From June 19-21, 2017, the NCBI will assist in a bioinformatics hackathon at the New York Genome Center (NYGC). This hackathon will focus on advanced bioinformatics analysis of next generation sequencing (NGS) data, proteomics and metadata. To apply for this hackathon, complete this application (approximately 10 minutes to complete). Applications are due Monday, May 22, 2017 by 5 PM ET.
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 bioinformatics analyses from high-throughput experiments. Some projects are available to other non-scientific developers, mathematicians or librarians.
The event is open to anyone selected for the hackathon and able to travel to the NYGC (see address below).
Potential subjects for this iteration are:
- Expanding and publicizing a Shiny app for visualizing protein correlation profiling data,
- building a pipeline for efficient partitioning of barcodes,
- creating a public JBrowse database for all Staphylococcus aureus genomes
- simulating tumor genomes,
- associating somatic mutations with clinical outcomes,
- simplifying access to shared-data repositories from Python, and
- building a pipeline for searching for virus-associated protein domains in NGS datasets.
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 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 course 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 Monday, May 22, 2017 by 5 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 May 24th by 5 pm ET, and have until May 25th 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 bars other data 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, 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.
- The hackathon may extend into the evening hours on Monday and/or Tuesday. Please make any necessary arrangements to accommodate this possibility.
Please contact firstname.lastname@example.org with any questions.
Venue: New York Genome Center, 101 6th Ave, New York, NY 10013