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. | Advertisement:
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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 resourcePinto P José et al., TNA4OptFlux – a software tool for the analysis of strain optimization strategies. BMC Research Notes (2013) doi:10.1186/1756-0500-6-175 Hernández-Lemus Enrique et al., Information theoretical methods for complex network structure reconstruction Complex Network Modeling. Complex Adaptive Systems Modeling (2013) doi:10.1186/2194-3206-1-8 Gonçalves Emanuel et al., CySBGN: A Cytoscape plug-in to integrate SBGN maps Networks analysis. BMC Bioinformatics (2013) doi:10.1186/1471-2105-14-17 Xie Li et al., Multiscale modeling of the causal functional roles of nsSNPs in a genome-wide association study: application to hypoxia SNP-SIG 2012: Identification and annotation of SNPs in the context of structure, function, and disease SNP-SIG 2012: Identification and annotation of SNPs in the context of structure, function, and disease. BMC Genomics (2013) doi:10.1186/1471-2164-14-S3-S9 Sun Xiuli et al., PMTED: a plant microRNA target expression database Knowledge-based analysis. BMC Bioinformatics (2013) doi:10.1186/1471-2105-14-174 |
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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