Computational Systems Biology
Sauro Lab
University of Washington
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Software Downloads:

1. SBW
2. JDesigner
3. Jarnac
5. Matlab Interface
6. Optimization
6. Bifurcation
maintained by Frank Bergmann

SBW AutoLayout

The SBW AutoLayout module automatically creates lucid layouts of biochemical models. The SBW AutoLayout module has a graphical user interface (GUI) and an application programming interface (API). The GUI provides a typical window application for using AutoLayout's functionality, while the API allows programmers to incorporate AutoLayout's functionality into their own programs.

Layout Features:

  • Automatically creates layouts for models
  • User controls parameters for automatic layout
  • Networks can be manually adjusted
  • Supports node (species) aliasing

Format Support:

  • Reads SBML Files
  • Supports layout information from SBML Layout Specification, JDesigner, and CellDesigner
  • Generates all necessary layout information for models with no previous layout information
  • Saves models and layout in SBML files that conforms to the SBML Layout Specification

Image Exporting:

  • Saves whole networks or screenshots of networks
  • Saves network images in raster formats (JPG, PNG, BMP)
  • Saves network images in vector format (PS)


For more information see the Features & Screenshots


The SBW AutoLayout module is installed with SBW. For more information see the SBW installation page.

The SBW AutoLayout module currently runs only on Windows, but we are working on Mac and Linux versions.

Documentation & Help


Deckard A, Bergmann FT, Sauro HM. Supporting the SBML layout extension. Bioinformatics. 2006 Oct 11;

sbw/autolayout.txt · Last modified: 2007/01/12 08:11 (external edit)

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