SARS-CoV-2 genomic data is critical for monitoring the viral spread and evolution of the COVID-19 pandemic, identifying newly emerging variants, and developing and evaluating the countermeasures. As of September 2022, over 13 million SARS-CoV-2 genomes have been sequenced across the world, making it the most sequenced pathogen ever. A cornerstone of genomic analysis is building a phylogeny, which demonstrates the relatedness of individual isolates to the rest of the sequenced genomes. However, the volume of SARS-CoV-2 genomes presents novel opportunities beyond phylogenies, as well as computational challenges to traditional methods of genomic analyses and visualization. Continue reading “NCBI-NIAID Beyond Phylogenies Codeathon was a success!”
Celebrating 1 Year of NCBI Virtual Outreach Events
We launched the NCBI Virtual Outreach Event series in the fall of 2021 to expand our online outreach to a worldwide audience of people who use NCBI resources for biological/biomedical research, science education, and clinical applications. Our virtual outreach events include interactive workshops, webinars, and codeathons. In the past year, we have hosted 34 virtual events and served over 1,600 participants (Figure 1).
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Petabyte-Scale Sequence Search: Metagenomics Benchmarking Codeathon Highlights
The National Institutes of Health (NIH) Office of Data Science Strategy (ODSS), the National Library of Medicine’s (NLM’s) National Center for Biotechnology and Information (NCBI), and the Department of Energy’s (DOE’s) Office of Biological and Environmental Research (BER) hosted scientists from around the world for a virtual Petabyte-Scale Sequence Search: Metagenomics Benchmarking Codeathon. The codeathon, held September 27-October 1, 2021, attracted experts from national laboratories including the Los Alamos National laboratory, research institutions including the Joint Genome Institute, and students from universities across the world to develop benchmarking approaches to address challenges in conducting large-scale analyses of metagenomic data.
Continue reading “Petabyte-Scale Sequence Search: Metagenomics Benchmarking Codeathon Highlights”
Computational Medicine Codeathon and AWS workshop at Chapel Hill in March
NIH is pleased to announce a computational medicine-focused codeathon. To apply, please complete the application form by February 25, 2020. We will also be offering a free workshop, AWS Technical Essentials, the day before the codeathon. Read on for more information about the event. Continue reading “Computational Medicine Codeathon and AWS workshop at Chapel Hill in March”
Single Cell in the Cloud Codeathon, Jan 15-17 at NYGC
NCBI is pleased to announce a single-cell focused codeathon at the New York Genome Center, January 15 -17. To apply, please complete the application form by December 30, 2019. Read on if you need more information about the event.
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Pangenome metadata scopeathon in San Diego, January 16-17
We will help run a scopeathon (January 16-17, 2020). This event focuses on planning and designing software to extract value from organismal and genera-level graph genomes by dynamically labeling with metadata. We’re seeking people who are interested in describing community level genomes as graphs, or solving problems involving complex phenotypic interactions with specific genomes. If this describes you, please apply! We also encourage people who will be in San Diego for the International Plant & Animal Genome XXVIII conference to apply. The event is open to anyone selected and willing to travel to San Diego. We will work with data from the following organism groups:
- Microbes (Bacteria and Archaea)
- Plants (corn/wheat, others)
Continue reading “Pangenome metadata scopeathon in San Diego, January 16-17”
Request for proposals: Single Cell in the Cloud codeathon at NYGC in January
The New York Genome Center is hosting an NCBI Single Cell in the cloud codeathon from January 15-17, 2020. Submissions for project proposals are due December 2nd.
Please submit your proposal and apply here.
What topics are in scope?
This codeathon will focus on single cell data, including RNA, DNA, and chromatin accessibility. We are particularly interested in proposals for pipelines and analysis of SRA data, data interoperability, and using machine learning techniques in clustering. We also welcome proposals for tutorial pipelines and educational tools. You will have access to computational resources in the Cloud to turn your idea into a working prototype. Visit our website for examples of previous codeathon projects.
Continue reading “Request for proposals: Single Cell in the Cloud codeathon at NYGC in January”
NIH Biomedical Data Science Codeathon in Pittsburgh, Jan 8-10
NCBI is pleased to announce a Biomedical Data Science Codeathon in collaboration with Carnegie Mellon in Pittsburgh, PA on January 8-10, 2020.
We’re specifically seeking people with experience working with complex diseases, precision medicine, and genomic analyses. 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. The event is open to anyone selected for the codeathon and willing to travel to Pittsburgh.
Potential topics include:
- Virus Genome Graph tools
- Image analysis pipelines
- RNAseq pipelines
- Cancer graph genomes
- Complex Disease Analysis
Continue reading “NIH Biomedical Data Science Codeathon in Pittsburgh, Jan 8-10”
Virus hunting in the cloud codeathon, v2
We are pleased to announce the second installment of the Virus Hunting Codeathon that will take place from November 4-6, 2019 at the University of Maryland in College Park.
The NCBI will help run this bioinformatics codeathon, hosted by the UMIACS and CBCB at the University of Maryland. The purpose of this event is to continue develop techniques, code, and pipelines to identify known, taxonomically definable, and novel viruses from metagenomic datasets on cloud infrastructure.
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 virological analyses from high-throughput experiments. We especially encourage people who have experience in Computational Virus Hunting or related fields to participate. The event is open to anyone selected for the codeathon and willing to travel to College Park (see below).
- Fast, federated indexing
- Big Query
- Metadata features
- Genome graphs for viruses
- Approximate taxonomic analysis
- Domain/HMM Boundary and Taxonomic Refinement
- Bringing together approximate taxonomy and domain models
- Sequence data quality metrics
- Phage-host interactions
We will provide the final list of projects before the codeathon starts.
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.