Announcing the first ever RNA-Seq in the Cloud hackathon!

Announcing the first ever RNA-Seq in the Cloud hackathon!

From March 11-13, 2019, the NCBI will help run a bioinformatics hackathon in the North Carolina Research Triangle hosted by the University of North Carolina, Chapel Hill (UNC).

Potential topics include:

  • technical metadata homogenization
  • a simple interface for using ontologies to make data searches more sensitive and specific
  • automated data analysis and visualization
  • novel isoform identification and comparison

We’re looking for people who have experience in working with subjects like these. If this describes you, please apply!

This event is for researchers, including students and postdocs, who use bioinformatics data or develop pipelines for large scale RNA-Seq analyses from high-throughput experiments. The event is open to anyone selected for the hackathon and willing to travel to UNC.


Working groups of five to six people will be formed into five to eight teams. These teams will build pipelines to analyze large datasets within a cloud infrastructure. We will unveil the projects before the hackathon starts. These projects will build upon previous NCBI hackathons and community 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.  We will meet throughout the hackathon to discuss progress on each of the topics, bioinformatics best practices, coding styles, etc.


We will add all pipelines, scripts, software, and programs generated in this hackathon to a public GitHub repository designed for that purpose.

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, BMC Bioinformatics, GigaScience, Genome Research or PLoS Computational Biology.


To apply, please complete this form (approximately 5 minutes to complete). Initial applications are due Friday, February 15th, 2019 by 3 pm PT. We will select participants based on the experience and motivation they provide on the form.

Prior participants and applicants are especially encouraged to apply. We will notify the first round of accepted applicants on February 19 by 3 pm PT. You will have until February 22 at noon PT to confirm your participation. If you confirm, please make sure it is highly likely you can attend the hackathon. 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: You will need to bring your own laptop to this program. A working knowledge of scripting (e.g., Shell, Python, R) is useful but not 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.

It’s unlikely that financial support for travel, lodging or meals is available for this event. Also, note that the hackathon may extend into the evening hours each day. Please make any necessary arrangements to accommodate this possibility.

There is no registration fee or cost associated with attending this event.

For more information, or with any questions, please contact Ben Busby.

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