%0 Journal Article %1 Saur_2003_355 %A Sauro, Herbert M %A Hucka, Michael %A Finney, Andrew %A Wellock, Cameron %A Bolouri, Hamid %A Doyle, John %A Kitano, Hiroaki %D 2003 %J OMICS %K Biochemistry; Biological; Computer Gov't, Gov't; Models, Non-P.H.S.; Non-U.S. Research Simulation; Software; Support, Systems Systems; Theory U.S. %N 4 %P 355--372 %R 10.1089/153623103322637670 %T Next generation simulation tools: the Systems Biology Workbench and BioSPICE integration. %U http://dx.doi.org/10.1089/153623103322637670 %V 7 %X 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.

@article{Saur_2003_355, 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.}, added-at = {2009-06-03T11:20:58.000+0200}, author = {Sauro, Herbert M and Hucka, Michael and Finney, Andrew and Wellock, Cameron and Bolouri, Hamid and Doyle, John and Kitano, Hiroaki}, biburl = {https://www.bibsonomy.org/bibtex/2761a73ff5aa7716c8fd8dd656b59a030/hake}, description = {The whole bibliography file I use.}, doi = {10.1089/153623103322637670}, file = {Saur_2003_355.pdf:Saur_2003_355.pdf:PDF}, interhash = {d6e962bb55e0cec28b789ee6c8bf1497}, intrahash = {761a73ff5aa7716c8fd8dd656b59a030}, journal = {OMICS}, keywords = {Biochemistry; Biological; Computer Gov't, Gov't; Models, Non-P.H.S.; Non-U.S. Research Simulation; Software; Support, Systems Systems; Theory U.S.}, number = 4, pages = {355--372}, pmid = {14683609}, timestamp = {2009-06-03T11:21:28.000+0200}, title = {Next generation simulation tools: the Systems Biology Workbench and BioSPICE integration.}, url = {http://dx.doi.org/10.1089/153623103322637670}, volume = 7, year = 2003 }