Skip Navigation



Bioinformatics Advance Access published online on May 18, 2006
Bioinformatics, doi:10.1093/bioinformatics/btl195
This Article
Right arrow Advance Access manuscript (PDF) Freely available
Right arrow All Versions of this Article:
22/15/1879    most recent
btl195v1
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 Gauges, R.
Right arrow Articles by Wegner, K.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Gauges, R.
Right arrow Articles by Wegner, K.
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 March 29, 2006
Revised May 10, 2006
Accepted May 15, 2006

Article

A model diagram layout extension for SBML

Ralph Gauges 1 *, Ursula Rost 1, Sven Sahle 1, and Katja Wegner 1

1 Bioinformatics and Computational Biochemistry, EML Research, Schloss-Wolfsbrunnen Weg 33, D-69118 Heidelberg, Germany

* To whom correspondence should be addressed.
Ralph Gauges, E-mail: Ralph.Gauges{at}eml-r.villa-bosch.de


  Abstract

Motivation: Since the knowledge about processes in living cells is increasing, modeling and simulation techniques are used to get new insights into these complex processes. During the last few years, the SBML file format has gained in popularity and support as a means of exchanging model data between the different modeling and simulation tools. In addition to specifying the model as a set of equations, many modern modeling tools allow the user to create and interact with the model in the form of a reaction graph. Unfortunately, the SBML file format does not provide for the storage of this graph data along with the mathematical description of the model.

Results: Therefore, we developed an extension to the SBML file format that makes it possible to store such layout information which describes position and size of objects in the graphical representation.

Availability: The complete specification can be found on [1]. Additionally, a complete implementation exists as part of libSBML [2].

Associate Editor: Martin Bishop
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
 BioinformaticsHome page
K. Kojima, M. Nagasaki, and S. Miyano
Fast grid layout algorithm for biological networks with sweep calculation
Bioinformatics, June 15, 2008; 24(12): 1433 - 1441.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
A. Deckard, F. T. Bergmann, and H. M. Sauro
Supporting the SBML layout extension
Bioinformatics, December 1, 2006; 22(23): 2966 - 2967.
[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.