NCBI-UCSC Genomics Hackathon April 2-4, 2018

NCBI-UCSC Genomics Hackathon April 2-4, 2018

From April 2 -4, 2018, the NCBI will help with a bioinformatics hackathon in Northern California hosted by the University of California, Santa Cruz (UCSC)!  The hackathon will focus on advanced bioinformatics analysis of next generation sequencing data, proteomics, and metadata.

This event is for researchers, including students and postdocs, who have already engaged in the use of bioinformatics data or in the development of pipelines for bioinformatics analyses from high-throughput experiments. Some projects are available to other non-scientific developers, mathematicians, or librarians.

The event is open to anyone selected for the hackathon and willing to travel to UCSC.

Working groups of five to six individuals will be formed into five to eight teams.  These teams will build pipelines and tools to analyze large datasets within a cloud infrastructure.  Potential subjects for this iteration include:

  • Developing a framework for nesting containerized bioinformatics workflows in cloud infrastructure.
  • Extending the GA4GH API to map fastq files
  • Machine learning pipelines for germline rare variants linked to phenotypes
  • A simple, open-source mapper for nanopore data
  • An automated pipeline for named entity recognition from biomedical literature

Please see the application form for more details and additional projects.


After a brief organizational session, teams will spend three days addressing a challenging set of scientific problems related to a group of datasets. Participants will analyze and combine datasets to work on these problems.


Datasets will come from public repositories or will be supplied by the project lead. During the hackathon, participants will have an opportunity to include other datasets and tools for analysis.  Please note, if you use your own data during the hackathon, we ask that you submit it to a public database within six months of the end of the event.


All pipelines and other scripts, software and programs generated in this hackathon will be added to a public GitHub repository. Manuscripts describing the design and usage of the software tools constructed by each team may be submitted to an appropriate journal such as the F1000Research hackathons channel.


To apply, complete this form (approximately 10 minutes to complete). Applications are due Friday March 9th, 2018 by 3 pm PT. Participants will be selected based on the experience and motivation they provide on the form.  Prior participants and applicants are especially encouraged to apply.  The first round of accepted applicants will be notified on March 12 by 3 pm PT, and have until March 14 at noon PT to confirm their participation. If you confirm, please make sure it is highly likely you can attend, as confirming and not attending prevents other data scientists from attending this event.  Please include a monitored email address, in case there are follow-up questions.

Note: Participants will need to bring their own laptop to this program. A working knowledge of scripting (e.g., Shell, Python, R) is necessary to be successful in this event. Employment of higher level scripting or programming languages may also be useful. Applicants must be willing to commit to all three days of the event.  No financial support for travel, lodging or meals is available for this event.  Also note that the hackathon may extend into the evening hours on Monday and/or Tuesday. Please make any necessary arrangements to accommodate this possibility.

Please contact and/or with any questions.

Venue: University of California, Santa Cruz

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