title: 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.
authors.affiliation: Keck Graduate Institute, Claremont, California 91711, USA.
authors.forename: Herbert M
authors.initials: HM
authors.lastname: Sauro
authors.forename: Michael
authors.initials: M
authors.lastname: Hucka
authors.forename: Andrew
authors.initials: A
authors.lastname: Finney
authors.forename: Cameron
authors.initials: C
authors.lastname: Wellock
authors.forename: Hamid
authors.initials: H
authors.lastname: Bolouri
authors.forename: John
authors.initials: J
authors.lastname: Doyle
authors.forename: Hiroaki
authors.initials: H
authors.lastname: Kitano
mesh_terms: D001669:Biochemical Phenomena; D001671:Biochemistry; D003198:Computer Simulation; D003199:Computer Systems; D008954:Models, Biological; D012984:Software; D013598:Systems Theory