Micro binfie podcast

Nabil and Lee have a quick chat about minimum spanning trees (MST). Eburst paper: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-10-152

We go over tree visualizations! * Microreact https://microreact.org/,https://www.phylocanvas.gl/ * grapetree https://github.com/achtman-lab/GrapeTree * Auspice/NextStrain https://nextstrain.org/ * Taxonium https://taxonium.org/ * Itol: https://itol.embl.de/ * PhyloViz https://online.phyloviz.net/index * Phandango https://jameshadfield.github.io/phandango/#/main

125 Kostas Konstantinidis returns to talk to us about ANI and metagenomics by Microbial Bioinformatics

We talk with Kostas! For more information please visit https://enve-omics.gatech.edu/

In this episode of the Micro Binfie Podcast, hosts Dr. Andrew Page and Dr. Lee Katz delve into the fascinating world of hash databases and their application in cgMLST (core genome Multilocus Sequence Typing) for microbial bioinformatics. The discussion begins with the challenges faced by bioinformaticians due to siloed MLST databases across the globe, which hinder synchronization and effective gen...

We discuss GAMBIT, software for accurately classifying bacteria and eukaryotes using a targeted k-mer based approach. GAMBIT software: https://github.com/gambit-suite/gambit GAMBIT suite: https://github.com/gambit-suite GAMBIT (Genomic Approximation Method for Bacterial Identification and Tracking): A methodology to rapidly leverage whole genome sequencing of bacterial isolates for clinical identi...

In this episode, Andrew Page and Lee Katz continue their conversation with Titus Brown, diving deeper into his work on k-mers, Sourmash, and open source software development: Topics discussed: K-mers for analyzing sequencing data, and how Sourmash builds on MinHash How Sourmash handles k-mers for metagenomic comparisons vs. MASH The modhash and bottom sketch approaches used in Sourmash Dealing wit...

In this final episode with Titus Brown, the conversation focuses on his work scaling metagenomic search with Sourmash: An overview of what Sourmash does - sketching and comparing large k-mer datasets How the sampling approach enables analyses like containment estimation Exciting capabilities of the Branchwater tool for multi-threaded real-time SRA search Scaling to search across millions of metage...

In this episode, Andrew Page and Lee Katz continue their chat with Titus Brown, focusing on taxonomy assignment in metagenomics: Topics discussed: Dealing with contamination and low quality genomes in reference databases Sourmash as a versatile search tool, not a curated database The need for high confidence in taxonomic assignment in public health Most microbial assignment tools have low specific...

Andrew, Nabil, and Lee react to the bioinformatics and the science overall in the 1993 film Jurassic Park. We looked at these YouTube clips: * https://youtu.be/mDTaykXudVI?si=I5aiUdBGStpIKHVC * https://youtu.be/RLz5Api676Y?si=D6nps33O42Fmk4Ac * https://youtu.be/0Nz8YrCC9X8?si=KNwkeFoS6Bu4LOpv * https://youtu.be/dxIPcbmo1_U?si=TOBw5AONYVCW0JzV * https://youtu.be/m1lc8GwBKFE?si=rj7Oiq51l2_dB6ro More...

In this episode of the Micro Binfie Podcast, Andrew Page and Lee Katz interview Titus Brown about his journey from studying math and physics as an undergrad to becoming a bioinformatician focusing on metagenomics and software development. Topics discussed: Titus' background in math, physics, digital evolution research, and developmental biology His transition into bioinformatics to analyze the inf...

The podcast discusses an article co-authored by Andrew Page, examining the use of GPT-4 for research publication. The conversation focuses on the authorship of articles generated by GPT-4 and the implications for academic publishing. Authorship and Ethics: Andrew discusses the question of authorship when AI-generated content is involved in research articles. He explores the ethical implications an...

