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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

Gruel Nadège et al., Polarity gene alterations in pure invasive micropapillary carcinomas of the breast. Breast Cancer Research (2014) doi:10.1186/bcr3653

Lescarbeau M Reynald et al., Quantitative analysis of castration resistant prostate cancer progression through phosphoproteome signaling Systems biology, post-genomic analysis and emerging technologies. BMC Cancer (2014) doi:10.1186/1471-2407-14-325

Xie Ling et al., Integrating microRNA and mRNA expression profiles in response to radiation-induced injury in rat lung Radiation Biology and Molecular Radiation Oncology. Radiation Oncology (2014) doi:10.1186/1748-717X-9-111

Azuaje J Francisco et al., Selecting biologically informative genes in co-expression networks with a centrality score Systems Biology. Biology Direct (2014) doi:10.1186/1745-6150-9-12

Sudhakar Padhmanand et al., Construction and verification of the transcriptional regulatory response network of Streptococcus mutans upon treatment with the biofilm inhibitor carolacton Prokaryote microbial genomics. BMC Genomics (2014) doi:10.1186/1471-2164-15-362

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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