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Next Generation Simulation Tools: The Systems Biology Workbench and BioSPICE Integration
Abstract
Researchers in quantitative systems biology make use of a large number of different software packages for modelling, analysis, visualization, and general data manipulation. In this paper, we describe the Systems Biology Workbench (SBW), a software framework that allows heterogeneous application components—written in diverse programming languages and running on different platforms—to communicate and use each others' capabilities via a fast binary encoded-message system. Our goal was to create a simple, high performance, opensource software infrastructure which is easy to implement and understand. SBW enables applications (potentially running on separate, distributed computers) to communicate via a simple network protocol. The interfaces to the system are encapsulated in client-side libraries that we provide for different programming languages. We describe in this paper the SBW architecture, a selection of current modules, including Jarnac, JDesigner, and SBWMeta-tool, and the close integration of SBW into BioSPICE, which enables both frameworks to share tools and compliment and strengthen each others capabilities.
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Citations
Cited by
COPASI—a COmplex PAthway SImulator
Hoops, S., Sahle, S., Gauges, R., Lee, C., Pahle, J., Simus, N., Singhal, M., Xu, L., Mendes, P., & Kummer, U. (2006) · Bioinformatics · doi:10.1093/bioinformatics/btl485 · Cited by 2,618
Cell-signalling dynamics in time and space
Kholodenko, B. N. (2006) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm1838 · Cited by 1,347
Genetic circuit design automation
Nielsen, A. A. K., Der, B. S., Shin, J., Vaidyanathan, P., Paralanov, V., Strychalski, E. A., Ross, D., Densmore, D., & Voigt, C. A. (2016) · Science · doi:10.1126/science.aac7341 · Cited by 1,020
The systems biology graphical notation.
Novère, N. L., Hucka, M., Mi, H., Moodie, S., Schreiber, F., Sorokin, A., Demir, E., Wegner, K., Aladjem, M. I., Wimalaratne, S. M., et al. (2009) · Nature Biotechnology · doi:10.1038/nbt.1558 · Cited by 903
Self-citationThe BioPAX community standard for pathway data sharing
Demir, E., Cary, M. P., Paley, S., Fukuda, K., Lemer, C., Vastrik, I., Wu, G., D'Eustachio, P., Schaefer, C., Luciano, J., et al. (2010) · Nature Biotechnology · doi:10.1038/nbt.1666 · Cited by 745
“However, BioPAX addresses this need by coor-dinating work (as described below) with the SBML and CellML mathematical modeling language communities 55,56 and a growing software tool set supporting biological process simulation 57 .”
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Metadata
- Authors
- Sauro, H. M., Hucka, M., Finney, A., Wellock, C., Bolouri, H., Doyle, J., & Kitano, H.
- Venue
- OMICS: A Journal of Integrative Biology
- Publisher
- SAGE Publications
- Published
- 2003-12
- Volume
- 7
- Issue
- 4
- Pages
- 355-372
- ISSN
- 1536-2310 (ISSN-L)
- 1557-8100
- OpenAlex
- W1495660511
- Cited by
- 285
- References
- 0
- FWCI
- 54.95
- Type
- journal article
- Language
- en
- Open access
- closed
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- Sauro, H. M., Hucka, M., Finney, A., Wellock, C., Bolouri, H., Doyle, J., & Kitano, H. (2003). Next Generation Simulation Tools: The Systems Biology Workbench and BioSPICE Integration. OMICS: A Journal of Integrative Biology. https://doi.org/10.1089/153623103322637670
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Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
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