République Française Inserm
Institut thématique Immunologie, inflammation, infectiologie et microbiologie

JPIAMR virtual Microbial Bioinformatics Hackathon 2021

The Joint Programming Initiative on Antimicrobial Resistance (JPIAMR) together with the Public Health Alliance for Genomic Epidemiology (PHA4GE) and CLIMB-BIG-DATA, we are organising :


JPIAMR webinar :

Microbial bioinformatics hackathon 

Bioinformatics tools and methods for AMR in bacteria

11-13 October 2021

3-7 pm London time (BST)


Register online on the JPIAMR website dedicated to the eventThere are 30 places available to attend this special interest group. 

At a minimum participants will be expected to know in advance how to use the Linux command line, have a good working knowledge of AMR, and have an understanding of genomics.



Together with the Public Health Alliance for Genomic Epidemiology (PHA4GE) and the Joint Programming Initiative on Antimicrobial Resistance (JPIAMR), we are organising the 7th Microbial Bioinformatics Hackathon with a special focus on Antimicrobial Resistance.

Antimicrobial resistance is a critical universal issue and scientists need reliable, fast, reproducible tools for their research. The aim of this hackathon is to improve upon/build/extend bioinformatics tools and methods for the AMR community. This year’s hackathon has a special focus on antimicrobial resistance in bacteria. 

We want to bring together international bioinformatics researchers, scientists and clinicians to collaborate and solve common problems that impact our community, as pathogens know no borders.


Potential topics

  • SNV variant detection standard for AMR (for example Mtb)
  • Alignment of AMR databases (programmatically merging and deduplicating).
  • Creation of standardised benchmarking datasets (genomic, metagenomic, assembled, unassembled)
  • Integrate hAMRonization into BioPython to ease widespread adoption
  • Extend open source AMR bioinformatics tools to improve consistency and interoperability (when the software says  ‘gene name’ it should mean the same thing everywhere).
  • GPU enabled AMR calling and analysis


Steering group 

Andrew Page, Quadram Institute, UK, representing CLIMB-BD and PHA4GE
Emma Griffiths, SFU, Canada, representing PHA4GE
Mark Pallen, Quadram Institute, UK, representing CLIMB-BD
Lisa Marchioretto, Quadram Institute, UK, representing CLIMB-BD
Finlay Maguire, Dalhousie University, Canada, representing PHA4GE
Jessica Boname, MRC, UK, representing JPIAMR and MRC