NCIBI Workshop Resources Page

The following are the resources and downloads that you will be using in the NCIBI "Try Our Tools" workshop (click here for details). Before the workshop, please download them to the laptop you will be bringing with you to the sessions. Included are the application and plugins for Cytoscape and the data sets and other background information relevant to the tutorials. To install Cytoscape on your laptop, please follow the instructions under "Pre-wokshop Cytoscape installation" below.

Pre-workshop Cytoscape installation

What is Cytoscape:

Cytoscape is an open source bioinformatics software platform for visualizing molecular interaction networks.

Prior to the workshop please follow the below instructions to load Cytoscape on the computer you will be using for the workshop.

Cytoscape with workshop plugins requirements:

Any modern version of Mac OS X, Windows, or Linux

Minimum recommended hardware configuration: 1GHz processor, 512MB RAM

Java 5 SE or Java 6 SE Runtime Environment - In general, Java SE 6 is faster than 5.
If your machine is compatible with the 6 series, please try version 6 here.

To launch the Cytoscape application:

Download and unzip to your local computer.

Linux / MAC OS X:

Run from the command line.

Windows XP or Vista::

Double-click cytoscape-runme.bat.


You can pass the .jar file to Java directly using the command "java -Xmx512M -jar cytoscape.jar -p plugins". The -Xmx512M flag tells java to allocate more memory for Cytoscape and the -p plugins option tells cytoscape to load all of the plugins in the plugins directory. Loading the plugins is important because many key features like layouts, filters and the attribute browser are included with Cytoscape as plugins in the plugins directory.


Workshop Files (Modules 1-4)


Below are the list of files you will need to download and access for each demonstration module during the workshop. Please follow the demonstrator's instructions.

Download all files in zip format (contains all workshop files listed below)

Download individual files
listed by module

Module 1:
Finding Literature Based on Relevant Interactions and Pathways

Related files:



Module 2:
Gene set enrichment testing and concept mapping

Related files:



Module 3:
Visually exploring protein interaction networks and pathway associations

Related files:





Module 4:
Exploring metabolomic data analysis tools

Related files:

Module4_ Metabolomics_Tutorial.pdf