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Apply by 17 Aug for the NIH Research Festival Collaborative Data Science and Machine Learning Hackathon!

Posted Aug 13, 2018 by Amanda J. Wilson
Category: National

From September 10-12 , 2018 with presentations at the NIH Research Festival on September 13th, the NCBI and NIH.AI will host a data science hackathon on the NIH Campus in Bethesda, Maryland!
This hackathon will be in collaboration with the newly formed intramural group NIH.AI ( and will focus on building tools for advanced analysis of biomedical datasets including text, images, next generation sequencing data, proteomics, and metadata with a specific emphasis on using machine learning when applicable. The event is open to anyone selected for the hackathon and willing to travel to Bethesda.  
While many participants of hackathons have already engaged in the use of large datasets or in the development of informatics tools, code, or pipelines, researchers who are in the early stages of their data science journey, including students and postdocs with a working knowledge of scripting (e.g., Shell, Python, R) are also encouraged to apply.  Some projects are available to non-scientific developers, mathematicians, or librarians.
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.  The hackathon runs from 9 am - 6 pm each day, with an optional social event on the evening of the second day.
Potential subjects for this event include:
Automated containerized bioinformatics workflows Machine-learning based metadata harmonization Automated machine learning for biomedical text mining Machine learning based production of training images to use in image analysis workflows
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 in order 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 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.
To apply, complete this form  ( (approximately 10 minutes to complete). Applications are due Friday August 17th, 2018 by 3 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 August 20th by 3 pm ET, and have until August 24th at 5 pm 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.  Please make any necessary arrangements to accommodate this possibility.
Please contact with any questions.
Those who are interested in hackathons, but unsure of their qualifications can attend pre-hackathons, offered several times per year.  Applications for those are available on the site

Individuals with disabilities who need Sign Language Interpreters and/or reasonable accommodation to participate in this event should contact Allissa Dillman and NLM,, 301-827-4311, and/or the Federal Relay (1-800-877-8339).

header for the NCBI hackathons github page


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