JSBML 1.0: providing a smorgasbord of options to encode systems biology models
Open accessAbstract
Summary: JSBML, the official pure Java programming library for the Systems Biology Markup Language (SBML) format, has evolved with the advent of different modeling formalisms in systems biology and their ability to be exchanged and represented via extensions of SBML. JSBML has matured into a major, active open-source project with contributions from a growing, international team of developers who not only maintain compatibility with SBML, but also drive steady improvements to the Java interface and promote ease-of-use with end users. Availability and implementation: Source code, binaries and documentation for JSBML can be freely obtained under the terms of the LGPL 2.1 from the website http://sbml.org/Software/JSBML. More information about JSBML can be found in the user guide at http://sbml.org/Software/JSBML/docs/. Contact: jsbml-development@googlegroups.com or andraeger@eng.ucsd.edu Supplementary information: Supplementary data are available at Bioinformatics online.
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- Authors
- Rodriguez, N., Thomas, A., Watanabe, L., Vazirabad, I. Y., Kofia, V., Gómez, H. F., Mittag, F., Matthes, J., Rudolph, J., Wrzodek, F., Netz, E., Diamantikos, A., Eichner, J., Keller, R., Wrzodek, C., Fröhlich, S., Lewis, N. E., Myers, C. J., Le Novère, N., Palsson, B. Ø., Hucka, M., & Dräger, A.
- Affiliations
- 1 European Bioinformatics Institute (EBI), Hinxton, UK,
- University of California San Diego (US)
- University of Utah (US)
- Marquette University (US)
- University of Toronto (CA)
- Boston University (US)
- European Bioinformatics Institute (GB)
- University of Tübingen (DE)
- Tel Aviv University (IL)
- Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK) (DE)
- California Institute of Technology (US)
- Corresponding author
- Thomas, Alex
- Dräger, Andreas
- ORCID
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2015-06-16
- Volume
- 31
- Issue
- 20
- Pages
- 3383-3386
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- PMC
- PMC4595895
- OpenAlex
- W2159739447
- Cited by
- 37
- References
- 24
- Citations by year
- 2025: 1 · 2024: 2 · 2023: 1 · 2022: 1 · 2021: 9 · 2020: 6 · 2019: 2 · 2018: 6 · 2017: 3 · 2016: 2 · 2015: 3
- FWCI
- 2.03
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Locations
- Bioinformatics (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- CaltechAUTHORS (California Institute of Technology) (submittedVersion, cc-by)
- eScholarship (California Digital Library) (submittedVersion, cc-by)
- eScholarship (California Digital Library) (submittedVersion)
- HighWire Press Open Archive (submittedVersion)
- Technical University of Denmark, DTU Orbit (Technical University of Denmark, DTU) (submittedVersion, other-oa)
- Funders
- National Science Foundation (0315756, 1218095)
- European Commission (332020, 242167)
- Deutsche Forschungsgemeinschaft
- Bundesministerium für Bildung und Forschung (0315756)
- Novo Nordisk
- Danmarks Tekniske Universitet
- Novo Nordisk Fonden (NNF10CC1016517)
- National Institutes of Health (HHSN272201000053C)
- Seventh Framework Programme (242167)
- Biotechnology and Biological Sciences Research Council (BBS/E/B/000C0419)
- National Institute of General Medical Sciences (GM070923, R01GM070923)
- National Institute of Allergy and Infectious Diseases (HHSN272201000053C)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene Regulatory Network Analysis
- Social Sciences › Decision Sciences › Information Systems and Management › Scientific Computing and Data Management
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Keywords
- SBML, Java library, model exchange, open source software
- MeSH terms
- Computer Simulation, Models, Biological, Programming Languages, Software, Systems Biology
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