SBML and CellML translation in Antimony and JSim
Open accessAbstract
Motivation: The creation and exchange of biologically relevant models is of great interest to many researchers. When multiple standards are in use, models are more readily used and re-used if there exist robust translators between the various accepted formats. Summary: Antimony 2.4 and JSim 2.10 provide translation capabilities from their own formats to SBML and CellML. All provided unique challenges, stemming from differences in each format’s inherent design, in addition to differences in functionality. Availability and implementation: Both programs are available under BSD licenses; Antimony from http://antimony.sourceforge.net/ and JSim from http://physiome.org/jsim/. Contact: lpsmith@u.washington.edu
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There is more third party support for SBML and it is semantically richer compared to CellML.
“There is more third party support for SBML and it is a semantically richer language compared to CellML [13, 28].”
From Adapting modeling and simulation credibility standards to computational systems biology (2023) · cites this paper as [28]
The Introduction (page unavailable) says CellML is not inherently semantically rich in the same way as SBML, supporting the semantic comparison. It describes software tools that import both formats but does not establish that SBML has more third-party support than CellML. (LLM, conf=0.87)
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Cites
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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
Self-citation
- Authors
- Smith, L. P., Butterworth, E., Bassingthwaighte, J. B., & Sauro, H. M.
- Affiliations
- University of Washington (US)
- Corresponding author
- Smith, Lucian P.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2013-11-08
- Volume
- 30
- Issue
- 7
- Pages
- 903-907
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- PMC
- PMC3967103
- OpenAlex
- W2139035000
- Cited by
- 18
- References
- 17
- Citations by year
- 2026: 1 · 2024: 1 · 2023: 1 · 2020: 1 · 2019: 1 · 2016: 5 · 2015: 1 · 2014: 6 · 2013: 1
- FWCI
- 1.94
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- public-domain
- Locations
- Bioinformatics (publishedVersion, public-domain)
- Europe PMC (PubMed Central) (publishedVersion, public-domain)
- PubMed Central (publishedVersion, public-domain)
- PubMed (publishedVersion)
- Funders
- National Institutes of Health
- National Heart, Lung, and Blood Institute (T15HL088516)
- National Institute of General Medical Sciences (P50GM094503, R01GM081070)
- National Institute of Biomedical Imaging and Bioengineering (1R01EB08407, R01EB008407)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene Regulatory Network Analysis
- Physical Sciences › Computer Science › Computational Theory and Mathematics › Modeling and Simulation Systems
- Social Sciences › Decision Sciences › Information Systems and Management › Scientific Computing and Data Management
- Keywords
- SBML, CellML, antimony, model translation, model exchange, model interoperability
- MeSH terms
- Computer Simulation, Models, Biological, Software, Cluster Analysis, Systems Biology
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