Paper Info
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.
Year
Venue
Keywords
2002
Pacific Symposium on Biocomputing
programming language,system biology,computational biology
Field
DocType
ISSN
Visualization,Computer science,Software system,Software,Bioinformatics,Data manipulation language,Computational biology,Resource-oriented architecture,Software development,Software framework,Communications protocol
Conference
2335-6936
Citations 
PageRank 
References 
21
3.55
0
Authors
6
Name
Order
Citations
PageRank
Hucka M11733170.84
Finney A2925111.69
Herbert M Sauro31330203.16
Bolouri H4849105.25
Doyle J C53437499.39
Hiroaki Kitano63515539.37