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Date/Time
Date(s) - 27/02/2014
2:00 pm - 4:00 pm

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This month, Thomas Down will be introducing us to his Biodalliance genome browser and telling us a bit about its development and Maximilian Haeussler will be discussing Unstructured data analysis, and the UCSC virtual machine.

All welcome, although please bear in mind that this is a BRCF meeting so content may be quite technical.

Here are some directions to Guy’s Tower.

Thomas Down
Biodalliance: Embeddable Genome Visualization

Thomas Down has a background in sequence analysis and epigenomics, and believes that we need more scientific software that’s a pleasure to use. He is currently working with Tim Hubbard at the Sanger Institute and KCL on genomic data visualisation.

Genome browsers are a vital part of the genomics workflow. Eyeballing data has proved indispensable for spotting unexpected correlations, formulating new hypotheses, or simply sanity-checking newly collected data. Advances in data-collection and analysis mean that the importance of visualisation, and the amount of data users want to see, is greater than ever. Dalliance (http://www.biodalliance.org/) is a web-based genome browser that combines high-performance and interactivity with a small footprint that allows for easy embedding — in larger applications, publications, or even presentations!

As well as introducing the tool itself and talking about some applications, I will explain how Dalliance is able to access a range of important genomics file formats, like BigWig and BAM files, in an efficient manner without any special server-side support.

Max Haeussler
UCSC Browser in a Box and the UCSC Publications tracks

Max Haeussler has a background in developmental biology and text mining and believes that we need more literature search engines that understand at least some molecular biology to make them a pleasure to use. He is currently working with David Haussler and develops for the UCSC Genome Browser at the University of California at Santa Cruz.

I will present two ongoing additions to the UCSC genome browser:

  • a small virtual machine that allows to run the UCSC genome browser website on (almost) any PC
  • the publication and webpages tracks resulting from the UCSC Genocoding project(http://genome.ucsc.edu and http://text.soe.ucsc.edu), for which we have obtained access to several million fulltext research articles and more than 40 billion webpages. The three genome annotation tracks link out from genomic locations to any scientific publication or web page that mentions a dbSNP id, protein or DNA sequence. I’m also presenting ongoing work to detect database accessions, gene mutations and protein interactions automatically in full text articles.