Helping biologists see the bigger picture in diverse cancer genomics data

We develop visualizations to help scientists to make sense of copious and diverse types of genomic data. Our web-based data browser helps scientists make inferences and test hypotheses. Unique and important in the medical genomics research field, we allow users to combine their private data securely with public data using a decoupled server-client architecture. We are funded for the next 5 years by the National Cancer Institute as a genomic data visualization center to develop tools to visualize the largest compendium of cancer genomics data, the Genomic Data Commons. While we are funded nationally, our users are international, with only 40% of our traffic coming from within the United States. Last month we had over 3,500 users. We are committed to open-source software from the beginning and aim to make our code as reusable as possible (e.g. our static interval tree, KM statistics and ICGC plugin).

Students we mentor will have the benefit of being part of both a small, focused development team and also having access to the community resources of the larger UCSC Genomics Institute, whose mission is to create advanced technologies and open-source genomics platforms to unravel evolutionary patterns, molecular processes and the underpinnings of disease. We are committed to working with students to ensure that they gain new knowledge and skills as well as contribute ideas and useful code to the project.

We are interested in finding long-term collaborators and growing our development team. If you're interested in doing your Google Summer of Code project on cancer genetics, statistics, data visualization, database query, or functional programing, please contact us as soon as possible. We want to help all students submit the best possible proposal.

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Technologies

  • javascript
  • react
  • clojure
  • d3
  • python

Topics

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UCSC Xena 2017 Projects

  • Akhil Kamath
    Transcript Centric View
    Currently UCSC Xena is designed in such a way that each row is a sample and columns are data types. Biologists often need to study the different...
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2017