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MEMOSys: Bioinformatics platform for genome-scale metabolic models

Stephan Pabinger123, Robert Rader1, Rasmus Agren4, Jens Nielsen4 and Zlatko Trajanoski123*

Author Affiliations

1 Institute for Genomics and Bioinformatics, Graz University of Technology, Petersgasse 14, 8010 Graz, Austria

2 Christian Doppler Laboratory for Genomics and Bioinformatics, Petersgasse 14, 8010 Graz, Austria

3 Division for Bioinformatics, Innsbruck Medical University, Schöpfstrasse 45, 6020 Innsbruck, Austria

4 Department of Chemical and Biological Engineering, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden

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BMC Systems Biology 2011, 5:20  doi:10.1186/1752-0509-5-20

Published: 31 January 2011

Abstract

Background

Recent advances in genomic sequencing have enabled the use of genome sequencing in standard biological and biotechnological research projects. The challenge is how to integrate the large amount of data in order to gain novel biological insights. One way to leverage sequence data is to use genome-scale metabolic models. We have therefore designed and implemented a bioinformatics platform which supports the development of such metabolic models.

Results

MEMOSys (MEtabolic MOdel research and development System) is a versatile platform for the management, storage, and development of genome-scale metabolic models. It supports the development of new models by providing a built-in version control system which offers access to the complete developmental history. Moreover, the integrated web board, the authorization system, and the definition of user roles allow collaborations across departments and institutions. Research on existing models is facilitated by a search system, references to external databases, and a feature-rich comparison mechanism. MEMOSys provides customizable data exchange mechanisms using the SBML format to enable analysis in external tools. The web application is based on the Java EE framework and offers an intuitive user interface. It currently contains six annotated microbial metabolic models.

Conclusions

We have developed a web-based system designed to provide researchers a novel application facilitating the management and development of metabolic models. The system is freely available at http://www.icbi.at/MEMOSys webcite.