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Next generation simulation tools: the Systems Biology Workbench and BioSPICE integration.
| Content Provider | Semantic Scholar |
|---|---|
| Author | Sauro, Herbert M. Hucka, Michael Finney, Andrew Wellock, Cameron Bolouri, H. Doyle, John Kitano, Hiroaki |
| Copyright Year | 2003 |
| 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. |
| File Format | PDF HTM / HTML |
| DOI | 10.1089/153623103322637670 |
| Alternate Webpage(s) | http://authors.library.caltech.edu/35134/1/Sauro_2003p355.pdf |
| Alternate Webpage(s) | http://sbw.kgi.edu/pdfs/Omics.pdf |
| Alternate Webpage(s) | http://www.sys-bio.org/pdfs/Omics.pdf |
| Alternate Webpage(s) | http://www.cds.caltech.edu/~mhucka/publications/Sauro:Omics:2003.pdf |
| Alternate Webpage(s) | http://www.cds.caltech.edu/~mhucka/publications/sauro2003next.pdf |
| PubMed reference number | 14683609 |
| Alternate Webpage(s) | https://doi.org/10.1089/153623103322637670 |
| Journal | Medline |
| Volume Number | 7 |
| Issue Number | 4 |
| Journal | Omics : a journal of integrative biology |
| Language | English |
| Access Restriction | Open |
| Content Type | Text |
| Resource Type | Article |
