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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