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The Systems Biology Research Tool: evolvable open-source software


Wright, J; Wagner, A (2008). The Systems Biology Research Tool: evolvable open-source software. BMC Systems Biology, 2:55.

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.

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.

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31 citations in Web of Science®
35 citations in Scopus®
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80 downloads since deposited on 23 Sep 2008
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Additional indexing

Item Type:Journal Article, refereed, original work
Communities & Collections:04 Faculty of Medicine > Department of Biochemistry
07 Faculty of Science > Department of Biochemistry

Special Collections > SystemsX.ch
Special Collections > SystemsX.ch > Research, Technology and Development Projects > YeastX
Dewey Decimal Classification:570 Life sciences; biology
Language:English
Date:June 2008
Deposited On:23 Sep 2008 07:31
Last Modified:03 Aug 2017 14:52
Publisher:BioMed Central
ISSN:1752-0509
Additional Information:Free full text article
Free access at:PubMed ID. An embargo period may apply.
Publisher DOI:https://doi.org/10.1186/1752-0509-2-55
PubMed ID:18588708

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Licence: Creative Commons: Attribution 2.0 Generic (CC BY 2.0)