viernes, 3 de febrero de 2017

NCBI to host genomics hackathon March 20-22

NCBI to host genomics hackathon March 20-22

National Institutes of Health, U.S. National Library of Medicine

NCBI to host genomics hackathon March 20-22

Thursday, February 2, 2017

From March 20th to 22nd, the NCBI will host a genomics hackathon on the NIH campus. To apply for this hackathon, complete this application (approximately 10 minutes to complete). Applications are due February 22nd by 1 PM ET.
This hackathon will primarily focus on advanced bioinformatics analysis of next generation sequencing data and metadata. This event is for students, postdocs and investigators or other researchers already engaged in the use of genomics data or pipelines for genomic analyses from next generation sequencing data. However, there are some projects available to other non-scientific developers, mathematicians or librarians. The event is open to anyone selected for the hackathon who is able to travel to NIH.
There will be 5-7 teams of 5-6 individuals. These teams will build pipelines and tools to analyze large datasets within a cloud infrastructure.
The potential subjects for this iteration are:
  • GA4GH - NCBI API Integration,
  • Global Screening Arrays,
  • Graph Genome Information Extraction,
  • Single Cell Methylation Data,
  • Generation of an automated gff3 parser,
  • integration of Immport metadata with specific genomic datasets,
  • And several others.
Please see the application for specific and evolving team projects.
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, primarily those housed at the NCBI. During the course, participants will have an opportunity to include other datasets and tools for analysis.
Please note, if you use your own data during the course, 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.
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 application (approximately 10 minutes to complete). Applications are due February 22nd by 1 pm ET.
Participants will be selected from a pool of applicants based on the experience and motivation they provide on the form. Prior participants and applicants are especially encouraged to reapply.
The first round of accepted applicants will be notified on February 24th by 5 pm ET, and have until February 27th at 1 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) 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 course may extend into the evening hours on Monday and/or Tuesday. Please make any necessary arrangements to accommodate this possibility.
Please contact with any questions.

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