Micro binfie podcast

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 spe...

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 p...

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 heal...

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....

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.

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 transit...

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 Biosc...

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.

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.

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...

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.

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...

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...

90 Public health bioinformatics on the cloud with WDL + Terra.bio by Microbial Bioinformatics

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...

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

87 Nextstrain, SARSCOV2 and dealing with a data deluge by Microbial Bioinformatics

86 What's next for nextstrain? by Microbial Bioinformatics

We are joined again by Prof Mark Pallen who takes us through his early experiences in high-throughput microbial genomics. Mark was pleased that he persuaded Nick Loman to join him in Birmingham. Mark tells us how they worked with George Weinstock to perform the first genome sequence analyses of Gram-negatives for genomic epidemiology—in this case of multi-drug resistant Acinetobacter baumannii. Af...

Mark Pallen explains how exciting it was to be in microbial bioinformatics around the turn of the millennium, as we gained genomes for the first time from model organisms and fearsome pathogens. He recounts working with his hero David Relman on the genome sequencing of the strange slow-growing organism called Tropheryma whipplei in competition with a French team. Mark moved to Belfast in late 1999...

We discuss mobile genetic elements in bacteria and find, its really hard. Its just a short chat as Lee lost power, but we will be back with a part 2 sometime soon.

In this episode we talk to Professor Mark Pallen, who discusses the highlights from his long career as a medical microbiologist turned bioinformatician. His bioinformatics journey began in 1977, the year Fred Sanger invented DNA sequencing-as-we know-it, when Mark was tasked with assembling some amino acid sequences under exam conditions. Mark explains how little was know about sequences at the ti...

We bring on Lingzi Xiaoli and Jill Hagey to talk about their benchmark datasets for SARS-CoV-2. Find out more at https://github.com/CDCgov/datasets-sars-cov-2. See our previous episode for part 1 of the conversation. * Previous paper for bacterial datasets can be found at https://peerj.com/articles/3893/ * Jill can be found on Twitter at @JillHagey and jvhagey.github.io * Lingzi can be found on Li...

We bring on Lingzi Xiaoli and Jill Hagey to talk about their benchmark datasets for SARS-CoV-2. Find out more at https://github.com/CDCgov/datasets-sars-cov-2 * Previous paper for bacterial datasets can be found at https://peerj.com/articles/3893/ * Jill can be found on Twitter at @JillHagey and jvhagey.github.io * Lingzi can be found on LinkedIn at https://www.linkedin.com/in/lingzi-xiaoli-27b871...

Dr Erin Young from the Utah Department of Health and Dr Kelsey Florek from the Wisconsin State Laboratory of Hygiene join us to talk about StaPH-B containers for public health bioinformatics. Its basically how to make biology easier for everyone! Github: https://github.com/StaPH-B