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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

Teku N Gabriel et al., Identification of core T cell network based on immunome interactome Systems physiology, pharmacology and medicine. BMC Systems Biology (2014) doi:10.1186/1752-0509-8-17

Steindorff Stecca Andrei et al., Identification of mycoparasitism-related genes against the phytopathogen Sclerotinia sclerotiorum through transcriptome and expression profile analysis in Trichoderma harzianum Eukaryote microbial genomics. BMC Genomics (2014) doi:10.1186/1471-2164-15-204

Korshkari Parpakron et al., ShrimpGPAT: a gene and protein annotation tool for knowledge sharing and gene discovery in shrimp Multicellular invertebrate genomics. BMC Genomics (2014) doi:10.1186/1471-2164-15-506

Otte A Kathrin et al., Proteomic analysis of Daphnia magna hints at molecular pathways involved in defensive plastic responses Proteomics. BMC Genomics (2014) doi:10.1186/1471-2164-15-306

Rajcevic Uros et al., Colorectal cancer derived organotypic spheroids maintain essential tissue characteristics but adapt their metabolism in culture. Proteome Science (2014) doi:10.1186/1477-5956-12-39

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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