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NCBI Hackathon @ University of Pittsburgh

HSLS is pleased to announce that the National Center for Biotechnology Information (NCBI) Hackathon is coming to the University of Pittsburgh on September 25-27, 2017! HSLS is working with numerous groups across campus to organize this event, including the Center for Research Computing (CRC), Computing Services and Systems Development (CSSD), School of Computing and Information (SCI), and University Library System (ULS).

What is an NCBI Hackathon? NCBI, in conjunction with the National Institutes of Health Office of Data Science, has created a forum in which individuals with expertise in various areas of science and software development meet for an intense few days to write useful, efficient pipelines to support biomedical research. For example, in the first Hackathon, held January 5-7, 2015, the Metagenomics Team aimed to identify all the viruses in metagenomic and mammalian samples, leading to a viral identification pipeline and code for a potential 10X-60X BLAST speedup for metagenomics analysis. All code is freely available on GitHub, a web service that provides publicly accessible, free-usage tiers for collaborative software development. Manuscripts describing the design and usage of the software tools created during the Hackathons are available on the F1000Research Hackathons channel.

Prior to Pittsburgh, the Hackathon was held at the New York Genome Center from June 19-21, 2017. Planned projects included associating somatic mutations with clinical outcomes, creating a public JBrowse database for all Staphylococcus aureus genomes, simplifying access to shared-data repositories from Python, and planning an educational curriculum for training librarians and other information professionals to teach advanced concepts and skills in data discovery and retrieval. The intent with the latter project was to turn the curriculum into a course during the Pittsburgh Hackathon, with the assistance of librarians who code.

If you are interested in participating in the Pittsburgh Hackathon, please keep an eye out for application materials by the end of July. For more information, or to find out what is required to become a team lead, contact the Molecular Biology Information Service.

~Carrie Iwema

Posted in the July 2017 Issue