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Bioinformatics Advance Access published online on October 11, 2006
Bioinformatics, doi:10.1093/bioinformatics/btl520
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© The Author (2006). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
Received August 11, 2006
Revised October 6, 2006
Accepted October 8, 2006

Applications note

Supporting the SBML layout extension

Anastasia Deckard 1, Frank T. Bergmann 1 *, and Herbert M. Sauro 1

1 Keck Graduate Institute, 535 Watson Dr, Claremont, CA 91711

* To whom correspondence should be addressed.
Frank T. Bergmann, E-mail: fbergman{at}kgi.edu


  Abstract

Motivation: Researchers studying large or complex biochemical networks would benefit from the ability to automatically create lucid visualizations and store them in a portable and widely accepted format.

Summary: Two modules, SBMLSupportLayout and SBWAutoLayout, support reading, creating, manipulating, and writing layout information for biochemical models. SBMLSupportLayout can read, update, add, and render model layout information. SBWAutoLayout can automatically layout models, graphically manipulate model layout, and generate layout information for models without layout information.

Availability: SBMLSupportLayout and SBWAutoLayout are distributed with the Systems Biology Workbench (SBW), which can be downloaded from http://www.sys-bio.org. Additionally, their visualization and layout capabilities are available online at http://www.sys-bio.org/Layout. Both modules run on Win32, Linux, and the Mac OS X version is forthcoming.

Associate Editor: Nikolaus Rajewsky
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