Micro binfie podcast
Episodes
54 SARS-CoV-2 In Canada and addressing data sharing and privacy
01 Apr 2021
Contributed by Lukas
The Canadians have taken over the podcast - AGAIN ! Join guest host Dr. Emma Griffiths, as she talks with Dr. Finn McGuire and Dr. William Hsiao abo...
53 SARS-CoV-2 surveillance in Canada with CANCOGEN
25 Mar 2021
Contributed by Lukas
The Canadians have taken over the podcast ! Join guest host Dr. Emma Griffiths, as she talks with Dr. Finlay McGuire and Dr. William Hsiao about the...
52 SARS-CoV-2 sequencing in Denmark with Mads Albertsen
18 Mar 2021
Contributed by Lukas
Denmark is one of the leading countries in the world forSARS-CoV-2 genomic surveillance. Prof Mads Albertsen chats to us about SARS-CoV-2 sequencing ...
51 SARSCOV2 Round-up 3 and updates from Denmark
11 Mar 2021
Contributed by Lukas
We discuss the latest developments in SARS-CoV-2 genomics over the last 2 weeks with Mads Albertsen and the latest developments in Denmark. Denmark c...
50 Atypical invasive non-typhoidal Salmonella in The Gambia
25 Feb 2021
Contributed by Lukas
Invasive non-typhoidal Salmonella is a significant public health challenge in Africa. We talk to Abdoulie Kanteh and Grant Mackenzie about their work ...
49 SARS-CoV-2 Tools and resources update
22 Feb 2021
Contributed by Lukas
We are joined by Peter van Heusden to discuss all the latest developments in SARS-CoV-2 genomics, particularly around tools and resources. We also dis...
48 SARS-CoV-2 More Variants of Concern and updates from Africa
20 Feb 2021
Contributed by Lukas
We discuss the latest developments in SARS-CoV-2 genomics over the last 2 weeks with Peter van Heusden, covering the growing list of Variants of Conce...
47 SARS-CoV-2 Rapid roundup and questions answered
08 Feb 2021
Contributed by Lukas
We present a rapid round up of SARS-CoV-2 questions and issues, hopefully with some answers, so that you can stay on top of the latest in SARS-CoV-2 g...
46 SARS-CoV-2 genomics resources
08 Feb 2021
Contributed by Lukas
We discuss recent updates to the best SARS-CoV-2 resources, so that you can stay on top of the latest bioinformatics and genomics tools. Recorded 5 Fe...
45 Software deep dive: Enterobase
04 Feb 2021
Contributed by Lukas
We chat with Nabil about EnteroBase, and learn about the background to the project, the general benefits of the platforms and some of the strange quir...
44 How to sequence SARS-CoV-2 using the ARTIC protocol with Joshua Quick
22 Jan 2021
Contributed by Lukas
Joshua Quick from the University of Birmingham talks about "How to sequence SARS-CoV-2 using the ARTIC protocol". This was part of a joint ARTICnetwor...
43 Why use genomics in an epidemic? with Sam Sheppard
21 Jan 2021
Contributed by Lukas
Sam Sheppard from the University of Bath presents at the ARTICnetwork & CLIMB-BIG-DATA workshop on COVID-19 data analysis, motivating why we should us...
42 Overcoming barriers to SARS-CoV-2 data analysis
20 Jan 2021
Contributed by Lukas
ARTICnetwork & CLIMB-BIG-DATA present a panel discussion on overcoming barriers to SARS-CoV-2 data analysis with Nick Loman and Will Rowe from the Uni...
41 SARS-CoV-2 Phylogenomics questions answered
19 Jan 2021
Contributed by Lukas
ARTICnetwork & CLIMB-BIG-DATA present a panel discussion on SARS-CoV-2 phylogenomics with Nick Loman from the University of Birmingham, Verity Hill fr...
40 A crash course in SARS-CoV-2 bioinformatics
18 Jan 2021
Contributed by Lukas
Over the last year we've learnt a lot about SARS-CoV-2 genomics. Lee extracts all the insider knowledge from our brains and we give him the honest tru...
39 Explaining the naming of SARS-CoV-2 new variants
16 Jan 2021
Contributed by Lukas
Andrew talks to Niamh Tumelty from the University of Cambridge about SARS-CoV-2 'new variants' and tries to clear up some of the confusion around all ...
