Cytoscape SBML Reader Plugin

Introduction

This directory contains a copy of the Cytoscape SBML Reader plugin, which allows you to load an SBML file from Cytoscape's File menu. Only level 1 SBML is currently supported. Many of the SBML's model attributes and relations are translated into Cytoscape node and edge attributes.

In order to achieve the best display of the model, and in addition to simply installing the plugin, two further steps are required:

  1. Use the SBML visual style. Visual styles are selected from the pulldown menu at the right side of the main menu bar. To use this style, however, you must first have a copy of it on your computer. The simplest way to get this, for now (October 2003) is to run the Java Web Start version of this reader (click here), which will automatically install the SBML visual style into the collection of visual styles Cytoscape maintains on your computer. (Before long, we will provide a web site from which you can download visual styles.)

  2. From the Layout menu, choose the Hierarchical option.

Installation Instructions

To use the SBML Reader plugin, you must first obtain a copy of Cytoscape, Version 1.1. You can download a copy from: http://www.cytsoscape.org. Once you have downloaded Cytoscape and verified that it works, proceed with the next steps.
  1. Copy the SBMLReader.jar file to your [Cytoscape_Home]/plugins directory.

  2. Restart Cytoscape. For example, on Unix/Linux or MacOS X, run:
    cytoscape.sh
    On Windows, run:
    cytoscape.bat