Microbial Virulence in the Cloud hackathon August 13 – 15 2019

Microbial Virulence in the Cloud hackathon August 13 – 15 2019

From August 13 – 15 2019, the NCBI will run a bioinformatics hackathon on the NIH campus!

We’re specifically looking for folks who have experience in working with computational microbial genomics, evolutionary biology, antimicrobial resistance, and similar genomic analysis.  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 large scale genomic analyses from high-throughput experiments (please note that the event itself will focus on open access public human).

Potential topics include:

  • Virulence Factor Characterization
  • Antimicrobial Resistance Characterization in Metagenomes
  • Automated Gene family characterization
  • NLP and Metadata Harmonization
  • Complex Population Structures
  • Gene Family Naming Conventions and Domain Mapping
  • Annotation of Novel Genomes Extracted from Metagenomes with Standalone PGAP
  • Identification of mobile elements carrying the antimicrobial resistance gene
  • Additional activities of virulence factors (e.g. resistance to other microorganisms)

Hackathon Logistics

The hackathon runs from 9 am – 5 pm each day, with the potential to extend into the evening hours each day.  There will also be optional social events at the end of each day. Working groups of five to six individuals, with various backgrounds and expertise, will be formed into five to eight teams with an experienced leader. These teams will build pipelines and tools to analyze large datasets within a cloud infrastructure. Each day, we will come together to discuss progress on each of the topics, bioinformatics best practices, coding styles, etc.

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

Note: Participants will need to bring their own laptop to this program. No financial support for travel, lodging, or meals is available for this event.


Datasets will come from public repositories, with a focus on ~83,000 metagenomic datasets in the sequence read archive that have been ported to cloud infrastructure, as well as derivative contigs of some 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 (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, BMC Bioinformatics, GigaScience, Genome Research or PLoS Computational Biology.


To apply, please complete this form.  Initial applications are due July 11th, 2019 by 3 pm ET, with rolling acceptance to follow based on space. 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 13th by 3 pm ET and have until July 16th noon ET to confirm their participation (especially qualified applicants or those traveling internationally may receive acceptances earlier). If you confirm, you must be willing to commit to all three days of the event, as confirming and not attending prevents other data scientists from attending this event.


Entrants retain ownership of all intellectual property rights (including moral rights) in the code submitted to as well as developed in the hackathon. Employees of the U.S. Government attending as part of their official duties retain no copyright in their work and their work is in the public domain in the U.S.

The Government disclaims any rights in the code submitted or developed in the hackathon.

Participants agree to publish the code and any related data in GitHub.

For more information or questions, please contact us at ncbi.hackathons@mail.nih.gov.

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