38 Ontologies - effective data sharing
07 Jan 2021
Contributed by Lukas
Dr Emma Griffiths and Dr João Carriço join us for part two of our crash course on ontologies with a focus on effective data sharing.
37 Ontologies - the secret sauce of bioinformatics
24 Dec 2020
Contributed by Lukas
Dr Emma Griffiths and Dr João Carriço join us to give us a crash course on ontologies, the bioinformatics secret sauce that makes all things work we...
36 Roary the pangenome pipeline
10 Dec 2020
Contributed by Lukas
We chat with Andrew about Roary, software for generating a pangenome, and learn about the background to the project, where the name comes from, hidden...
35 The Wandering Bioinformatician
26 Nov 2020
Contributed by Lukas
Have you ever wanted to pack in your job and move to the other side of the world? We chat to Phil Ashton on his travels as a bioinformatician, going f...
34 Moving from wet to dry with Phil Ashton
12 Nov 2020
Contributed by Lukas
We chat with Phil Ashton about his move from the wet lab into the dry lab to become a bioinformatician, and his experiences with working in public hea...
33 The untrained monkey
29 Oct 2020
Contributed by Lukas
Someone shows up at your door wanting to get a nature paper in bioinformatics and they only have a week, where do you start? We talk bioinformatics tr...
32 Looking behind Majora's Mask and nation wide tracking of SARS-CoV-2 genomics
15 Oct 2020
Contributed by Lukas
Nick Loman, Sam Nicholls and Radosław Popławski join us to discuss building systems to support the analysis of hundreds of thousands of SARS-CoV-2 g...
31 Large scale sequencing of SARS-CoV-2 genomes from one region
01 Oct 2020
Contributed by Lukas
We chat to Justin O'Grady, Andrew Page and Alison Mather about how they went about sequencing 1500 SARS-CoV-2 genomes from one small region in the UK ...
30 How we made the podcast on our 1st birthday
17 Sep 2020
Contributed by Lukas
To help us celebrate a full year of the podcast after our first episode on September 19, 2019, we go into how we started the podcast. We talk about a...
29 Mashtree software deep dive
10 Sep 2020
Contributed by Lukas
Paper: https://joss.theoj.org/papers/10.21105/joss.01762 Repository: https://github.com/lskatz/mashtree We chat to the author of Mashtree, bioinforma...
28 BRIG the BLAST Ring Image Generator
27 Aug 2020
Contributed by Lukas
We chat to Nabil-Fareed Alikhan about the bioinformatics software he authored called BRIG, the BLAST Ring Image Generator. Software: http://brig.sour...
27 SNP-sites: rapid efficient extraction of SNPs from multi-FASTA alignments
13 Aug 2020
Contributed by Lukas
We chat to the author of SNP-sites, bioinformatics software for extracting SNPs from a multi-FASTA alignment. Sounds simple but behind all of our soft...
26 SARS-CoV-2 contextual data specification for open genomic epidemiology
13 Aug 2020
Contributed by Lukas
We talk to Dr Emma Griffiths (UBC), Dr Ruth Timme (FDA) and Dr Duncan MacCannell (CDC) about the PHA4GE SARS-CoV-2 contextual data specification for o...
25 Sustainable bioinformatics software
30 Jul 2020
Contributed by Lukas
How do you make bioinformatics software sustainable so that we can move our field from academic research into hospitals and doctors offices? We discus...
24 Experimental projects lead to experimental software
16 Jul 2020
Contributed by Lukas
Experimental projects lead to experimental software. We discuss the issues around the sustainability of academic bioinformatics software. How it curre...
23 CoronaHiT: large scale multiplexing of SARS-CoV-2 genomes on Nanopore
02 Jul 2020
Contributed by Lukas
We chat with the authors of CoronaHiT which lets you sequence up to 94 SARS-CoV-2 samples on a single MinION flowcell. This reduces the cost of sequen...
22 Assembly after party
25 Jun 2020
Contributed by Lukas
When you get an assembly the fun doesnt stop there. You then have to fix it up and see how good it is. In this episode we discuss scaffolding, gapfill...
