Sign up to save your podcasts
Or
Share Studying Superbugs – Juliette Hayer on Baargin
Share to email
Share to Facebook
Share to X
Share to email
Share to Facebook
Share to X
Or
Studying Superbugs – Juliette Hayer on Baargin
#3: Juliette Hayer joins Arfon and Abby to discuss Baargin, an open source tool she created to analyze bacterial genomes, especially those resistant to antibiotics.
Juliette is a PhD Researcher at the French Research
Institute for Sustainable Development (IRD, Institut de Recherche pour le Développement), at the MIVEGEC research unit, where she implements computational biology methods for bacterial genomics and metagenomics to understand the circulation and transmission of antimicrobial resistance.
You can find Juliette on GitHub (@jhayer), ResearchGate, and X (@juliette_hayer).
Episode Highlights
stands for Bacterial Assembly and Antimicrobial Resistance Genes
Detection in Nextflow. She developed it to analyze the genomes of
drug-resistant bacteria in various environments.
assembling genomes for multiple strains simultaneously using
high-throughput sequencing technologies.
into next-generation sequencing, the assembly of short reads, and the
emergence of long-read technologies for comprehensive genome analysis.
the primary audience for Baargin, emphasizing its user-friendliness for
researchers producing genome data.
Nextflow in bioinformatics and its popularity, highlighting its
benefits for scalable and reproducible workflows.
open source principles, advocating for transparency, reproducibility,
and collaborative contributions in research.
studies, including the identification of drug-resistant E. coli
transmission in Chile and ongoing projects in Vietnam and Cambodia.
publishing in the Journal of Open Source Software (JOSS), emphasizing
the focus on code and transparent review processes.
significance of documentation in software development, with Juliette
highlighting its critical role in ensuring usability.
to Baargin, mentioning that comfort with git and Nextflow is essential
for potential contributors.
Baargin, including adding tools for predicting resistance genes,
improving detection of mobile genetic elements, and enhancing
multi-locus sequence typing.
Links
relevant extended-spectrum beta-lactamase–producing Escherichia coli
among livestock, dogs, and wildlife in Chile: https://doi.org/10.1016/j.jgar.2023.07.009
---
Supercharge your research with the latest scientific software showcased in the Journal of Open Source Software (JOSS). Hear directly from authors on their work, their motivations, and new ways open source software can accelerate your work.
Hosted by editor-in-chief Arfon Smith and founding editor Abby Cabunoc Mayes, each episode features an interview with different authors of published papers in JOSS. Tune in to learn about the latest developments in research software engineering and open science, and how they are changing the way research is conducted.
New episodes every other Thursday.
View all episodes
By The Journal of Open Source Software#3: Juliette Hayer joins Arfon and Abby to discuss Baargin, an open source tool she created to analyze bacterial genomes, especially those resistant to antibiotics.
Juliette is a PhD Researcher at the French Research
Institute for Sustainable Development (IRD, Institut de Recherche pour le Développement), at the MIVEGEC research unit, where she implements computational biology methods for bacterial genomics and metagenomics to understand the circulation and transmission of antimicrobial resistance.
You can find Juliette on GitHub (@jhayer), ResearchGate, and X (@juliette_hayer).
Episode Highlights
stands for Bacterial Assembly and Antimicrobial Resistance Genes
Detection in Nextflow. She developed it to analyze the genomes of
drug-resistant bacteria in various environments.
assembling genomes for multiple strains simultaneously using
high-throughput sequencing technologies.
into next-generation sequencing, the assembly of short reads, and the
emergence of long-read technologies for comprehensive genome analysis.
the primary audience for Baargin, emphasizing its user-friendliness for
researchers producing genome data.
Nextflow in bioinformatics and its popularity, highlighting its
benefits for scalable and reproducible workflows.
open source principles, advocating for transparency, reproducibility,
and collaborative contributions in research.
studies, including the identification of drug-resistant E. coli
transmission in Chile and ongoing projects in Vietnam and Cambodia.
publishing in the Journal of Open Source Software (JOSS), emphasizing
the focus on code and transparent review processes.
significance of documentation in software development, with Juliette
highlighting its critical role in ensuring usability.
to Baargin, mentioning that comfort with git and Nextflow is essential
for potential contributors.
Baargin, including adding tools for predicting resistance genes,
improving detection of mobile genetic elements, and enhancing
multi-locus sequence typing.
Links
relevant extended-spectrum beta-lactamase–producing Escherichia coli
among livestock, dogs, and wildlife in Chile: https://doi.org/10.1016/j.jgar.2023.07.009
---
Supercharge your research with the latest scientific software showcased in the Journal of Open Source Software (JOSS). Hear directly from authors on their work, their motivations, and new ways open source software can accelerate your work.
Hosted by editor-in-chief Arfon Smith and founding editor Abby Cabunoc Mayes, each episode features an interview with different authors of published papers in JOSS. Tune in to learn about the latest developments in research software engineering and open science, and how they are changing the way research is conducted.
New episodes every other Thursday.