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Bioinformatics Advance Access published online on March 16, 2006
Bioinformatics, doi:10.1093/bioinformatics/btl091
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© The Author (2006). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
Received January 3, 2006
Revised March 7, 2006
Accepted March 7, 2006

Applications note

WebCell: a web-based environment for kinetic modeling and dynamic simulation of cellular networks

Dong-Yup Lee 1 {dagger}, Choamun Yun 2 {dagger}, Ayoun Cho 3, Bo Kyeng Hou 4, Sunwon Park 5, and Sang Yup Lee 6 *

1 Department of Chemical and Biomolecular Engineering, Metabolic and Biomolecular Engineering National Research Laboratory, 373-1 Guseong-dong, Yuseong-gu, Daejeon 305-701, Korea; Bioinformatics Research Center, 373-1 Guseong-dong, Yuseong-gu, Daejeon 305-701, Korea; Present address: Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore 117576, and Bioprocessing Technology Institute, Agency for Science and Technology Research (A*STAR), 20 Biopolis Way, #06-01, Centros, Singapore 138668
2 Department of Chemical and Biomolecular Engineering, Metabolic and Biomolecular Engineering National Research Laboratory, 373-1 Guseong-dong, Yuseong-gu, Daejeon 305-701, Korea; Bioinformatics Research Center, 373-1 Guseong-dong, Yuseong-gu, Daejeon 305-701, Korea
3 Department of Chemical and Biomolecular Engineering, Metabolic and Biomolecular Engineering National Research Laboratory
4 Bioinformatics Research Center, 373-1 Guseong-dong, Yuseong-gu, Daejeon 305-701, Korea
5 Department of Chemical and Biomolecular Engineering, Metabolic and Biomolecular Engineering National Research Laboratory,
6 Department of Chemical and Biomolecular Engineering, Metabolic and Biomolecular Engineering National Research Laboratory, 373-1 Guseong-dong, Yuseong-gu, Daejeon 305-701, Korea; Bioinformatics Research Center, 373-1 Guseong-dong, Yuseong-gu, Daejeon 305-701, Korea; Department of BioSystems, Korea Advanced Institute of Science and Technology, 373-1 Guseong-dong, Yuseong-gu, Daejeon 305-701, Korea

* To whom correspondence should be addressed.
Sang Yup Lee, E-mail: leesy{at}kaist.ac.kr


  Abstract

Summary: WebCell is a web-based environment for managing quantitative and qualitative information on cellular networks, and for interactively exploring their steady-state and dynamic behaviors in response to systemic perturbations. It is designed as a user-friendly web interface, allowing users to efficiently construct, visualize, analyze and store reaction network models, thereby facilitating kinetic modeling and in silico simulation of biological systems of interest. A collected model library is also available to provide comprehensive implications for cellular dynamics of the published models.

Availability: WebCell is accessible at http://webcell.kaist.ac.kr or http://webcell.org.

Associate Editor: Alfonso Valencia

{dagger}These authors contributed equally to this work.


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