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Cytoscape Training: A Comprehensive Overview

During Cytoscape workshop February 2015
Cytoscape Training: A Comprehensive Overview


Marci Brandenburg, MS, MSI, Bioinformationist,  Taubman Health Sciences Library University of Michigan, taught a hands-on workshop about the use of Cytoscape, an open source molecular interactions visualization tool, on February 9-10, 2015. Cytoscape allows for the exploration of molecular interactions and biological pathways and integrates these networks with annotations, gene expression profiles, and other data.


The workshop was devided into three half-day sessions:

  • Cytoscape:  Going from Raw Data to a Publishable Image, covered  core functions, such as learning how to import network and attribute data, change visual properties to easily distinguish biologically significant relationships, create a legend for the image, and manually add nodes/edges.
  • Cytoscape:  A Focus on Apps, covered a variety of applications, such as the Reactome FI (Reactome Functional Interaction and pathway enrichment tool), BiNGO (Gene Ontology Tool), MCODE (cluster finding tool), and more.
  • Analyzing Metabolomic and Gene Data, covered metabolomics-specific resources, including MetScape (Cytoscape app for visualizing and interpreting metabolomic data), MetDisease (Cytoscape app for annotating metabolic network with MeSH disease terms), and Metab2MeSH (tool for annotating compounds with MeSH concepts).

Fifteeen faculty and graduate students participated in this workshop, which was evaluated with very high marks.

The workshop was hosted by the Center for Information Technologies and Telecommunications, a Key Activity of the RCMI Center for Collaborative Research in Health Disparities of the University of Puerto Rico Medical Sciences Campus.
Acknowledgement of Funding

This program is funded by RCMI grant G12 MD007600 (National Institute on Minority Health and Health Disparities) from the National Institutes of Health.  Please use this number to acknowledge support.

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