From August 14th – 16th, the NCBI, with involvement from several NIH institutes, will host a Biomedical Data Science hackathon at the National Library of Medicine on the NIH campus. The hackathon will primarily focus on medical informatics, advanced bioinformatics analysis of next generation sequencing data and metadata. To apply for this event, complete this application (approximately 10 minutes to complete). Applications are due Tuesday, July 11, 2017 by 4 PM ET.
This event is for students, postdocs and investigators or other researchers already engaged in the use of medical informatics data or pipelines for genomic analyses from next generation sequencing data. Some projects are available to other non-scientific developers, cybersecurity experts, mathematicians or librarians.
The event is open to anyone selected for the hackathon, and willing to travel to NIH.
Potential subjects for this iteration are:
- defining single cell expression profiles and extracting them from tissues,
- building robots to extract genomic signatures from primary datasets,
- locating antibiotic resistance signatures in metagenomic data,
- building a pipeline to make legacy code security compliant,
- defining complex phenotypes from primary datasets,
- developing an interactive viewer for gene expression in aging,
- integrating phenvar.colorado.edu with Clinvar, Electronic Medical Records, and Ontologies,
- and possibly others.
Please see the application for specific and evolving team projects.
There will be 5-7 teams comprised of 5-6 individuals. These teams will build pipelines and tools to analyze large datasets within a cloud infrastructure.
After a brief organizational session, teams will spend three days analyzing 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. 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. A manuscript outlining 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 Tuesday, July 11, 2017 by 4 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 13th by 5 pm ET, and have until July 17th at 4 pm ET to confirm their participation. If you confirm, please make sure it is highly likely you can attend, as confirming and not attending bars other scientists from attending this event. Please include a monitored email address, in case there are follow-up questions.
- Participants will need to bring their own laptop to this program.
- A working knowledge of scripting (e.g., Shell, Python) 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.
- The hackathon may extend into the evening hours on Monday and/or Tuesday. Please make any necessary arrangements to accommodate this possibility.
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