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rpetit3 merged 2 commits into from
Jun 5, 2026
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Add presentations #19

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add recent presentations
rpetit3 Jun 5, 2026
85c934e
fix qs and ws dependabot alerts (#11, #12)
rpetit3 Jun 5, 2026
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11 changes: 10 additions & 1 deletion impact/presentations.md
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Expand Up @@ -22,9 +22,14 @@ Slides: [PDF](https://datasets.bactopia.io/media/2023-bactopia-edlb-workshop.pdf

## Talks

- _Bactopia: a Flexible Pipeline for Complete Analysis of Bacterial Genomes (June 2026)_
A talk presented by [Dr. Robert A Petit III](https://www.robertpetit.com) at the
[Centre for Pathogen Genomics Bioinformatics Seminar](https://biomedicalsciences.unimelb.edu.au/departments/microbiology-Immunology/research/centre-for-pathogen-genomics). This talk provided a full overview of Bactopia. Including the main pipeline, Bactopia Tools, and the external libraries (e.g. bactopia-py, nf-bactopia). A look into LLM usage in Bactopia was also provided.
Slides: [PDF](https://datasets.bactopia.io/media/2026-rp3-cpg-binfies-bactopia.pdf)

- _How we avoided AI slop in Bactopia (April 2026)_
A talk presented by [Dr. Robert A Petit III](https://www.robertpetit.com) at the [Nextflow Summit Boston 2026](https://summit.nextflow.io/2026/boston/overview/). This talk walked through growing pains of utilizing LLMs during the development of Bactopia, as well as the steps to ensure effective usage of LLMs in the future.
Video: _coming soon!_
Video: [YouTube](https://www.youtube.com/watch?v=m_AwgTzVBqY)
Slides: [PDF](https://datasets.bactopia.io/media/2026-rp3-bactopia-nf-summit.pdf)

- _Bactopia - Enhancing and expanding the Bactopia framework (October 2024)_
Expand Down Expand Up @@ -79,6 +84,10 @@ Slides: [Web](https://bit.ly/3lQpZKo), [PDF](https://datasets.bactopia.io/media/

## Posters

- _Bactopia v4: A Scalable Bacterial Genome Surveillance Pipeline (May 2026)_
A poster presented by [Dr. Robert A Petit III](https://www.robertpetit.com) at the [SFA²F 2026](https://www.sfafmeeting.org/) outlining the latest changes in Bactopia.
Slides: [PDF](https://datasets.bactopia.io/media/2026-bactopia-poster.pdf)

- _Bactopia v4: A Scalable Bacterial Genome Surveillance Pipeline (May 2026)_
A poster presented by [Dr. Robert A Petit III](https://www.robertpetit.com) at the [APHL 2026](https://www.aphl.org/conferences/annualmeeting/Pages/default.aspx) outlining the latest changes in Bactopia.
Slides: [PDF](https://datasets.bactopia.io/media/2026-bactopia-poster.pdf)
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37 changes: 8 additions & 29 deletions package-lock.json
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4 changes: 3 additions & 1 deletion package.json
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Expand Up @@ -53,6 +53,8 @@
},
"overrides": {
"serialize-javascript": "^7.0.5",
"uuid": "^14.0.0"
"uuid": "^14.0.0",
"qs": "^6.15.2",
"ws": "^8.20.1"
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}
}