogens, Institute for Biomedical Informatics (IBMI), University of Tübingen, Tübingen, Germany.ORCID 0000-0001-9579-7267
Yuichiro InagakiManagement & IT Consulting Division, Mizuho Information & Research Institute, Inc., Tokyo, Japan.ORCID 0000-0003-4011-8487
Wolfram LiebermeisterUniversité Paris-Saclay, INRAE, MaIAGE, Jouy-en-Josas, France.ORCID 0000-0002-2568-2381
Allyson L ListerOxford e-Research Centre (OeRC), Department of Engineering Science, University of Oxford, Oxford, UK.ORCID 0000-0002-7702-4495
Daniel LucioCollege of Sciences, NC State University, Raleigh, NC, USA.ORCID 0000-0002-8912-7213
Eric MjolsnessDepartment of Computer Science, University of California, Irvine, CA, USA.ORCID 0000-0002-9085-9171
Carole J ProctorInstitute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK.ORCID 0000-0002-1366-1399
Karthik RamanDepartment of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology (IIT) Madras, Chennai, India.ORCID 0000-0002-9311-7093
Nicolas RodriguezThe Babraham Institute, Cambridge, UK.ORCID 0000-0002-9290-7894
Clifford A ShafferDepartment of Computer Science, Virginia Tech, Blacksburg, VA, USA.ORCID 0000-0003-0001-0295
Bruce E ShapiroDepartment of Mathematics, California State University, Northridge, CA, USA.
Joerg StellingDepartment of Biosystems Science and Engineering, SIB Swiss Institute of Bioinformatics, ETH Zürich, Basel, Switzerland.ORCID 0000-0002-1145-891X
Neil SwainstonInstitute of Integrative Biology, University of Liverpool, Liverpool, UK.ORCID 0000-0001-7020-1236
Naoki TanimuraScience Solutions Division, Mizuho Information & Research Institute, Inc., Tokyo, Japan.
John WagnerIBM Research Australia, Melbourne, Vic., Australia.
Martin Meier-SchellersheimLaboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.ORCID 0000-0002-8754-6377
Herbert M SauroDepartment of Bioengineering, University of Washington, Seattle, WA, USA.ORCID 0000-0002-3659-6817
Bernhard PalssonDepartment of Bioengineering, University of California San Diego, La Jolla, CA, USA.ORCID 0000-0003-2357-6785
Hamid BolouriSystems Immunology, Benaroya Research Institute at Virginia Mason, Seattle, WA, USA.
Hiroaki KitanoThe Systems Biology Institute, Tokyo, Japan.ORCID 0000-0002-3589-1953
Akira FunahashiDepartment of Biosciences and Informatics, Keio University, Yokohama, Kanagawa, Japan.ORCID 0000-0003-0605-239X
Henning HermjakobEuropean Bioinformatics Institute, European Molecular Biology Laboratory (EMBL-EBI), Hinxton, UK.ORCID 0000-0001-8479-0262
John C DoyleComputing and Mathematical Sciences, California Institute of Technology, Pasadena, CA, USA.ORCID 0000-0002-1828-2486
Michael HuckaComputing and Mathematical Sciences, California Institute of Technology, Pasadena, CA, USA.ORCID 0000-0001-9105-5960
SBML Level 3 Community members
Funding
TR&D 3 - Network Guided Machine LearningP41GM103504 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI IDEKER, TREY · 2012 to 2024
$17.3MTrainingP41GM103712 · NIGMS · UNIVERSITY OF PITTSBURGH AT PITTSBURGH · PI FAEDER, JAMES · 2012 to 2021
$16.3MRobust Software Components for Model Organism DatabasesR01GM075742 · NIGMS · SRI INTERNATIONAL · PI KARP, PETER D · 2005 to 2019
$12.0MTR&D3: Standards and Tools for Simulator Composition and Credibility portalP41EB023912 · NIBIB · UNIVERSITY OF WASHINGTON · PI Ion I. Moraru, HERBERT M. SAURO · 2018 to 2026
$11.4MTR&D4 Spatial Modeling: Modeling Framework for Cell MotilityP41GM103313 · NIGMS · UNIVERSITY OF CONNECTICUT SCH OF MED/DNT · PI LOEW, LESLIE M · 2012 to 2018
$9.7MProject I: Immunity to Influenza in Primary Lung Epithelial CellsU19AI117873 · NIAID · ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI · PI SEALFON, STUART C. · 2015 to 2019
$8.6MContinued Support of Essential SBML Software and Community ResourcesR01GM070923 · NIGMS · CALIFORNIA INSTITUTE OF TECHNOLOGY · PI HUCKA, MICHAEL · 2004 to 2018
$8.0MGENOMICALLY BASED MODELS FOR ANTIBIOTIC DEVELOPMENTR01GM057089 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI PALSSON, BERNHARD O · 1998 to 2021
$6.9MCOPASI software for modeling and simulation of biochemical networksR01GM080219 · NIGMS · VIRGINIA POLYTECHNIC INST AND ST UNIV · PI HOOPS, STEFAN, MENDES, PEDRO · 2007 to 2019
$5.4MSoftware for collaborative construction, simulation, and analysis of mechanistic computational models of biological systemsR35GM119770 · NIGMS · UNIVERSITY OF NEBRASKA LINCOLN · PI Tomas Helikar · 2016 to 2026
$4.4MHardening Software for Rule-based models-Competitive RevisionR01GM111510 · NIGMS · NORTHERN ARIZONA UNIVERSITY · PI HLAVACEK, WILLIAM S, POSNER, RICHARD G · 2014 to 2023
$2.8MToward whole-cell models for precision medicine and synthetic biologyR35GM119771 · NIGMS · ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI · PI KARR, JONATHAN ROSS · 2016 to 2020
$2.1MBiotechnology and Biological Sciences Research Council BB/M017702/1Biotechnology and Biological Sciences Research Council BB/N019482/1Cancer Research UK 26815NIAID NIH HHS U19 AI117873NIBIB NIH HHS P41 EB023912NIBIB NIH HHS U24 EB028887NIGMS NIH HHS P41 GM103313NIGMS NIH HHS P41 GM103504NIGMS NIH HHS P41 GM103712NIGMS NIH HHS R01 GM057089NIGMS NIH HHS R01 GM070923NIGMS NIH HHS R01 GM075742NIGMS NIH HHS R01 GM080219NIGMS NIH HHS R01 GM095485NIGMS NIH HHS R01 GM111510NIGMS NIH HHS R01 GM123032NIGMS NIH HHS R35 GM119770NIGMS NIH HHS R35 GM119771
Abstract
Systems biology has experienced dramatic growth in the number, size, and complexity of computational models. To reproduce simulation results and reuse models, researchers must exchange unambiguous model descriptions. We review the latest edition of the Systems Biology Markup Language (SBML), a format designed for this purpose. A community of modelers and software authors developed SBML Level 3 over the past decade. Its modular form consists of a core suited to representing reaction-based models and packages that extend the core with features suited to other model types including constraint-based models, reaction-diffusion models, logical network models, and rule-based models. The format leverages two decades of SBML and a rich software ecosystem that transformed how systems biologists build and interact with models. More recently, the rise of multiscale models of whole cells and organs, and new data sources such as single-cell measurements and live imaging, has precipitated new ways of integrating data with models. We provide our perspectives on the challenges presented by these developments and how SBML Level 3 provides the foundation needed to support this evolution.
Indexed as
AnimalsHumansLogistic ModelsModels, BiologicalSoftwareSystems Biologycomputational modelingfile formatinteroperabilityreproducibilitysystems biology
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