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.
- 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
View additional tutorials for resources in
Recent BioMed Central research articles citing this resource
Benso Alfredo et al., An extended gene protein/products boolean network model including post-transcriptional regulation 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-S5
Chou Wei-Chun et al., Visual gene-network analysis reveals the cancer gene co-expression in human endometrial cancer Transcriptomic methods. BMC Genomics (2014) doi:10.1186/1471-2164-15-300
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
Kasavi Ceyda et al., A system based network approach to ethanol tolerance in Saccharomyces cerevisiae. BMC Systems Biology (2014) doi:10.1186/s12918-014-0090-6
Ying Huanchun et al., Risk miRNA screening of ovarian cancer based on miRNA functional synergistic network. Journal of Ovarian Research (2014) doi:10.1186/1757-2215-7-9
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.
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.