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Bioinformatics Advance Access originally published online on August 17, 2009
Bioinformatics 2009 25(21):2850-2852; doi:10.1093/bioinformatics/btp496
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© The Author 2009. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

WEbcoli: an interactive and asynchronous web application for in silico design and analysis of genome-scale E.coli model

Tae-Sung Jung 1,2, Hock Chuan Yeo 2, Satty G. Reddy 2, Wan-Sup Cho 1 and Dong-Yup Lee 2,3,*

1 Department of Information Industrial Engineering, CBITRC, Chungbuk National University, Cheongju Chungbuk 361-763, Korea, 2 Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, #06-01, Centros, Singapore 138668 and 3 Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore 117576

* To whom correspondence should be addressed.


  Abstract

Summary: WEbcoli is a WEb application for in silico designing, analyzing and engineering Escherichia coli metabolism. It is devised and implemented using advanced web technologies, thereby leading to enhanced usability and dynamic web accessibility. As a main feature, the WEbcoli system provides a user-friendly rich web interface, allowing users to virtually design and synthesize mutant strains derived from the genome-scale wild-type E.coli model and to customize pathways of interest through a graph editor. In addition, constraints-based flux analysis can be conducted for quantifying metabolic fluxes and charactering the physiological and metabolic states under various genetic and/or environmental conditions.

Availability: WEbcoli is freely accessible at http://webcoli.org.

Contact: cheld{at}nus.edu.sg

Associate Editor: Martin Bishop

Received on May 26, 2009; revised on August 12, 2009; accepted on August 13, 2009

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