Skip Navigation

Bioinformatics 2008 24(16):i227-i233; doi:10.1093/bioinformatics/btn275
This Article
Right arrow Full Text Freely available
Right arrow FREE Full Text (Print PDF) Freely available
Right arrow Comments: Submit a response
Right arrow Alert me when this article is cited
Right arrow Alert me when Comments are posted
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 Monteiro, P. T.
Right arrow Articles by de Jong, H.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Monteiro, P. T.
Right arrow Articles by de Jong, H.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© The Author 2008. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Temporal logic patterns for querying dynamic models of cellular interaction networks

Pedro T. Monteiro 1,2,3, Delphine Ropers 1, Radu Mateescu 1, Ana T. Freitas 2 and Hidde de Jong 1,*

1INRIA Grenoble - Rhône-Alpes, 655 Av. de l’Europe, Montbonnot, 38334 St. Ismier Cedex, France, 2IST/INESC-ID, 9 Rua Alves Redol, 1000-029 Lisbon, Portugal and 3Université Claude Bernard Lyon 1, 43 Bvd. du 11 Nov. 1918, 69622, Villeurbanne Cedex, France

*To whom correspondence should be addressed.


  Abstract

Motivation: Models of the dynamics of cellular interaction networks have become increasingly larger in recent years. Formal verification based on model checking provides a powerful technology to keep up with this increase in scale and complexity. The application of modelchecking approaches is hampered, however, by the difficulty for nonexpert users to formulate appropriate questions in temporal logic.

Results: In order to deal with this problem, we propose the use of patterns, that is, high-level query templates that capture recurring biological questions and can be automatically translated into temporal logic. The applicability of the developed set of patterns has been investigated by the analysis of an extended model of the network of global regulators controlling the carbon starvation response in Escherichia coli.

Availability: GNA and the model of the carbon starvation response network are available at http://www-helix.inrialpes.fr/gna

Contact: Hidde.de-Jong{at}inrialpes.fr


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


This article has been cited by other articles:


Home page
 Brief BioinformHome page
A. Csikasz-Nagy
Computational systems biology of the cell cycle
Brief Bioinform, July 1, 2009; 10(4): 424 - 434.
[Abstract] [Full Text] [PDF]


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.