Structural Variant Hackathon


NCBI is pleased to announce a Structural Variant Hackathon at the Baylor College of Medicine, Houston Texas, immediately before ASHG on October 11-13, 2019.

We’re specifically looking for folks who have experience in working with structural variants, complex disease, precision medicine, and similar genomic analysis.  If this describes you, please apply! 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 large scale genomic analyses from high-throughput experiments (please note that the event itself will focus on open access public human data).

Potential topics include:

  • Mapping structural variants to public databases
  • Calculating the heritability of different types of structural variants
  • CNV effect on isoform expression
  • Assembly accuracy for metagenomics
  • Quality assessment in large cohorts

The hackathon runs from 9 am – 6 pm each day, with the potential to extend into the evening hours each day. There will also be optional social events at the end of each day. Working groups of five to six individuals, with various backgrounds and expertise, will be formed into five to eight teams with an experienced leader. These teams will build pipelines and tools to analyze large datasets within a cloud infrastructure. Each day, we will come together to discuss progress on each of the topics, bioinformatics best practices, coding styles, etc.

There will be no registration fee associated with attending this event.

Note: Participants will need to bring their own laptop to this program. No financial support for travel, lodging, or meals is available for this event.

Continue reading

Virus hunting in the cloud: A hackathon story at ASV 2019


Are you going to ASV 2019?

If you are, join us in a few days for a workshop on the virus hunting hackathon we helped run earlier this year.

Session: Workshop #19: Virus Discovery

Program Number: W-19-8

Time: Sunday, July 21, 7:00 PM CDT

Location: Mayo Auditorium

In this workshop, Dr. Rodney Brister will talk about how 41 scientists from 21 organizations worked to improve the usability of SRA data, identifying datasets that included known viruses and viral signals. Not only is that information now being integrated into a public search interface, but the approach used is also being refined in future hackathons so it can be applied to all SRA datasets.

We hope to see you there!

Microbial Virulence in the Cloud hackathon August 13 – 15 2019


From August 13 – 15 2019, the NCBI will run a bioinformatics hackathon on the NIH campus!

We’re specifically looking for folks who have experience in working with computational microbial genomics, evolutionary biology, antimicrobial resistance, and similar genomic analysis.  If this describes you, please apply! 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 large scale genomic analyses from high-throughput experiments (please note that the event itself will focus on open access public human).

Continue reading

Presentation on NCBI’s genome browser at Rocky Mountain Genomics Hackcon


On June 18, 2019, NCBI’s Sanjida Rangwala will demonstrate the rich data visualization capabilities of NCBI’s genome browser at a conference that is part of the Rocky Mountain Genomics Hackcon.  As mentioned in a previous post, NCBI staff will also participate in an NCBI-style Hackathon  as part of the larger event.  The genome browser presentation and demonstration will show you how to create visuals that provide insights and show connections among genes, transcripts, variation,  epigenomics and GWAS data from NCBI sources. You will also see  how you can upload your own data and embed NCBI viewers on your own pages.

NCBI to help with Rocky Mountain Genomics HackCon, June 17 – 21, 2019


The NCBI will participate in a one-day conference on June 18, 2019 and a hackathon, June 19-21, 2019 as a part of Rocky Mountain Genomics Hackcon 2019 at the BioFrontiers Institute in Boulder Colorado.

The conference will feature technical speakers in precision medicine, metagenomics, and advanced RNA-Seq analysis, as well as an exhibitor and poster session. The hackathon will focus on creating visualization tools for exploratory data analysis.

Many people who attend these events have experience working with large datasets or the development of informatics tools, code, or pipelines; however, researchers who are in earlier stages of their data science journey, including students and postdocs are also encouraged to apply. 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 Boulder, Colorado.  

Please visit the Rocky Mountain Genomics Hackcon 2019 site for more details and information on how to attend.

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

Continue reading

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.