title: The ERATO Systems Biology Workbench: enabling interaction and exchange between software tools for computational biology.
abstract: Researchers in computational biology today make use of a large number of different software packages for modeling, analysis, and data manipulation and visualization. In this paper, we describe the ERATO Systems Biology Workbench (SBW), a software framework that allows these heterogeneous application components--written in diverse programming languages and running on different platforms--to communicate and use each others' data and algorithmic capabilities. Our goal is to create a simple, open-source software infrastructure which is effective, easy to implement and easy to understand. SBW uses a broker-based architecture and 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 the SBW architecture and the current set of modules, as well as alternative implementation technologies.
authors.affiliation: Control and Dynamical Systems, 107-81, California Institute of Technology, CA 91125, USA.
authors.forename: M
authors.initials: M
authors.lastname: Hucka
authors.forename: A
authors.initials: A
authors.lastname: Finney
authors.forename: H M
authors.initials: HM
authors.lastname: Sauro
authors.forename: H
authors.initials: H
authors.lastname: Bolouri
authors.forename: J
authors.initials: J
authors.lastname: Doyle
authors.forename: H
authors.initials: H
authors.lastname: Kitano
mesh_terms: D019295:Computational Biology / Q000379:methods*; D003195:Computer Communication Networks; D003198:Computer Simulation; D003199:Computer Systems; D011381:Programming Languages; D012984:Software; D013269:Stochastic Processes; D014584:User-Computer Interface