Visualising biological data

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Image from www.cytoscape.org

Biocomputing expert John “Scooter” Morris will be in Australia to teach at two workshops in Melbourne and Sydney later this month.

Scooter is based at the University of California, San Francisco, where he is the executive director of the Resource for Biocomputing, Visualization, and Informatics. His research focuses on the visualization of diverse biological data in ways that can communicate important properties about underlying properties.

The major vehicle for that visualization has been Cytoscape ( www.cytoscape.org ), an open source platform for integration and visualization of biological data—particularly biological data that can be mapped onto networks of various different kinds. Scooter is a member of the core development team for Cytoscape, and he and his team have also developed a number of plug-ins for the Cytoscape platform, allowing researchers to link visualisation of pathways and networks with visualisation of molecular structures (structureViz), cluster data for easier visualisation and analysis (clusterMaker), and extend the Cytoscape platform into chemical informatics (chemViz).

While in Australia, Scooter will be teaching at two workshops:

The EMBL Australia Master Class on Protein Sequence Analysis, 21-25 October, Garvan Institute of Medical Research (NSW)

Cytoscape Workshop hosted by SBI Australia, 28 October, Monash Conference Centre, 30 Collins St, Melbourne (Victoria)

This 1-day workshop will cover the following:

1) Introductory tutorial on the analysis and visualization of biological networks, including the background for network biology;

2) Hands-on tutorial introduction to Cytoscape;

3) Demonstration and hands-on use cases of Cytoscape, with numerous example use cases showing what is possible.

4) Master class: Bring your own data, cancer pathway data, proteomics data, mass spectrometry pull downs, etc. Traditional genomics data is welcome (e.g. expression data), but please note that this data is usually not particularly well-suited to networks visualisation. The Master Class will also include demos of Cytoscape features in development, and Cytoscape scripting.

We can also play with looking at structures as network and throw in some cheminformatics if there is interest.

Places are limited, please reserve your place

Cytoscape is an open source software platform for visualizing molecular interaction networks and biological pathways and integrating these networks with annotations, gene expression profiles and other state data. Cytoscape is currently the primary package used throughout the world for visualizing and analyzing Biological networks of many types. The Cytoscape consortium recently released the first major revision of Cytoscape in 10 years: Cytoscape 3.0 and the next release, Cytoscape 3.1 was just released in beta and promises several new, exciting features for integration and visualization of biological networks.

Although Cytoscape was originally designed for biological research, now it is a general platform for complex network analysis and visualization.

Scooter is the Executive Director, Resource on Biocomputing, Visualization, and Informatics, at the University of California, San Francisco. His major interests are in the visualization of diverse biological data in ways that can communicate important properties about underlying properties. The major vehicle for that visualization has been Cytoscape, an open source platform for integration and visualization of biological data, particularly biological data that can be mapped onto networks of various different kinds. Some examples of our work in this area include: • structureViz , which provides a linkage between the network view commonly used for visualization of pathways, protein-protein interaction networks, or protein similarity networks and the structural view commonly used by structural biologists to manipulate, analyze, and compare macromolecular structures. • clusterMaker , which unifies a number of different clustering techniques commonly used by biologists for segregating proteins into groups, performing expression profiling, and more recently epistatic mini-array profiles (EMAPs). • chemViz, extends the capabilities of Cytoscape into the domain of cheminformatics. chemViz displays 2D diagrams of compounds specified by InCHI or SMILES strings. chemViz can also calculate Tanimoto similarities of compounds and use the values to create chemical similarity networks.

Scooter also participates in the ongoing development of Cytoscape as a member of the core development team, contributing a number of plugins and extensions to Cytoscape to improve the general functionality as well as usability.

In 2005, Scooter was awarded the ACM/SIGCHI Lifetime Service Award for service to the field of Human Computer Interaction.

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