Women-led Biodata Science Hackathon May 8-10, 2019


NCBI is excited to host our first Women-led Hackathon, a collaborative biodata science event organized by women on the NIH Campus in Bethesda, Maryland!

NIH has a strong interest in enhancing the diversity of the scientific workforce, and women in particular are underrepresented in data science.  This women-led NCBI initiative strongly encourages researchers, especially women, at any stage of their data science journey to apply for this inaugural event. Past hackathon participants have ranged from students and postdocs with a working knowledge of scripting (e.g. Shell, Python, R) to those already engaged in the use of large datasets or in the development of informatics tools, code, or pipelines.

Potential topics include:

  • An open store for variant and gene prioritization tools
  • Variable Tracking and Schema Capturing to make Biomedical Research Data ‘FAIR’
  • Molecular language: discovery of cell-to-cell communication molecules from RNA-Seq data
  • dsVirus variant discovery and annotation pipeline
  • Design of ICD-9 to 10 conversion function for the R package ‘icd’
  • Hiding in plain sight — unannotated structural variants in public genomic data sets

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Follow “Pangenomics in the Cloud” hackathon projects on GitHub


NCBI is on the West Coast this week (March 25 – 27) for “Pangenomics in the Cloud,” a three-day hackathon hosted by the University of California, Santa Cruz.

Graphs are the name of the game here! The teams will be building graphs, managing coordinates between samples and defining and identifying and marking haplotypes, and looking at population specific variants.

Please follow along on our GitHub, fork and make pull requests during and after the event, and stay tuned for updates on the findings.

Pangenomics in the Cloud hackathon, March 25-27, 2019


We are pleased to announce the first ever pangenomics, graphs and haplotypes hackathon.

From March 25-27, 2019, the NCBI will help run a bioinformatics hackathon in Santa Cruz, California, hosted by the University of California, Santa Cruz (UCSC).  Potential topics include:

  • Building large scale graphs from pangenomes using several assembly methods
  • Simplification of mapping
  • Resolving haplotypes
  • Identification of population-specific structural variants
  • Defining haplotype-specific expression, visualization, and coordination with the GRC

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Announcing the first ever RNA-Seq in the Cloud hackathon!


From March 11-13, 2019, the NCBI will help run a bioinformatics hackathon in the North Carolina Research Triangle hosted by the University of North Carolina, Chapel Hill (UNC).

Potential topics include:

  • technical metadata homogenization
  • a simple interface for using ontologies to make data searches more sensitive and specific
  • automated data analysis and visualization
  • novel isoform identification and comparison

We’re looking for people who have experience in working with subjects like these. If this describes you, please apply!

This event is for researchers, including students and postdocs, who use bioinformatics data or develop pipelines for large scale RNA-Seq analyses from high-throughput experiments. The event is open to anyone selected for the hackathon and willing to travel to UNC. Continue reading

Florida (USF) Biological Data Science “IronHack” February 25-27, 2019


From February 25-27, 2019, NCBI will help with a Data Science hackathon at USF in Tampa Florida!

The hackathon will focus on the genomics of Iron-linked Rare Diseases as well as large scale RNA-Seq indexing and analysis. This event is for researchers, including students and postdocs, who have already engaged in the use of large datasets or in the development of pipelines for 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 willing to travel to Tampa.

Working groups of five to six individuals will be formed into five to eight teams. These teams will build or expand on pipelines and tools to analyze large datasets within a cloud infrastructure. Example subjects for such hackathons include:

  • Integrative pipelines to analyze large scale RNA-Seq experiments
  • Visualization tools for mapping phenotypes to genotypes
  • Rapid clinical diagnostics tools
  • Structural variant mining with single molecule sequencing 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.

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Apply now to join the Seattle Biological Data Science FHackathon February 4-6, 2019


From February 4-6, 2019, the NCBI will help with a data science hackathon at the Fred Hutchinson Cancer Research Center in Seattle. To apply, complete this form (approximately 10 minutes to complete). Initial applications are due Friday, January 11th by 11 pm ET.

The hackathon will focus on genomics as well as general data science. This event is for researchers, including students and postdocs, who have already engaged in the use of large datasets or in the development of pipelines for analyses from high-throughput experiments. Some projects are available to other non-scientific developers, mathematicians, or librarians.

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Virus Hunting Data Science Hackathon next week in San Diego


From January 9th – 11th, the NCBI will help run a bioinformatics hackathon in Southern California hosted by the Computational Sciences Research Center at San Diego State University. We reached out to the global computational biology and virology community as part of this effort to make data more accessible.

The hackathon teams look forward to leveraging metagenomic datasets in the cloud to find data based on organismal content and update taxonomy – but most of all – hunt down new viruses!

Follow along with the event with NCBI tweets and see our work on GitHub.