SoCal Hackathon 2019

We are pleased to announce the second installment of the SoCal Bioinformatics Hackathon.

From 9-11 January, 2019, the NCBI will help run a bioinformatics hackathon in Southern California hosted by the Computational Sciences Research Center at San Diego State University!  We are going to put a few hundred thousand metagenomic datasets on cloud infrastructure and identify known, taxonomically definable and novel viruses!  We’re specifically looking for folks who have experience in Computational Virus Hunting or Adjacent Fields! If this describes you, please apply! This event is for researchers, including students and postdocs, who are already engaged in the use of bioinformatics data or in the development of pipelines for virological analyses from high-throughput experiments. The event is open to anyone selected for the hackathon and willing to travel to SDSU (see below).


Working groups of five to six individuals will be formed into five to eight teams.  These teams will build pipelines to analyze large datasets within a cloud infrastructure. The projects will be unveiled before the hackathon starts, and will build off of previous NCBI hackathons.


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 in order to work on these problems. We will be writing code and solving problems.

Throughout the three days will breakout to discuss progress on each of the topics, bioinformatics best practices, coding styles, etc.


Datasets will come from public repositories, with a focus on metagenomics datasets in the sequence read archive that have been ported to cloud infrastructure, as well as derivative contigs of the above.


All pipelines and other scripts, software, and programs generated in this hackathon will be added 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.  Ideally, we will present a virological index from these datasets on cloud infrastructure.

San Diego State University

Founded in 1897, San Diego State University is a public institution of higher education located in Southern California. SDSU is the oldest and largest university in San Diego and the third largest in the state.

SDSU is conveniently located eight stops along the same trolley line (the green line) as the Town and Country Hotel, home of the 2019 PAG


To apply, please complete this form (approximately 5 minutes to complete). Initial applications are due Wednesday, December 12th, 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 December 14 by 3 pm PT, and have until December 17 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 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.

No 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. Depending on the number of people that need accommodation, we will attempt to get a group rate at one of the local hotels. Please indicate on the registration form if you need a hotel room.

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

For more information, or with any questions, please contact Ben Busby ( ), Kyle Levi (, and Rob Edwards ( with any questions.