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 intersection of ChatGPT's capabilities with Write the Docs, a documentation system widely used by devel...
Nov 04, 2023•26 min
Lee and Andrew are at the Global Microbial Identifier conference (GMI13) in Vancouver Canada. On day 3 we catch up with Dr Ruth Timme.
Sep 18, 2023•8 min
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.
Sep 17, 2023•8 min
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.
Sep 16, 2023•21 min
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 interfere with genuinely evaluating a candidate's knowledge during interviews. Drawing parallels with calcul...
Jul 06, 2023•27 min
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 boilerplate programs, drafting documents, to summarizing vast tracts of data. Andrew talks about his...
Jun 22, 2023•31 min
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 track of things. The hosts caution against starting with trendy languages that are constantly changing...
Jun 08, 2023•30 min
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). Link to paper: https://www.nature.com/articles/s41564-022-01214-9 History paper: https://www.scienc...
May 25, 2023•46 min
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 Bioinformatics at the University of Innsbruck in the departments of Microbiology and the Digital Sc...
May 11, 2023•33 min
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 the conversation by sharing that she enjoys research and solving problems with different tools. The t...
Apr 27, 2023•15 min
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 in Norwich UK.
Apr 20, 2023•44 min
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 around it. They began by explaining the original Kraken, which uses an exact camera matching process an...
Apr 06, 2023•22 min
We are talking about KRAKEN - the taxonomic classification software and in the hot seat are Dr Jennifer Lu and Natalia Rincon from Johns Hopkins University Center for Computational Biology. The MicroBinfie podcast welcomed Dr. Jennifer Lu and Natalia Rincon to discuss Kraken, a taxonomic classification software. Developed in 2013-2014, Kraken easily identifies and assigns sequencing reads to a specific species, genus, or general bacteria. Its efficiency in classifying millions or billions of rea...
Mar 23, 2023•27 min
Ed Feil is a professor of bacterial evolution at the University of Bath, and Natacha Couto, a data scientist at the Center of Genomic Pathogen Surveillance at the University of Oxford. We delve into the concept of multi-locus sequence typing (MLST) in bacterial population genetics. They highlight how the MLST method allows for defining strains based on partial sequences that range up to 500 base pairs. The method measures differences between loci for each strain, offering an allele number while ...
Mar 09, 2023•40 min
The hosts of the MicroBinfie podcast invite Dr Natacha Couto (University of Oxford) and Professor Ed Feil (University of Bath) as special guests to discuss the concept of "One Health". One Health is a comprehensive approach that seeks to manage the problem of antimicrobial resistance (AMR) by addressing the use of antibiotics in healthcare, agriculture, and the environment. It aims to improve health outcomes across all sectors to create a better planet. However, the diagrams often used to repres...
Feb 23, 2023•36 min
We celebrate having 100 episodes! We look back at the history of our podcast and then talk about what the future might hold. Then: Lee gets his revenge by having Andrew and Nabil pronounce words local to him. We very briefly mentioned this paper: https://www.nature.com/articles/s41586-022-05543-x Nabil was trying to remember this particular site and remembered it after recording: https://phagesdb.org/phages/
Feb 09, 2023•52 min
At the 8th Microbial Bioinformatics Hackathon in Bath we talked to a live panel with Kristy Horan, Torsten Seemann, Finlay Maguire and Andrew Page about bioinformatics from the frontlines. We apologise for the poor audio quality, it was recorded in a room with 20 people in the background so at points it got a bit loud, however we felt you might enjoy the discussion regardless.
Jan 26, 2023•39 min
We interview Frank Ambrosio. He is embarking on a lifestyle of nomadic bioinformatics, living his best life. * https://www.linkedin.com/in/francis-ambrosio/ In this episode of the MicroBinfie podcast, Frank Ambrosio, a bioinformatician working for Theiagen as a traveling bioinformatician, joins co-hosts Andrew Nabil and Lee to talk about his journey into bioinformatics. Frank shares how he transitioned from being a lab technician and microbiologist to analyzing his own data and pursuing a master...
Jan 12, 2023•43 min
We discuss recent advancements in genome sequencing technologies, based on what we've been hearing at conferences and within the community. The Microbial Bioinformatics podcast brought together three experts, Andrew, Lee, and Nabil, to discuss the latest advances in sequencing technologies. The team explored the new developments in the market, including a cutting-edge instrument from Element Biosciences that captured Nabil's attention. Andrew analyzed the adaptive sequencing feature in Illumina ...
Dec 29, 2022•17 min
We've been busy attending in-person conferences such as IMMEM XIII and ASM NGS so we thought we'd give you some of our reflections. We discuss waste water surveillance, hybrid conferences and metadata amongst other things.
Dec 22, 2022•36 min
For the first time ever all 3 MicroBinfies are together in person to record an episode. We are joined by Torsten Seemann for a conversation about how what we do in research can get lost in translation when applied to public health. We discuss what we did with SARS-CoV-2 genomics and somehow end up chatting about geography and language. Hope you enjoy.
Dec 08, 2022•42 min
Over the past few weeks scientists have been swapping Twitter for Mastodon. Our very own Nabil-Fareed Alikhan talks about his experience with setting up and running a Mastodon server called https://mstdn.science which is one of the places where scientists have moved over to. We are joined by Emma Hodcroft to get an independent scientists view on the whole thing. In the MicroBinfie podcast, Andrew and Nabil discuss the migration of academics from Twitter to a new platform called Mastodon, with Na...
Nov 17, 2022•28 min
We go through bug reports and issues and give insights into how bioinformaticians dig into them. We suggest the underlying problems and possible solutions and also provide tips on how to file better bug reports.
Nov 10, 2022•17 min
Often the hard part of bioinformatics isnt the analysis, its getting all of the software you need setup and installed. Come with us on this journey and avoid dependancy hell. In the MicroBinfie podcast, the hosts discuss the struggles of installing, managing, and dealing with dependencies with bioinformatics software. In the past, software installations were a nightmare, and it was common to edit lines of code and manage dependencies manually, causing conflicts like diamond dependency. To ease t...
Oct 27, 2022•36 min
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 track of things. The hosts caution against starting with trendy languages that are constantly changing...
Oct 13, 2022•30 min
90 Public health bioinformatics on the cloud with WDL + Terra.bio by Microbial Bioinformatics
Sep 29, 2022•44 min
Today on the @microbinfie podcast, we talk about WDL with @sevinsky and @DannyJPark. We learn what widdle means to Andrew and his kids. Joel takes a shot at Lyve-SET and you'll never guess what happens next. In the MicroBinfie podcast, we discuss the workflow description language (WDL) commonly used to describe bioinformatics pipelines in a portable and cross-environmental way. The starting point is the presumption that tools are already containerized, and WDL helps to bind them together. The gu...
Sep 15, 2022•26 min
This is an extended directors cut of our chat with Dr Henk den Bakker about Sepia. Its a summer holiday bonus. Some URLs Get Sepia here: https://github.com/hcdenbakker/sepia Some information on the food safety informatics group at UGA: https://www.denglab.site/ Rust: https://www.rust-lang.org/ Kalamari: https://github.com/lskatz/kalamari CAMI: https://www.nature.com/articles/nmeth.4458
Aug 04, 2022•53 min
87 Nextstrain, SARSCOV2 and dealing with a data deluge by Microbial Bioinformatics
Jul 21, 2022•28 min
86 What's next for nextstrain? by Microbial Bioinformatics
Jul 07, 2022•23 min
