This codeathon is a collaborative effort between the National Center for Biotechnology Information (NCBI) and the National Institute of Allergy and Infectious Diseases (NIAID).

Date and Time:  September 23th to 27th, 2024 11 AM - 5 PM (EST)

Details:  Codeathons aim to spark innovation and creative problem-solving by assembling experts to rapidly develop solutions to problems, such as deployable pipelines or bioinformatics services that will empower scientists in the fight against antimicrobial resistance (AMR).

Projects in this codeathon will use data from the National Database of Antibiotic Resistant Organisms (NDARO), a collaborative, cross-agency, centralized hub for researchers to access AMR data to facilitate real-time surveillance of pathogenic organisms.  Teams will be encouraged to explore NDARO and related data from the NCBI Pathogen Detection project (such as that found in the Isolates, MicroBIGG-E, and Antibiotic Susceptibility Test (AST) Browsers).

This event will bring together researchers with expertise in bacteriology and antimicrobial resistance and with skills in areas such as bioinformatics, data science, and data visualization. The codeathon will be collaborative rather than competitive, with teams sharing ideas and technical expertise.

During the week-long codeathon, teams of 5-10 people will collaborate on solutions for the following objectives:

• Identify loss-of-function genetic variations that contribute to AMR.
• Find and classify mobile genetic elements that contribute to AMR in draft genomes.  Note: This work could integrate sequence data with epidemiological, transmission and antibiotic sensitivity testing data to identify patterns and directions of co-migrating of AMR genes or plasmids.
• Elucidate AMR biomarkers for historically hard-to-predict bacterial species (e.g., Acinetobacter, Pseudomonas).

This event is an interactive platform where people with diverse backgrounds and expertise can collaborate, network and potentially foster new collaborations and career opportunities.

At the end of the event, teams will present their work to each other and representatives from the National Institutes of Health (NIH). After the codeathon, all team products will be publicly available through the NCBI Codeathons’ GitHub site.


NCBI Outreach Team: 

• Alexa Salsbury, PhD is the lead for this codeathon. Her background is in structural biology, computational chemistry, biophysics, CADD, and data science.
• Rana Morris, PhD is a NCBI Subject Matter Expert and is providing support for this codeathon. With over 20 years of experience at NCBI, her background includes biochemistry, molecular and cellular biology, genetics, genomics, diagnostic development, and coordination of genetics/genomics components in clinical trials.

NCBI Systems-Cloud Team: 

• Brian Koser is the Cloud Team Lead for this codeathon. He is a Cloud Administrator at NCBI and has been supporting cloud-based data sharing projects at NIH for the past thirteen years.
• Do Hyung Kim, PhD is a new NCBI Cloud team member assisting cloud-related tasks to support codeathon research projects. He has previously worked in several fields including cellular biology, as well as cancer and virus research. 
   
   

More information about this event is available on our NCBI Outreach Events Page.

If you have questions about this codeathon, please email us at codeathons@ncbi.nlm.nih.gov.