diff --git a/impact/presentations.md b/impact/presentations.md index e2f58d60..68b0d3a8 100644 --- a/impact/presentations.md +++ b/impact/presentations.md @@ -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)_ @@ -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) diff --git a/package-lock.json b/package-lock.json index 81688b08..4aed4afa 100644 --- a/package-lock.json +++ b/package-lock.json @@ -16714,9 +16714,9 @@ } }, "node_modules/qs": { - "version": "6.14.2", - "resolved": "https://registry.npmjs.org/qs/-/qs-6.14.2.tgz", - "integrity": "sha512-V/yCWTTF7VJ9hIh18Ugr2zhJMP01MY7c5kh4J870L7imm6/DIzBsNLTXzMwUA3yZ5b/KBqLx8Kp3uRvd7xSe3Q==", + "version": "6.15.2", + "resolved": "https://registry.npmjs.org/qs/-/qs-6.15.2.tgz", + "integrity": "sha512-Rzq0KEyX/w/tEybncDgdkZrJgVUsUMk3xjh3t5bv3S1HTAtg+uOYt72+ZfwiQwKdysThkTBdL/rTi6HDmX9Ddw==", "license": "BSD-3-Clause", "dependencies": { "side-channel": "^1.1.0" @@ -19628,27 +19628,6 @@ "url": "https://github.com/sponsors/sindresorhus" } }, - "node_modules/webpack-dev-server/node_modules/ws": { - "version": "8.20.0", - "resolved": "https://registry.npmjs.org/ws/-/ws-8.20.0.tgz", - "integrity": "sha512-sAt8BhgNbzCtgGbt2OxmpuryO63ZoDk/sqaB/znQm94T4fCEsy/yV+7CdC1kJhOU9lboAEU7R3kquuycDoibVA==", - "license": "MIT", - "engines": { - "node": ">=10.0.0" - }, - "peerDependencies": { - "bufferutil": "^4.0.1", - "utf-8-validate": ">=5.0.2" - }, - "peerDependenciesMeta": { - "bufferutil": { - "optional": true - }, - "utf-8-validate": { - "optional": true - } - } - }, "node_modules/webpack-merge": { "version": "6.0.1", "resolved": "https://registry.npmjs.org/webpack-merge/-/webpack-merge-6.0.1.tgz", @@ -19881,16 +19860,16 @@ } }, "node_modules/ws": { - "version": "7.5.10", - "resolved": "https://registry.npmjs.org/ws/-/ws-7.5.10.tgz", - "integrity": "sha512-+dbF1tHwZpXcbOJdVOkzLDxZP1ailvSxM6ZweXTegylPny803bFhA+vqBYw4s31NSAk4S2Qz+AKXK9a4wkdjcQ==", + "version": "8.21.0", + "resolved": "https://registry.npmjs.org/ws/-/ws-8.21.0.tgz", + "integrity": "sha512-Vsp28b7DRcimFQvrqu2Wek3z1iYxDCWqHYB8Qsnk/S4RfaCQzPGPyBNuVjJV3cd6UiKtUtp6sNM77gWvzcCH+g==", "license": "MIT", "engines": { - "node": ">=8.3.0" + "node": ">=10.0.0" }, "peerDependencies": { "bufferutil": "^4.0.1", - "utf-8-validate": "^5.0.2" + "utf-8-validate": ">=5.0.2" }, "peerDependenciesMeta": { "bufferutil": { diff --git a/package.json b/package.json index e0b2e3bf..7bb1753d 100644 --- a/package.json +++ b/package.json @@ -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" } }