HighLights

NCIBI "Try Our Tools" Virtual Workshop

You can try out selected NCIBI tools by following along with a tutorial booklet and downloading the relevant sample data files and required software. The tutorials are organized into 4 modules (see below) and each module has a video of the workshop associated with it that you may view before hand or simultaneously. Facilitated by technology advances that NCIBI uses to integrate data from diverse sources and heterogeneous formats, the workshops will allow you to explore 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.

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 cytoscape-ncibi-workshop.zip and unzip to your local computer.

Linux / MAC OS X:

Run cytoscape-runme.sh from the command line.

Windows XP or Vista::

Double-click cytoscape-runme.bat.

Alternatively:

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 and the tutorial booklet you will need to download and access for each demonstration module during the workshop. Please follow the demonstrator's instructions in the video and/or the tutorial.