Jan 5, 2016

A portable library to support the SBML Layout Extension

BioRxiv : the Preprint Server for Biology
J Kyle MedleyHerbert M Sauro

Abstract

The SBML layout extension enables SBML models to encode layout information which describes the graphical depiction of model elements. In this application note, we describe libSBNW, a portable library that supports the SBML layout extension and can automatically generate layout for SBML models. The library can be used to automatically generate layout information for SBML models lacking it, or to edit coordinate information already encoded in a model. We provide C and Python APIs to allow other applications to host the library or to use it directly from the Python console. We show that the library is sufficient for creating a graphical application for displaying and editing layout information. The library is open-source and licensed under the BSD 3-clause license. Project source code, downloads, documentation and binaries for Windows and Mac OS X are available at \href{https://github.com/sys-bio/sbnw}{https://github.com/sys-bio/sbnw}. The library is also included in Tellurium, available at http://tellurium.analogmachine.org/. Video tutorials are available at http://0u812.github.io/sbnw/tutorials/.

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