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Linking the Molecular & Cellular Levels:
Bioinformatics & Computational Biology at the Wodak Lab

Proteins are some of the most fascinating and complex macromolecules in living systems that play extraordinarily diverse roles in sustaining life. These roles are mediated through the interactions that proteins make both with themselves and with other molecular constituents of the cell.

The focus of our laboratory is on investigating the principles that govern these interactions. We use molecular simulation and modeling techniques to study protein-protein protein-DNA and protein-ligand interactions at the atomic scale. We furthermore analyze the properties of known protein structures and sequences in order to gain insight into how evolution has shaped the functional specificity of proteins.

In parallel to these molecular level investigations we are actively engaged in developing quantitative and integrative computational approaches for analyzing physical and functional interactions between proteins, protein complexes and biochemical pathways at the cellular level. All our research activities closely combine the development of methods and software tools with their application to important biological problems with relevance to human health.

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Netility: Network Visualization with Neo4j and Cytoscape Web

Network visualization is one our focuses at the Wodak Lab. Primarily we have used Cytoscape, for which we have two plugins: GenePro and OrthoNets. Recently, the Bader Lab released Cytoscape Web, a Flash based tool to help people build visualizations right in the browser.
Cytoscape Web is a tremendous step forward for developers looking for ways to integrate visualizations into their web applications. Prior to this, one was often forced to rely on Java Applets or Java Webstart, which, while allowing to start them from a web page, are, after launch, completely divorced from their initial context. With Cytoscape Web a web application can continue to interact with the visualisation via JavaScript. Cytoscape Web also provides a nice light-weight alternative to the desktop version of Cytoscape that can be for many people, rather daunting to use, when all they want is a quick network view, and not a lot of options or analysis.

At the lab we've used Cytoscape Web in a new application called Netility to help create views of protein interaction networks, including their relationships to diseases and domains for two of our applications: iRefWeb and DAnCER.


Of course visualization is only part of the problem. You must first have data. In an early version of Netility a standard relational database was used, querying for nodes from the existing tables in iRefWeb. However, the schema for iRefWeb does store information as nodes and edges, and this made for complicated and unnatural queries.

Rather than create a new set of tables that defined proteins, interactions, disease, domains, etc. as nodes with relationships we decided to try Neo4j which was designed as a (NoSql) database specifically for graphs. Because Neo4j is a graph database, what were originally awkward SQL queries become natural network traversals.

Challenges still remain in Netility, some of which I'll discuss in a future post.

Brian Turner
Wodak Lab
Posted by: starclosure
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