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.
https://joss.theoj.org/
episode 3: 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
- [00:02:21] Introduction to Baargin: Juliette explains that Baargin 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.
- [00:06:20] Multiplex Sequencing: Juliette discusses the challenge of assembling genomes for multiple strains simultaneously using high-throughput sequencing technologies.
- [00:07:21] Next-Gen Sequencing and Assembly: The conversation delves into next-generation sequencing, the assembly of short reads, and the emergence of long-read technologies for comprehensive genome analysis.
- [00:09:59] Target Audience: Juliette identifies microbiologists as the primary audience for Baargin, emphasizing its user-friendliness for researchers producing genome data.
- [00:12:50] Nextflow in Bioinformatics: Juliette explains the role of Nextflow in bioinformatics and its popularity, highlighting its benefits for scalable and reproducible workflows.
- [00:17:03] Open Source Philosophy: Juliette shares her commitment to open source principles, advocating for transparency, reproducibility, and collaborative contributions in research.
- [00:19:20] Research Using Baargin: Juliette discusses her published studies, including the identification of drug-resistant E. coli transmission in Chile and ongoing projects in Vietnam and Cambodia.
- [00:20:14] Publishing in JOSS: Juliette describes the benefits of publishing in the Journal of Open Source Software (JOSS), emphasizing the focus on code and transparent review processes.
- [00:23:27] Documentation Importance: The hosts discuss the significance of documentation in software development, with Juliette highlighting its critical role in ensuring usability.
- [00:26:03] Contributions and Skills: Juliette welcomes contributions to Baargin, mentioning that comfort with git and Nextflow is essential for potential contributors.
- [00:28:27] Future Roadmap: Juliette outlines plans for extending Baargin, including adding tools for predicting resistance genes, improving detection of mobile genetic elements, and enhancing multi-locus sequence typing.
Links
- JOSS paper: https://joss.theoj.org/papers/10.21105/joss.05397
- Baargin code repository: https://github.com/jhayer/baargin
- Nextflow: https://www.nextflow.io/
- Study using Baargin: Multiple clonal transmissions of clinically 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
- Juliette on GitHub (@jhayer), ResearchGate, and X (@juliette_hayer).
- The Journal of Open Source Software (Twitter/X, blog)
- @arfon on (fosstodon, Linkedin, GitHub, website)
- @abbycabs on (Twitter/X, hachyderm, bsky, Linkedin, GitHub, website)