NYGC NCBI-style bioinformatics hackathon August 6-8, 2018


From August 6-8, 2018, the NCBI will help with a data science hackathon at the New York Genome Center in Manhattan. The hackathon will focus on genomics as well as general Data Science. This event is for researchers, including students and postdocs, who have already engaged in the use of large datasets or in the development of pipelines for 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 New York City.

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. Example subjects for such hackathons include:

  • A tool to find RNA-Seq and epigenomics for BioSamples with underlying structural variants
  • Searching for novel virus families
  • Building a Database of DNA Repair Sites and Mechanisms
  • Patient de-identification for human neuroimaging (MRI)
  • Data provenance of pipelines involving SRA or ClinVar data
  • Metrics to compare (cancer) clinical trial search results
  • Unambiguous detection of bacterial plasmids from pathogenic bacteria with PacBio

Please see the application form for more details and additional projects. The project list will continue to evolve and will be updated on the application form.

Organization

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

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.

Products

All pipelines and other scripts, software and programs generated in this hackathon will be added to a public GitHub repository designed for that purpose (github.com/NCBI-Hackathons). 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.

Application

To apply, complete this form (approximately 10 minutes to complete). Applications are due Friday, July 13th by 9 pm ET. 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 July 16th, and have until July 18th at noon ET 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 ben.busby@nih.gov with any questions.

Venue: New York Genome Center, 101 6th Ave, New York, NY 10013

Additional Projects: If you have an additional project you would like to see added to the form, please submit it here.

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