94 The great scientific Mastodon migration
Micro binfie podcast
by Microbial Bioinformatics
1w ago
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 ..read more
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93 - Roary Troubleshooting And Issues
Micro binfie podcast
by Microbial Bioinformatics
2w ago
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 ..read more
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92 - Avoid dependency hell and get up and running fast
Micro binfie podcast
by Microbial Bioinformatics
1M ago
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 ..read more
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90 Public health bioinformatics on the cloud with WDL + Terra.bio
Micro binfie podcast
by Microbial Bioinformatics
2M ago
90 Public health bioinformatics on the cloud with WDL + Terra.bio by Microbial Bioinformatics ..read more
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89 What do we do with WDL?
Micro binfie podcast
by Microbial Bioinformatics
2M ago
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 ..read more
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88 - Sepia directors cut
Micro binfie podcast
by Microbial Bioinformatics
4M ago
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 ..read more
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87 Nextstrain, SARSCOV2 and dealing with a data deluge
Micro binfie podcast
by Microbial Bioinformatics
4M ago
87 Nextstrain, SARSCOV2 and dealing with a data deluge by Microbial Bioinformatics ..read more
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86 What's next for nextstrain?
Micro binfie podcast
by Microbial Bioinformatics
5M ago
86 What's next for nextstrain? by Microbial Bioinformatics ..read more
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85 Breaking the dogma with bioinformatics
Micro binfie podcast
by Microbial Bioinformatics
5M ago
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. After winning an Ion Torrent sequencer in a competition, Mark and Nick then contributed some pioneering genomic analyses of the German STEC outbreak. One of their studies involved crowd sourced approach ..read more
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84 Bioinformatics in the noughties with Mark Pallen
Micro binfie podcast
by Microbial Bioinformatics
6M ago
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 collaborating with another Englishman working on the island of Ireland, Tim Foster in Dublin. Pallen describes the addictive exhilaration of using PSI-BLAST to find new sortases and sortase substrate ..read more
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