From July 11-13, 2018, NCBI will help with a data science hackathon at the Northwestern Feinberg School of Medicine campus in downtown Chicago. This hackathon focuses on genomics and general data science analyses including text, image, and sequence processing. The event is for researchers, including students and postdocs, who already use large datasets or develop pipelines for analyses from high-throughput experiments. Some projects are available to other non-scientific developers, mathematicians or librarians. The hackathon is open to anyone selected for the hackathon and willing to travel to Chicago.
Please note that this event will occur directly after the ISMB 2018 meeting.
Working groups of five to six individuals will be formed into five to eight teams. These teams will build pipelines and tools to analyze large datasets within a cloud infrastructure. Example subjects for such hackathons include:
- Prediction of infection-prone metagenomic states
- Endogenous Retroviral Expression in Cancer
- Expression of Structural Variants in Sepsis
- An Online Bioinformatics Pipeline Design Engine
- Disease clustering from literature based on limited training data (phenotypic information)
- Graphical User Interface for Gene Expression calculated on the fly from raw data
Please see the application form for more details and additional projects. The project list will continue to evolve and will be updated on the application form.
Organization
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
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.
Products
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.
Application
To apply, complete this form (approximately 10 minutes to complete). Initial applications are due Tuesday May 21, 2018 by 9 pm ET, and a second round of applications will be accepted by Friday, June 15th, 2018. Participants will be selected based on the experience and motivation they provide on the form. Prior participants and applicants are especially encouraged to apply. For each round, participants will be asked to confirm their attendance shortly after acceptance. 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. Also note that the hackathon may extend into the evening hours on Monday and/or Tuesday. Please make any necessary arrangements to accommodate this possibility.
Please contact ben.busby@nih.gov
with any questions.
Venue: Northwestern University Feinberg School of Medicine
Supported by the Division of Pulmonary and Critical Care Medicine and the Galter Health Sciences Library & Learning Center
Additional Projects: If you have an additional project you would like to see added to the form, please submit it here .
