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Open Access Highly Accessed Software

The Systems Biology Research Tool: evolvable open-source software

Jeremiah Wright12* and Andreas Wagner123

Author Affiliations

1 Department of Biochemistry, University of Zurich, Zurich, Switzerland

2 Swiss Institute of Bioinformatics, Lausanne, Switzerland

3 Sante Fe Institute, Sante Fe, New Mexico, USA

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BMC Systems Biology 2008, 2:55  doi:10.1186/1752-0509-2-55

Published: 29 June 2008

Abstract

Background

Research in the field of systems biology requires software for a variety of purposes. Software must be used to store, retrieve, analyze, and sometimes even to collect the data obtained from system-level (often high-throughput) experiments. Software must also be used to implement mathematical models and algorithms required for simulation and theoretical predictions on the system-level.

Results

We introduce a free, easy-to-use, open-source, integrated software platform called the Systems Biology Research Tool (SBRT) to facilitate the computational aspects of systems biology. The SBRT currently performs 35 methods for analyzing stoichiometric networks and 16 methods from fields such as graph theory, geometry, algebra, and combinatorics. New computational techniques can be added to the SBRT via process plug-ins, providing a high degree of evolvability and a unifying framework for software development in systems biology.

Conclusion

The Systems Biology Research Tool represents a technological advance for systems biology. This software can be used to make sophisticated computational techniques accessible to everyone (including those with no programming ability), to facilitate cooperation among researchers, and to expedite progress in the field of systems biology.