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OpenHelix

An open-source software platform used for visualization and analysis of molecular interaction and network data

Tutorial and training materials by OpenHelix

Learn to use Cytoscape, an open-source software platform used for visualization and analysis of molecular interaction and network data. Cytoscape uses a graphical user interface with floatable panels to easily manage your network data. Graphical data displays and text attributes provide detailed information about interactions of interest. Customizable features enable extensive visualization and manipulation opportunities. This platform also offers plugin capability to increase functionality, and has an active user community developing and maintaining the software.

Note: This tutorial corresponds to Cytoscape 2.x versions. We are monitoring the releases of the 3.x software and will provide updates in the future.

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You'll learn:

  • how to navigate and use the graphical user interface
  • to import network data from different sources
  • how to create a network layout and import attributes for your network
  • how to find and load plugins to add functionality to your network analysis


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Recent BioMed Central research articles citing this resource

Song Xiaoming et al., Genes associated with agronomic traits in non-heading Chinese cabbage identified by expression profiling Genomics and evolution. BMC Plant Biology (2014) doi:10.1186/1471-2229-14-71

Hooper E Joan et al., A survey of software for genome-wide discovery of differential splicing in RNA-Seq data. Human Genomics (2014) doi:10.1186/1479-7364-8-3

Liu Hui et al., Detection of type 2 diabetes related modules and genes based on epigenetic networks Selected articles from the Twelfth Asia Pacific Bioinformatics Conference (APBC 2014): Systems Biology The Twelfth Asia Pacific Bioinformatics Conference (APBC 2014). BMC Systems Biology (2014) doi:10.1186/1752-0509-8-S1-S5

Dogan V Meeshanthini et al., The effect of smoking on DNA methylation of peripheral blood mononuclear cells from African American women Human and rodent genomics. BMC Genomics (2014) doi:10.1186/1471-2164-15-151

Han Dohyun et al., Characterization of the membrane proteome and N-glycoproteome in BV-2 mouse microglia by liquid chromatography-tandem mass spectrometry Proteomics. BMC Genomics (2014) doi:10.1186/1471-2164-15-95

More about the resource:

The Cytoscape Consortium is a collaboration between the Institute for Systems Biology (Hood lab), the University of California San Diego (Ideker lab), Memorial Sloan-Kettering Cancer Center (Sander lab), the Institut Pasteur (Schwikowski lab), Agilent Technologies (Adler lab) and the University of California, San Francisco (Conklin lab), with support from grant agencies and corporate sponsors. Cytoscape is a downloadable Java application that can run on Linux, Windows, and Mac OS systems.


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The materials and slides offered can not be resold or used for profit purposes. Reproduction, distribution and/or use is strictly limited to instructional purposes only and can not be used for for monetary gain or wide distribution.
Copyright 2009, OpenHelix, LLC.

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