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Bioinformatics Advance Access originally published online on October 11, 2006
Bioinformatics 2006 22(23):2966-2967; 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

Supporting the SBML layout extension

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

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

*To whom correspondence should be addressed.

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.

Contact: fbergman{at}kgi.edu

Received on August 11, 2006; revised on October 6, 2006; accepted on October 8, 2006

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