Introduction

Cytoscape is an open source bioinformatics software platform for visualizing molecular interaction networks and integrating these interactions with gene expression profiles and other state data.

Reposition is an open source Cytoscape Plugin for the reuse of existing Cytoscape network layouts in new Cytoscape projects.

Features Reposition v0.01

Reposition is developed and maintained by Matthias Koenig at the Computational Systems Biochemistry group of the Charite Berlin.

Project homepage:
http://www.charite.de/sysbio/people/koenig/software/reposition/help/.
Project hosted at:
http://sourceforge.net/projects/reposition/.

Installation

Install

Reposition is avaiblable for download at http://sourceforge.net/projects/reposition/.

[1] Download the latest version and move Reposition-vx.x.jar into the Cytoscape plugin directory, which is located in the Cytoscape installation directory under plugins
$CYTO_INSTALL/plugins/.

The plugin is loaded automatically during the next start of Cytoscape.

Uninstall

[1] Remove Reposition-vx.x.jar from the Cytoscape plugin directory $CYTO_INSTALL/plugins/.

Update / Change Version

[1] Remove the old Reposition-vx.x.jar from the Cytoscape plugin directory $CYTO_INSTALL/plugins/ and replace with the new version of the plugin.

Usage guide

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After installation the Reposition plugin is integrated into Cytoscape at startup and is available via the plugin menu.

1. First the network to which the layout should be applied has to be loaded and selected. For example a given SBML file of the network. Open a new Cytoscape Session
File -> New -> Session and load the network
File -> Import -> Network (multiple file types)...

2. Apply the layout from a given session file
Select the Reposition Plugin from the menu
Plugins -> Reposition
and select the Cytoscape Session file (*.cys) with the layout.

The positional information from the selected Cytoscape session is applied to the current network. The mapping of the layout is performed based on the xPosition and yPosition associated with the node identifiers. Nodes in the network with no positional information in the selected session file are mapped to standard positions.

The selected visual style of the Cytoscape session file is transferred to the new network. The behaviour is the same as an VisualStyle export of the old network and an import of the VisualStyle in the new network.

All node and edge attributes from the old network are mapped to the new network. If the new network already has a value for the (id, attribute) combination the value is kept.

The nodes in the new network which are not part of the Cytoscape session file get no positional information and have a default location in the layout. The node attributes are also not available for such nodes, because the necessary information is not available in the old network.

Additional Resources

Links

Reposition
http://www.charite.de/sysbio/people/koenig/software/reposition/help/index.html
http://sourceforge.net/projects/reposition/
http://www.charite.de/sysbio/people/koenig/

Cytoscape
http://www.cytoscape.org/

Cytoscape plugins
http://chianti.ucsd.edu/cyto_web/plugins/index.php

Development

Subversion Access

The project is open source. Everybody can participate.

This project's SourceForge.net Subversion repository can be checked out through SVN with the following instruction set:
svn co https://reposition.svn.sourceforge.net/svnroot/reposition reposition

Bugs in Reposition-v0.1

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Comming Features in SBMLReader2

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