Micro binfie podcast
Technology
About
Microbial Bioinformatics is a rapidly changing field marrying computer science and microbiology. Join us as we share some tips and tricks we’ve learnt over the years. If you’re student just getting to grips to the field, or someone who just wants to keep tabs on the latest and greatest - this podcast is for you. The hosts are Dr. Lee - a bioinformatician in the United States, Dr. Nabil-Fareed Alikhan from the University of Oxford (UK), and Prof. Andrew Page from Origin Sciences (UK) and bring together years of experience in microbial bioinformatics.The opinions expressed here are our own and do not necessarily reflect the views of University of Oxford or Origin Sciences.Intro music : Werq - Kevin MacLeod (incompetech.com)Licensed under Creative Commons: By Attribution 3.0 Licensehttp://creativecommons.org/licenses/by/3.0/Outro music : Scheming Weasel (faster version) - Kevin MacLeod (incompetech.com)Licensed under Creative Commons: By Attribution 3.0 Licensehttp://creativecommo
Episodes
- 152 - Deacon part 2
In this follow-up Software Deep Dive episode, we continue our conversation with Dr. Bede Constantinides (University of Birmingham) about the design and implementation of Deacon, a fast host-read removal tool for metagenomics. Deacon uses m…
- 151 - Deacon part 1
In this Software Deep Dive episode, we talk with Dr. Bede Constantinides (University of Birmingham) about Deacon, a tool for removing host DNA reads from metagenomic datasets. We discuss why host read removal is a deceptively difficult pro…
- 150 - Genomicx
In this episode, Lee, Nabil, and Andrew experiment with “vibe coding” bioinformatics tools using AI coding assistants. The goal: quickly build useful genomics utilities that run entirely in the browser via WebAssembly, without requiring co…
- 149 - Bridging AI & Biosciences
Join hosts Kieren Sharma (Artificially Ever After podcast, University of Bristol) and Andrew Page (MicroBinfie podcast, Origin Sciences) for a compelling live panel discussion exploring the dynamic intersection of artificial intelligence a…
- 148 - NextFlow debate 3
Final part of our discussion/debate on NextFlow
- 147 - NextFlow debate 2
Part two of debating NextFlow
- 146 - NextFlow debate 1
Andrew, Nabil, and Lee debate about NextFlow!
- 145 - micro binfie Pathoplexus part 2
Nabil and Lee bring a guest host Clint to talk with some of the people behind Pathoplexus http://pathoplexus.org/ * Dr. Emma Hodcroft - https://pathoplexus.org/about/eb * Dr. Theo Sanderson - https://pathoplexus.org/about/development-team…
- 144 - micro binfie Pathoplexus part 1
Nabil and Lee bring a guest host Clint to talk with some of the people behind Pathoplexus http://pathoplexus.org/ * Dr. Emma Hodcroft - https://pathoplexus.org/about/eb * Dr. Theo Sanderson - https://pathoplexus.org/about/development-team…
- 143 - where we catch up on our professional lives
143 - where we catch up on our professional lives by Microbial Bioinformatics
- 142 - Microbinfie - genomeqc
The crew talks about the genomeqc ecosystem. Check it out at https://happykhan.github.io/qualibact/ Errata: The project name was chaned to qualibact and is no longer genomeqc as mentioned on the episode.
- 140 Exploring Clinical Metagenomics
In this episode of the Podcast, hosts Lee Katz and Andrew Page delve into the intricacies of clinical metagenomics. Joined by experts Torsten Seemann and Finlay Maguire, they explore the challenges and methodologies involved in identifying…
- 139 Lassa virus genomics
On this episode we are joined by Sara Zufan to discuss her PhD journey and recent projects. The episode covers various research experiences and challenges in the field, including the rapid detection of AMR using nanopore sequencing, COVID-…
- 138 Decoding Tetracycline Resistance in MRSA
In this episode of the Micro Binfie Podcast, host Andrew Page takes listeners to the heart of the microbial genomics hackathon in Bethesda, Maryland, for an engaging conversation with special guest Megan Phillips, a PhD student from Emory…
- 137 Contagion part 2
In a two-part discussion, the hosts analyze the movie Contagion from their expert perspectives, focusing on the film's portrayal of epidemiology and genomics. They note that the movie compresses timelines for dramatic effect, speeding up t…
- 135 Assembling ATCC bacterial strains
In this episode of the Micro Binfie podcast, host Andrew Page is joined by Nikhita Puthuveetil, Senior Bioinformatician at the American Type Culture Collection (ATCC). They delve into ATCC's ambitious project of sequencing a vast array of…
- 141 hackathon panel
Andrew, Lee, Torsten, and Fin muse over the future of MLST, Illumina, and Nanopore at the ASM NGS Hackathon
- 136 Contagion part 1
In a two-part discussion, the hosts analyze the movie Contagion from their expert perspectives, focusing on the film's portrayal of epidemiology and genomics. They note that the movie compresses timelines for dramatic effect, speeding up t…
- 134 Diving into MRSA, Genomics, and Public Health
In this episode of the Micro Binfie Podcast, host Andrew Page speaks with Dr. Brooke Talbot, a recent PhD graduate from Emory University, about her research on Staphylococcus aureus, with a focus on MRSA and antibiotic resistance. Brooke s…
