NCIBI - "Try Our Tools" Virtual Workshops 2009 ARCHIVE

At our Annual Research Meeting in 2009, we ran tutorial workshops with over 75 participants. We have made these tutorials – 4 modules -  and videos of the workshops available from this page below. Some tutorials are undergoing updating and will be updated by May, 2010.

Each tutorial shows how our tools facilitate and augment analysis for such questions as.

  • What proteins interact and in what pathways?
  • What compounds and reactions in a pathway may be associated with a set of genes?
  • What interactions may play a mechanistic role in a disease?
  • What articles are relevant to given genes, interactions or diseases?
  • What genes are significantly enriched for a concept or for the same set of concepts?

Before you begin the workshops, you will need to download and install the application Cytoscape on your computer. To install Cytoscape please follow the instructions under "Pre-wokshop Cytoscape installation" below.

Virtual Workshops

Below are the list of files and the tutorial booklet you will need to download and access for each demonstration module during the workshop.


Virtual Workshop Module 1Module 1:
Finding Literature Based on Relevant Interactions and Pathways

(Featured tools: MiMI & MiMI Plugin for Cytoscape)

Related files:
Launch Module 1 video



Virtual Workshop Module 2Module 2:
Gene set enrichment testing and concept mapping

(Featured tool: ConceptGen)

Related files:

Launch Module 2 video




Virtual Workshop Module 3Module 3:
Visually exploring protein interaction networks and pathway associations

(Featured tool: MiMI Plugin for Cytoscape)

Related files:

Launch Module 3 video



Virtual Workshop Module 4Module 4:
Exploring metabolomic data analysis tools

(Featured tool: MetScape Plugin for Cytoscape)

Related files:
Module4_ Metabolomics_Tutorial.pdf

Launch Module 4 video


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

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.