Next generation simulation tools: the Systems Biology Workbench and BioSPICE integration.
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.
Sauro
Herbert M
HM
Keck Graduate Institute, Claremont, California 91711, USA.
Hucka
Michael
M
Finney
Andrew
A
Wellock
Cameron
C
Bolouri
Hamid
H
Doyle
John
J
Kitano
Hiroaki
H
D001669:Biochemical Phenomena; D001671:Biochemistry; D003198:Computer Simulation; D003199:Computer Systems; D008954:Models, Biological; D012984:Software; D013598:Systems Theory