The DOI matches its Crossref record; 11 of the 11 references it cites were found in a registry or an index.
Evolving a lingua franca and associated software infrastructure for computational systems biology: the Systems Biology Markup Language (SBML) project
Abstract
Biologists are increasingly recognising that computational modelling is crucial for making sense of the vast quantities of complex experimental data that are now being collected. The systems biology field needs agreed-upon information standards if models are to be shared, evaluated and developed cooperatively. Over the last four years, our team has been developing the Systems Biology Markup Language (SBML) in collaboration with an international community of modellers and software developers. SBML has become a de facto standard format for representing formal, quantitative and qualitative models at the level of biochemical reactions and regulatory networks. In this article, we summarise the current and upcoming versions of SBML and our efforts at developing software infrastructure for supporting and broadening its use. We also provide a brief overview of the many SBML-compatible software tools available today.
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Cites
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Self-citationA N EW A PPROACH TO D ECODING L IFE : Systems Biology
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COBRApy: COnstraints-Based Reconstruction and Analysis for Python
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Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology
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Corpus annotation for mining biomedical events from literature
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Rules for Modeling Signal-Transduction Systems
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Self-citationBio-PEPA: A framework for the modelling and analysis of biological systems
Ciocchetta, F., & Hillston, J. (2009) · Theoretical Computer Science · doi:10.1016/j.tcs.2009.02.037 · Cited by 335
Metadata
- Authors
- Hucka, M., Finney, A., Doyle, J. C., Kitano, H., Kovitz, B. L., Shapiro, B. E., Funahashi, A., Matthews, J., Bornstein, B. J., Keating, S. M., & Schilstra, M. J.
- Venue
- Systems Biology
- Published
- 2004-06-01
- Volume
- 1
- Issue
- 1
- Pages
- 41-53
- ISSN
- 1741-2471 (ISSN-L)
- 1741-248X
- OpenAlex
- W2100525485
- Cited by
- 232
- References
- 11
- FWCI
- 6.01
- Type
- journal article
- Language
- en
- Open access
- closed
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- The paper
- Hucka, M., Finney, A., Doyle, J. C., Kitano, H., Kovitz, B. L., Shapiro, B. E., Funahashi, A., Matthews, J., Bornstein, B. J., Keating, S. M., & Schilstra, M. J. (2004). Evolving a lingua franca and associated software infrastructure for computational systems biology: the Systems Biology Markup Language (SBML) project. Systems Biology. https://doi.org/10.1049/sb%3A20045008
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