About this Class

This 2-day workshop, including a BYOD (Bring Your Own Data) exercise, will provide an introduction and hands-on training for Cytoscape, which is an open source software platform for visualizing  networks and integrating these networks with annotations, gene expression profiles and other state data.

With over 800 publications citing Cytoscape, it has become the primary tool for visualization of networks, including biological pathways, protein-protein interaction data, protein similarity data, cell-cell, and even residue-residue interactions. In this workshop, you'll learn the basics of network analysis and visualization, utilizing Cytoscape to import network data from public resources such as STRING, Reactome, or Wikipathways, creating input files with network data in Excel format. You will also be able to augment network data with your own experimental results or data downloaded from sites such as cBioPortal. Once imported, you'll learn how to analyze the results using a variety of Cytoscape "apps" and visualize the data in a form useful for exploring the data or for producing meaningful images for presentations or publications. This workshop includes significant opportunity for hands-on exploration of Cytoscape and for working with your own data, so bring in Excel spreadsheets or CSV files with your experimental (for example, spreadsheet with data from microarray) or downloaded data that you would like to see visualized in a network. The Cytoscape core download provides a basic set of features for data integration, analysis, and visualization. Additional features are available as Apps (formerly called Plugins). The App Store has a collections of apps, which are groupings of apps useful for particular analyses. Apps are available for network and molecular profiling analyses, new layouts, additional file format support, scripting, and connection with databases.

The main website is here: http://www.cytoscape.org/.

An example of a recent publication is here: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4906568/ [Yin, Ji-Gang et al. “Gene Expression Profiling Analysis of Ovarian Cancer.” Oncology Letters 12.1: 405–412. 16 Aug. 2016]

You can review the complete list of publications here: http://cytoscape-publications.tumblr.com/

Scooter Morris, a member of the Cytoscape Team from USCF, will be here to provide training for this workshop, which promises to be very exciting and useful for the CCR scientific community.

Important: Attendees are required to pre-load the necessary software (listed below) on the laptop (PC, Mac) they will bring to the workshop. If you plan to attend, please try to do this ahead of the workshop. Depending on your level of computer privileges, you may need to submit a request to the NCI Service Desk (https://service.cancer.gov) to complete installation of JAVA, Cytoscape and the Omics App.

Listed below are the links to download the requirements, in this particular order:

[1] Latest JAVA (Version 8) for your platform: http://www.oracle.com/technetwork/java/javase/downloads/jre8-downloads-2...

• Note for 64 bit Windows users – please download the *64* bit Java version, as Oracle still downloads the 32-bit version by default.
• The *64* bit version is at: http://javadl.oracle.com/webapps/download/AutoDL?BundleId=211999

[2] Latest version of Cytoscape 3.4.0: http://www.cytoscape.org/download-platforms.html

• Please choose the correct platform (Windows, MacOS, Linux).

[3] Link to download the Omics ‘App’ for workshop: http://apps.cytoscape.org/apps/omicsanalysiscollection

• This can also be done after opening Cytoscape: Click on Apps --> Apps Manager --> OmicsAnalysisCollection --> Install

Date: September 1-2, 2016 (Thursday and Friday)

Time and Location:

September 1 - 9:30 am - 4:00 pm; Bldg 10, FAES Classrooms 1 & 2

September 2 - 9:30 am - 12:30 pm; Bldg 10, FAES Classrooms 6 & 7

Workshop Agenda

Day 1: 9:30 am – 12:30 pm

• Introductions and setup (15 minutes)
• Biological Networks (60 minutes): Understanding the terminology and basis of network theory as well as approaches for network construction
  • Network Taxonomy
  • Analytical Approaches
  • Visualization

Break

• Introduction to Cytoscape [Hands-on] (60 minutes): Fundamental aspects of the tool and walk through the analysis steps
  • Data model
  • Basic user interface
  • Visual Styles
  • Apps and the App Store
• App Demos and Use Cases (30 minutes)
• Clustering
• Over-representation analysis

Lunch Break

Day 1: 1:30 pm – 4:30 pm

• Introduction to Cytoscape II (45 minutes): Perform different demos that are built into the tool and have attendees do hands-on tutorials
• Tips & Tricks (15 minutes)
• Working with Data (30 minutes)
  • Importing networks (STRING)
  • Importing networks (Excel)
  • Adding data to networks

Break

• Analysis with Microarray Data (30 minutes)
• In-depth Examples with Your Data
• Questions and Answers

Day 2: 9:30 am -12:30 pm

• Refresher for topics covered on Day 1
• From Public Data to Cytoscape
• “Bring Your Own Data" (BYOD): In-depth analysis of user data
  • Specific cases based on user-driven requests
  • Two excel files are available below as examples
    • TCGA Breast Cancer Data from 2015 - both mRNA and protein expression data

Files

• tcga_breast2015_mRNA.xls: |
• tcga_breast2015_protein.xls: |