21 Setting up coronavirus sequencing for real-time public health surveillance
16 Jun 2020
Contributed by Lukas
We chat to Justin O'Grady and Andrew Page on how to get a SARS-CoV-2 sequencing effort off the ground in the middle of a pandemic and go on to sequenc...
20 Assembly read healing
11 Jun 2020
Contributed by Lukas
Preprocessing of sequence data in advance of de novo assembly is a critical step to improving the final quality of your assembly. We chat about read t...
19 Microbinfies assemble
28 May 2020
Contributed by Lukas
Short read de novo assembly is discussed in this podcast. We cover the history of assembly and how short read assemblers have evolved into what we use...
18 Panel - Has Nanopore rendered onsite Illumina obsolete?
14 May 2020
Contributed by Lukas
A panel discussion held in MRC Gambia at The London School of Hygiene and Tropical Medicine, recorded in front of a live audience of scientists in Jan...
17 Bayesian magic in practice
30 Apr 2020
Contributed by Lukas
The second part of the dark world of Bayesian magic with Dr Conor Meehan, Dr. Leo Martins and Dr Nabil-Fareed Alikhan.
16 The theory behind Bayesian Magic
16 Apr 2020
Contributed by Lukas
The dark world of Bayesian magic with Dr Conor Meehan, Dr. Leo Martins and Dr Nabil-Fareed Alikhan.
15 Bioinformatics war stories
02 Apr 2020
Contributed by Lukas
We share short war stories about bioinformatics from the trenches of research. We share tales about a mystery massive Listeria outbreak, bubbles on fl...
14 La resistance lives on: The AMR deep dive
19 Mar 2020
Contributed by Lukas
Kate Baker talks AMR
13 Questions not to ask
05 Mar 2020
Contributed by Lukas
Someone asks a simple question like "What programming language should I learn?", without realising just how difficult it is to answer. We discuss diff...
12 Phylogenetics with the arborists part 2
20 Feb 2020
Contributed by Lukas
12 Phylogenetics with the arborists part 2 by Microbial Bioinformatics
11 Phylogenetics with the arborists part 1
06 Feb 2020
Contributed by Lukas
11 Phylogenetics with the arborists part 1 by Microbial Bioinformatics
10 History of file formats
23 Jan 2020
Contributed by Lukas
10 History of file formats by Microbial Bioinformatics
09 Nobel prize or contamination
09 Jan 2020
Contributed by Lukas
Have you made a nobel prize winning discovery, or are you just looking at contamination. We discuss common sources of contamination in genome sequenci...
08 Looking back at 2019
26 Dec 2019
Contributed by Lukas
So it's the end of 2019 and we thought we'd like to pause and look back at what we were working on . What resonated with us and where we think the mi...
07 Wham, BAM, thank you SAM.
12 Dec 2019
Contributed by Lukas
This episode we discuss the ubiquitous Sequence Alignment Map (SAM)format
06 Writing good bioinformatics software with Torsten Seemann
28 Nov 2019
Contributed by Lukas
Torsten Seemann joins us to discuss how to write good bioinformatics software. Torsten is the author of many popular bioinformatics tools such as Prok...
05 History of Genotyping - Decentralised Future
14 Nov 2019
Contributed by Lukas
Modern genotyping is discussed in this second part.
04 History of Genotyping - The early years
31 Oct 2019
Contributed by Lukas
Genotyping is at the foundation of modern microbiology. We discuss all of the techniques used in the preNGS era.
03 FASTQ - all your bases are belong to us
17 Oct 2019
Contributed by Lukas
FASTQ files are the foundation of modern bioinformatics. Tune into an informal chat between Lee, Nabil and Andrew as they tell the story of how FASTQs...
02 What bioinformatics software not to write part 2
03 Oct 2019
Contributed by Lukas
In this episode we identify areas of “Peak-bioinformatics”. There are a lot of existing bioinformatics software out there - more often than not th...
01 What bioinformatics software not to write part 1
19 Sep 2019
Contributed by Lukas
In this episode we identify areas of “Peak-bioinformatics”. There are a lot of existing bioinformatics software out there - more often than not th...
00 Trailer
17 Sep 2019
Contributed by Lukas
The Micro Binfie poscast is available at SoundCloud (https://soundcloud.com/microbinfie) or you can subscribe via iTunes: https://podcasts.apple.com/...