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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

Ortuño M Francisco et al., Advances in bioinformatics and biomedical engineering - special issue of IWBBIO 2013 Selected articles from the 1st International Work-Conference on Bioinformatics and Biomedical Engineering-IWBBIO 2013 1st International Work-Conference on Bioinformatics and Biomedical Engineering-IWBBIO 2013. Theoretical Biology and Medical Modelling (2014) doi:10.1186/1742-4682-11-S1-I1

Tomescu A Oana et al., Integrative omics analysis. A study based on Plasmodium falciparum mRNA and protein data Selected articles from the High-Throughput Omics and Data Integration Workshop High-Throughput Omics and Data Integration Workshop. BMC Systems Biology (2014) doi:10.1186/1752-0509-8-S2-S4

Noh Haneul et al., Prediction of miRNA-mRNA associations in Alzheimer’s disease mice using network topology Human and rodent genomics. BMC Genomics (2014) doi:10.1186/1471-2164-15-644

Chinenov Yurii et al., Glucocorticoid receptor coordinates transcription factor-dominated regulatory network in macrophages Human and rodent genomics. BMC Genomics (2014) doi:10.1186/1471-2164-15-656

dos Santos Castro Lilian et al., Comparative metabolism of cellulose, sophorose and glucose in Trichoderma reesei using high-throughput genomic and proteomic analyses David Wilson. Biotechnology for Biofuels (2014) doi:10.1186/1754-6834-7-41

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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