We continue our conversation with Wytamma Wirth about write-the and all things AI. It starts with discussing the usage of language models, specifically ChatGPT, in writing boilerplate code, and how it can assist in generating code snippets, unit tests, and even documentation strings. The participants also explore the potential of incorporating it into code editors to make coding more efficient and...

In this episode, we dive deep into the world of automated code documentation and conversion using ChatGPT through the write-the software developed by Dr Wytamma Wirth from The University of Melbourne. Our guest, an experienced software engineer, takes us on a journey through the challenges and nuances of writing code documentation and the role AI can play in easing this process. We explore the int...

Lee and Andrew are at the Global Microbial Identifier conference (GMI13) in Vancouver Canada. On day 3 we catch up with Dr Ruth Timme.

Andrew and Lee are at the Global Microbial Identifier conference (GMI13) in Vancouver Canada. We talk to Dr William Hsiao, one of the organisers of the conference.

Andrew and Lee are at the Global Microbial Identifier conference 13 in Vancouver Canada. On the first day they talked to Dr Finlay Maguire and Dr Emma Griffiths about microbial genomics and Tim Hortons.

In this episode there is a comprehensive discussion on the influence of AI, especially GPT-4, in the sphere of microbial bioinformatics. They reflect on a study testing GPT-4's problem-solving capabilities, which raises concerns about its potential impact on employment practices and academic integrity. There's speculation that AI's proficiency in tackling standard technical problems could interfer...

In this episode of the Micro Binfie Podcast, titled "AI Unleashed: Navigating the Opportunities and Challenges of AI in Microbial Bioinformatics", Lee, Nabil, and Andrew unpack the implications of generative predictive text AI tools, notably GPT, on microbial bioinformatics. They kick off the conversation by outlining the various applications of AI tools in their work, which range from generating...

The MicroBinfie podcast discusses the top programming languages for bioinformatics. Andrew, Lee, and Nabil agree that Python is a great starting point for its consistency and rigor. Its strict syntax is ideal for teaching programming fundamentals that are essential in any language. In contrast, Perl encourages multiple ways of doing the same thing, creating confusion and difficulties in keeping tr...

We are back talking about systematics, and SeqCode; a nomenclatural code for prokaryotes described from sequence data. Marike Palmer is a Postdoctoral researcher in the School of Life Sciences at the University of Nevada Las Vegas and Miguel Rodriguez is an Assistant Professor of Bioinformatics at the University of Innsbruck in the departments of Microbiology and the Digital Science Center (DiSC)....

Today we are talking about systematics, and specifically SeqCode; a nomenclatural code for prokaryotes described from sequence data. Joining us to talk about it are co-authors on the recent publication. Marike Palmer and Miguel Rodriguez. Marike Palmer is a Postdoctoral researcher in the School of Life Sciences at the University of Nevada Las Vegas and Miguel Rodriguez is an Assistant Professor of...

An honest discussion about the up and downsides of doing a postdoc in front of an audience of first year PhD students. Guests Dr Emma Waters, Dr Heather Felgate and Dr Muhammad Yasir are joined by Dr Andrew Page. It was recorded in front of a live audience of PhD students at the Microbes, Microbiomes and Bioinformatics doctoral training program in the Quadram Institute in Norwich UK. Emma starts t...

This is a panel discussion on mobile genetic elements, guest chaired by Dr Muhammad Yasir with guests Dr Emma Waters, Dr Heather Felgate and Dr Andrew Page. We cover AMR, Salmonella Typhi and Staphylococci and outbreaks and the role of MGEs. It was recorded in front of a live audience of PhD students at the Microbes, Microbiomes and Bioinformatics doctoral training program in the Quadram Institute...

We talk about KRAKEN the taxonomic classification software and the software suite around it and are joined by Jennifer Lu and Natalia Rincon from Johns Hopkins University Center for Computational Biology. Dr. Jennifer Lu and Natalia Rincon from the Kraken software development team were interviewed on the MicroBinfie podcast. They discussed the various versions of Kraken and the tools developed aro...