Tag: Codeathon

NCBI & NIAID Join Forces to Co-Host Virtual AMR Codeathon

Resistance is Futile: A codeathon to combat antimicrobial resistance

Do you perform antimicrobial resistance (AMR) research, or would you like to join a team to work on microbial and AMR data analysis? NCBI is joining forces with the National Institute of Allergy and Infectious Diseases (NIAID) to co-host a virtual codeathon, Resistance is Futile: A codeathon to combat antimicrobial resistance, which will take place September 23-27, 2024. Continue reading “NCBI & NIAID Join Forces to Co-Host Virtual AMR Codeathon” →

Celebrating the Building Transparent ML/AI Solutions for Biological Research Codeathon

Machine Learning and Artificial Intelligence (ML/AI) are reshaping data science and scientific discovery. Recognizing the important role of collaboration and knowledge sharing in this space, NCBI hosted the “Building transparent ML/AI solutions to advance biological research codeathon” from February 26 to March 1, 2024. This virtual event brought together biologists, developers, and data scientists passionate about using responsible AI in biological research. Continue reading “Celebrating the Building Transparent ML/AI Solutions for Biological Research Codeathon” →

Successful NCBI-NIAID Codeathon Explored VCF Files in Population Genomics

Variant Call Format (VCF) files provide a crucial way to record and share information about genetic variants across samples. NCBI joined forces with the National Institute of Allergy and Infectious Diseases (NIAID) to co-host the VCF Files for Population Genomics Codeathon (July 31 – August 4). The codeathon focused on innovative methods for harnessing VCF files to analyze large datasets using the COVID-19 Genome Sequence Dataset, sourced from the National Library of Medicine (NLM) and NCBI’s SARS-CoV-2 Variant Calling Pipeline. This virtual event was a booming success and brought together experts in viral evolution, molecular epidemiology, and population genomics.

We received outstanding participation and engagement!

62 participants from academia, government, and industries across the world
8 teams collaborated and worked on the projects listed below
5,000+ views of final presentations
100+ strong applicants
21 different countries represented

Continue reading “Successful NCBI-NIAID Codeathon Explored VCF Files in Population Genomics” →

A Successful Codeathon! Collaborating to Expand Expertise in African Life Scientists

Exciting update! We recently collaborated with the African Society for Bioinformatics and Computational Biology (ASBCB) for their spring OMICS Codeathon, and it was a great success. ASBCB is a professional association dedicated to the advancement of bioinformatics and computational biology in Africa. Codeathons are events focused on technology and software development, where participants work collaboratively to solve problems.

The ASBCB codeathon program serves as a grassroots training initiative for expanding expertise among African life scientists. It aims to equip participants with valuable skills and knowledge in life science and biotechnology by using research projects, public datasets, and peer-to-peer learning. Continue reading “A Successful Codeathon! Collaborating to Expand Expertise in African Life Scientists” →

NCBI-NIAID Beyond Phylogenies Codeathon was a success!

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).

Continue reading “Celebrating 1 Year of NCBI Virtual Outreach Events” →

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” →

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:

Viruses
Microbes (Bacteria and Archaea)
Human
Plants (corn/wheat, others)
Animals

Continue reading “Pangenome metadata scopeathon in San Diego, January 16-17” →