Keck Computational Systems Biology

Some experimental settings:

Gravity:

Edge Length:

Use Magnetism

Use Boundary

Use Grid

SBML Layout Viewer

About the Layout Viewer (show more...)

This site takes an SBML File and renders it according to the SBML Layout Extension, or the JDesigner annotations.An experimental support for CellDesigner Model annotations (Annotation Version 2.5) has been added.

November 2007: The Render Extension used has been updated, so it would support also the render extension as proposed by the Eml Team. The advantage for visitors to this website is, that now the full rendering is available as SVG (Previously only the Layout (positions & dimensions) were available as SVG).

Update: The Layout algorithm used on this site has now been published: Supporting the SBML layout extension Anastasia Deckard; Frank T. Bergmann; Herbert M. Sauro, Bioinformatics 2006; doi: 10.1093/bioinformatics/btl520 Read more here: Full Article

This updated version of the Web Application features a different Layout algorithm implementing the the Becker-Rojas layout algorithms for reaction nets(Bioinformatics, vol. 17, no. 5, 2001, p. 461-467). This algorithm has been implemented by Katja Wegner (EML Research).

Now supporting TikZ

5/28/2010: The Layout viewer web application has been updated to also export the layout information in TikZ format. For this the open source converter sbml2tikz is used as library.

SBML File to visualize:
Image Format:
Overwrite Rendering with SBGN Stylesheet
Missing Reactant / Product:

Original Size | Scaled x2 | 640x480 | 1024x768 | SVG Export (experimental)

NEW: provided by sbml2tikz: TikZ Export | PDF Export

First version of the Render Extension schema:	level1.xsd
Information on the SBML Layout Extension:	villa-bosch.de
JDesigner1 annotation documentation:	JDSBMLEx.pdf
Get Loaded Model	Get Loaded Model with Layout/Render Extension

NOTE: This application runs on a development machine. Thus it is likely that I will be working while you are using this application. Hence clashes are possible. So please see this site as a demonstration feature. You also can find this Web application under: http://sys-bio.org/Layout with the advantage that i won't be working on the same machine ...