Best Micro Binfie Podcast Podcasts (2024)

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 glob…

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122 GAMBIT: Genomic Approximation Method for Bacterial Identification and Tracking 17:29

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4M ago17:29

17:29

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

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121 K-mers, Sourmash, and Open Source Software - More Conversations with Titus Brown 20:03

5M ago20:03

20:03

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 MinHashHow Sourmash handles k-mers for metagenomic comparisons vs. MASHThe modhash and bottom …

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120 Scaling Metagenomic Search with Sourmash - Conversations with Titus Brown 25:25

5M ago25:25

25:25

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 datasetsHow the sampling approach enables analyses like containment estimationExciting capabilities of the Branchwater tool for multi-threaded real-time SRA sea…

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119 The Challenges of Microbial Taxonomy - Conversations with Titus Brown 22:53

6M ago22:53

22:53

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 databasesSourmash as a versatile search tool, not a curated databaseThe need for high confidence in taxonomic assignment in public healthMost…

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118 Real bioinformaticians react to Jurassic Park 1:00:44

6M ago1:00:44

1:00:44

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://y…

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117 From Math to Metagenomics - Titus Brown on Career Journeys and Software Solutions 20:12

7M ago20:12

20:12

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 biologyHis tr…

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116 AI Authorship and Ethics in Academic Publishing for Genomics 32:27

7M ago32:27

32:27

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 a…

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115 Write-the: speeding up software development for bioinformatics 24:22

8M ago24:22

24:22

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 i…

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114 Write-the: Automating Code Documentation ChatGPT 25:35

8M ago25:35

25:35

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 c…

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113 Global Microbial Identifier conference with Ruth Timme 8:11

9M ago8:11

8:11

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

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112 Global Microbial Identifier conference with Will Hsiao 7:35

9M ago7:35

7:35

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.By Microbial Bioinformatics

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111 Global Microbial Identifier with Finlay Maguire and Emma Griffiths 21:08

9M ago21:08

21:08

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.By Microbial Bioinformatics

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110 ChatGPT: The Bioinformatics Calculator 26:47

12M ago26:47

26:47

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 ta…

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109 AI Unleashed: Navigating the Opportunities and Challenges of AI in Microbial Bioinformatics 30:56

1y ago30:56

30:56

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…

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Encore: What language should I learn? 29:48

1y ago29:48

29:48

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,…

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108 SeqCode: a nomenclatural code for prokaryotes described from sequence data 45:59

1y ago45:59

45:59

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 M…

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107 Systematics and naming of prokaryotes in the era of sequencing 33:16

1y ago33:16

33:16

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…

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106 Why on earth would you do a PostDoc? 15:19

1y ago15:19

15:19

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 t…

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105 Mobile genetic elements panel discussion 43:54

1y ago43:54

43:54

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 d…

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104 The Kraken software suite 21:50

1y ago21:50

21:50

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 vario…

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103 Release the Kraken 27:09

1+ y ago27:09

27:09

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…

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102 Early days of MLST 40:15

1+ y ago40:15

40:15

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…

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101 One Health with Natacha Couto and Ed Feil 36:29

1+ y ago36:29

36:29

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, agricul…

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100th episode 52:26

1+ y ago52:26

52:26

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-xNabil was trying to remember this particular site and r…

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99 Stories from the frontlines of bioinformatics 39:07

1+ y ago39:07

39:07

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 enj…

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98 Nomadic bioinformatics with Frank 42:39

1+ y ago42:39

42:39

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 …

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97 Advances in sequencing technologies 17:12

1+ y ago17:12

17:12

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, inclu…

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96 IMMEM XIII and ASM NGS conference roundup 35:34

1+ y ago35:34

35:34

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.By Microbial Bioinformatics

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95 Lost in Translation with Torsten Seemann 41:49

1+ y ago41:49

41:49

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 enj…

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94 The great scientific Mastodon migration 28:19

1+ y ago28:19

28:19

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 th…

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93 - Roary Troubleshooting And Issues 16:47

1+ y ago16:47

16:47

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.By Microbial Bioinformatics

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92 - Avoid dependency hell and get up and running fast 35:30

1+ y ago35:30

35:30

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 installat…

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91 - What language should I learn? 29:48

1+ y ago29:48

29:48

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,…

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90 Public health bioinformatics on the cloud with WDL + Terra.bio 44:19

1+ y ago44:19

44:19

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

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89 What do we do with WDL? 26:08

2y ago26:08

26:08

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…

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88 - Sepia directors cut 53:01

2y ago53:01

53:01

This is an extended directors cut of our chat with Dr Henk den Bakker about Sepia. Its a summer holiday bonus.Some URLsGet Sepia here: https://github.com/hcdenbakker/sepiaSome information on the food safety informatics group at UGA: https://www.denglab.site/Rust: https://www.rust-lang.org/Kalamari: https://github.com/lskatz/kalamariCAMI: https://ww…

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87 Nextstrain, SARSCOV2 and dealing with a data deluge 27:56

2y ago27:56

27:56

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

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86 What's next for nextstrain? 22:55

2y ago22:55

22:55

86 What's next for nextstrain? by Microbial BioinformaticsBy Microbial Bioinformatics

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85 Breaking the dogma with bioinformatics 27:15

2y ago27:15

27:15

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 o…

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84 Bioinformatics in the noughties with Mark Pallen 22:14

2y ago22:14

22:14

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…

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83 A short journey into mobile genetic elements 17:39

2y ago17:39

17:39

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.By Microbial Bioinformatics

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82 Bioinformatics moments before the millennium 39:57

2y ago39:57

39:57

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 expl…

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81 The people behind the benchmark datasets for SARS-CoV-2 9:27

2y ago9:27

9:27

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 a…

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80 Benchmark datasets for SARS-CoV-2 43:05

2y ago43:05

43:05

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 h…

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79 StaPH-B: Stable containers for public health bioinformatics 28:17

2y ago28:17

28:17

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-BBy Microbial Bioinformatics

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78 StaPH-B: state public health bioinformatics 25:33

2y ago25:33

25:33

Dr. Erin Young and Dr Kelsey Florek join us to talk about StaPH-B, a US state public health bioinformatics group. They also give some insights into the popular SARS-CoV-2 pipeline cecret.Website: staphb.org/Cecret Pipeline: github.com/CDCgov/SC2CLIAKelsey explains that StaPH-B was created to facilitate collaborations between bioinformaticians in st…

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77 Genomics for a new era 38:16

2+ y ago38:16

38:16

Today we’re talking about some exciting new developments in the area of comparative genomics. We are joined by Dr. Zamin Iqbal who is a Research Group Leader at the European Bioinformatics Institute and Dr. Grace Blackwell who is jointly at the European Bioinformatics Institute, in Zam’s group and Nick Thomson’s team at Wellcome Sanger Institute…

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