Skip Navigation



Bioinformatics Advance Access published online on October 11, 2006
Bioinformatics, doi:10.1093/bioinformatics/btl497
This Article
Right arrow Advance Access manuscript (PDF) Freely available
Right arrow Supplementary Data
Right arrow All Versions of this Article:
22/23/2918    most recent
btl497v1
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Sanford, C.
Right arrow Articles by Parkinson, J.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Sanford, C.
Right arrow Articles by Parkinson, J.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© The Author (2006). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
Received June 1, 2006
Revised September 21, 2006
Accepted September 27, 2006

Article

Cell++ - simulating biochemical pathways

Chris Sanford 1 #, Matthew L. K. Yip 2 #, Carl White 1, and John Parkinson 3 *

1 Hospital for Sick Children, 555 University Avenue, Toronto, ON, M5G 1X8, Canada; Department of Medical Genetics and Microbiology, University of Toronto, Toronto, ON, Canada
2 Hospital for Sick Children, 555 University Avenue, Toronto, ON, M5G 1X8, Canada
3 Hospital for Sick Children, 555 University Avenue, Toronto, ON, M5G 1X8, Canada; Department of Medical Genetics and Microbiology, University of Toronto, Toronto, ON, Canada; Department of Biochemistry, University of Toronto, ON, Canada


  Abstract

Motivation: With the generation of a wealth of information detailing cellular components, their functions and interactions, there is a growing need for the development of new computational tools capable of interpreting these data within spatial and dynamic contexts. Here, we introduce Cell++, a novel stochastic simulation environment with the capacity to study a wide variety of biochemical processes within a spatial context.

Results: Focusing on three case studies, we highlight the potential impact of spatial organization in the evolution and engineering of signaling and metabolic pathways. In addition to altering signaling and metabolic efficiency, simulations also demonstrated features consistent with the phenomenon of metabolic channeling.

Availability: Cell++ is licensed under the GNU general public license (GPL) and has been successfully implemented under Linux and IRIX operating systems. Source code together with a simple tutorial is available at http://www.compsysbio.org/CellSim/.

Associate Editor: Martin Bishop

#These authors contributed equally to this work


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?




Disclaimer:
Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.