- 133 The Role of Bioinformatics in Public Health and Disease Outbreaks
In this episode of the Micro Binfie podcast, host Andrew Page talks with Dr. Erin Young, a bioinformatician at the Utah Public Health Laboratory, recorded during the 10th Microbial Bioinformatics Hackathon in Bethesda, Maryland. Erin share…
- 132 Unlocking the Secrets of Antimicrobial Resistance in Metagenomes
In this episode of the Micro Binfie podcast, host Andrew Page is live from the 10th Microbial Bioinformatics Hackathon in Bethesda, Maryland. He sits down with David Mahoney, a PhD student from Dalhousie University in Halifax, Nova Scotia.…
- 131 Bioinformatics Evolution: Torsten Seemann on Snippy, Open-Source Support, and Global Genomics
In this episode of the Micro Binfie Podcast, host Andrew Page catches up with Torsten Seemann at the 10th Microbial Bioinformatics Hackathon in Bethesda, Maryland. They discuss the rapid evolution of bioinformatics, the challenges faced by…
- 130 Exploring Genomic Innovation and Machine Learning in Public Health
In this episode of the Micro binfie Podcast, host Andrew Page sits down with Tim Dallman at the 10th Bioinformatics Hackathon in Bethesda, Maryland. Tim shares insights from his work at Utrecht University in the Netherlands, where he focus…
- 129 Genomics on the Frontier: Bactopia, Bioinformatics, and Pathogen Surveillance with Robert Petit
Host Andrew Page is joined by Robert Petit from the Wyoming Public Health Laboratory. Robert, a key developer of the Bactopia pipeline, shares insights into how this end-to-end tool is transforming bacterial genomic surveillance. They dive…
- 128 Haiti cholera outbreak with Christine Lee and Cynney Walters
Andrew and Lee talk with Christine and Cynney about the Haiti cholera outbreak Cynney Walters: https://www.linkedin.com/in/cynney-walters-763111190 Walters et al, "Genome sequences from a reemergence of Vibrio cholerae in Haiti, 2022 revea…
- 127 Minimum spanning trees
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
- 126 Tree viz
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: htt…
- 125 Kostas Konstantinidis returns to talk to us about ANI and metagenomics
125 Kostas Konstantinidis returns to talk to us about ANI and metagenomics by Microbial Bioinformatics
- 124 Kostas Konstantinidis talks to us about ANI and metagenomics
We talk with Kostas! For more information please visit https://enve-omics.gatech.edu/
- 123 The Revolution of Hash Databases in cgMLST
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. T…
- 122 GAMBIT: Genomic Approximation Method for Bacterial Identification and Tracking
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 App…
- 121 K-mers, Sourmash, and Open Source Software - More Conversations with Titus Brown
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…
- 120 Scaling Metagenomic Search with Sourmash - Conversations with Titus Brown
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 analy…
- 119 The Challenges of Microbial Taxonomy - Conversations with Titus Brown
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 vers…
- 118 Real bioinformaticians react to Jurassic Park
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=D6nps33O42Fmk…
- 117 From Math to Metagenomics - Titus Brown on Career Journeys and Software Solutions
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.…
- 116 AI Authorship and Ethics in Academic Publishing for Genomics
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. Autho…
- 115 Write-the: speeding up software development for bioinformatics
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…
- 114 Write-the: Automating Code Documentation ChatGPT
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 eng…
- 113 Global Microbial Identifier conference with Ruth Timme
Lee and Andrew are at the Global Microbial Identifier conference (GMI13) in Vancouver Canada. On day 3 we catch up with Dr Ruth Timme.
- 112 Global Microbial Identifier conference with Will Hsiao
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.
- 111 Global Microbial Identifier with Finlay Maguire and Emma Griffiths
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.
- 110 ChatGPT: The Bioinformatics Calculator
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…
- 109 AI Unleashed: Navigating the Opportunities and Challenges of AI in Microbial Bioinformatics
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, notab…
- Encore: What language should I learn?
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 funda…
- 108 SeqCode: a nomenclatural code for prokaryotes described from sequence data
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 Migu…
- 107 Systematics and naming of prokaryotes in the era of sequencing
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.…
- 106 Why on earth would you do a PostDoc?
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 o…
- 105 Mobile genetic elements panel discussion
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 MGE…
- 104 The Kraken software suite
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…