Systems biology markup language: Level 2 and beyond
Abstract
The SBML (systems biology markup language) is a standard exchange format for computational models of biochemical networks. We continue developing SBML collaboratively with the modelling community to meet their evolving needs. The recently introduced SBML Level 2 includes several enhancements to the original Level 1, and features under development for SBML Level 3 include model composition, multistate chemical species and diagrams.
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SBML is the most widely used model format and the de facto language for systems biology models.
“The most widely used model format is SBML (Systems Biology Markup Language) [10, 13, 17, 18].”
From Adapting modeling and simulation credibility standards to computational systems biology (2023) · cites this paper as [18]
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Le Novere, N. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkj092 · Cited by 762 · see citing works
Minimum information requested in the annotation of biochemical models (MIRIAM)
Novère, N. L., Finney, A., Hucka, M., Bhalla, U. S., Campagne, F., Collado-Vides, J., Crampin, E. J., Halstead, M., Klipp, E., Mendes, P., et al. (2005) · Nature Biotechnology · doi:10.1038/nbt1156 · Cited by 622 · see citing works
Self-citationCellML: its future, present and past
Lloyd, C. M., Halstead, M. D. B., & Nielsen, P. F. (2004) · Progress in Biophysics and Molecular Biology · doi:10.1016/j.pbiomolbio.2004.01.004 · Cited by 499 · see citing works
Rules for Modeling Signal-Transduction Systems
Hlavacek, W. S., Faeder, J. R., Blinov, M. L., Posner, R. G., Hucka, M., & Fontana, W. (2006) · Science's STKE · doi:10.1126/stke.3442006re6 · Cited by 350 · see citing works
Self-citationDynamical modeling and multi-experiment fitting with PottersWheel
Maiwald, T., & Timmer, J. (2008) · Bioinformatics · doi:10.1093/bioinformatics/btn350 · Cited by 231 · see citing works
Modeling formalisms in Systems Biology
Machado, D., Costa, R. S., Rocha, M., Ferreira, E. C., Tidor, B., & Rocha, I. (2011) · AMB Express · doi:10.1186/2191-0855-1-45 · Cited by 189 · see citing works
Schaber, J., & Klipp, E. (2011) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2010.09.014 · Cited by 33 · see citing works
Adapting modeling and simulation credibility standards to computational systems biology
Tatka, L. T., Smith, L. P., Hellerstein, J. L., & Sauro, H. M. (2023) · Journal of Translational Medicine · doi:10.1186/s12967-023-04290-5 · Cited by 25 · see citing works
- Authors
- Finney, A., & Hucka, M.
- Affiliations
- University of Hertfordshire (GB)
- California Institute of Technology (US)
- Corresponding author
- Finney, A.
- ORCID
- Hucka, M.
- Venue
- Biochemical Society Transactions
- Publisher
- Portland Press Ltd.
- Published
- 2003-12-01
- Volume
- 31
- Issue
- 6
- Pages
- 1472-1473
- ISSN
- 0300-5127 (ISSN-L)
- 1470-8752
- OpenAlex
- W2082621456
- Cited by
- 187
- References
- 0
- Citations by year
- 2026: 1 · 2025: 1 · 2023: 1 · 2021: 4 · 2020: 2 · 2019: 5 · 2018: 4 · 2017: 3 · 2016: 9 · 2015: 7 · 2014: 8 · 2013: 12 · 2012: 6
- FWCI
- 5.83
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Biochemical Society Transactions (publishedVersion)
- PubMed (publishedVersion)
- CaltechAUTHORS (California Institute of Technology) (submittedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene Regulatory Network Analysis
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Microbial Metabolic Engineering and Bioproduction
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Keywords
- SBML, biochemical network models, model exchange format, model composition, model diagrams
- MeSH terms
- Programming Languages, Computational Biology
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
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