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.
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.
We are pleased to announce the first ever Computational Medicine in the Cloud Hackathon! NCBI will help run a bioinformatics hackathon in Baltimore, Maryland hosted by the Johns Hopkins University.
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
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.
This May, the NCBI will host a women’s collaborative biodata science hackathon on the NIH Campus in Bethesda, Maryland!
We are now collecting project proposals focusing on building tools and pipelines for advanced analysis of biomedical datasets including text, images, next generation sequencing data, proteomics, and metadata. Proposals for tutorial pipelines and educational tools for advanced analysis are also welcome. Submit your project proposal by March 4, 2019.
We are pleased to announce the first ever pangenomics, graphs and haplotypes hackathon.
- 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
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 “Announcing the first ever RNA-Seq in the Cloud hackathon!”
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.