Microbial Bioinformatics is a rapidly changing field marrying computer science and microbiology. Join us as we share some tips and tricks we’ve learnt over the years. If you’re student just getting to grips to the field, or someone who just wants to keep tabs on the latest and greatest - this podcast is for you. The hosts are Dr. Lee - a bioinformatician in the United States, Dr. Nabil-Fareed Alikhan from the University of Oxford (UK), and Prof. Andrew Page from Origin Sciences (UK) and bring…
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- Seebot https://github.com/happykhan/seebot - Ten quick tips to SNIFF out sustainable and secure scientific software | PLOS Computational Biology https://bsky.app/profile/stephenturner.us/post/3mqpkezwzls2m - Ten recommendations for creating usable bioinformatics command line software https://link.springer.com/article/10.1186/2047-217X-2-15
In this follow-up Software Deep Dive episode, we continue our conversation with Dr. Bede Constantinides (University of Birmingham) about the design and implementation of Deacon, a fast host-read removal tool for metagenomics. Deacon uses minimizers and k-mer set membership queries instead of alignment, allowing it to filter reads extremely quickly while balancing sensitivity and specificity. The…
In this Software Deep Dive episode, we talk with Dr. Bede Constantinides (University of Birmingham) about Deacon, a tool for removing host DNA reads from metagenomic datasets. We discuss why host read removal is a deceptively difficult problem, the limitations of alignment-based approaches, and how Deacon evolved from Bede's earlier tool Hostile. The conversation covers practical issues such as…
In this episode, Lee, Nabil, and Andrew experiment with “vibe coding” bioinformatics tools using AI coding assistants. The goal: quickly build useful genomics utilities that run entirely in the browser via WebAssembly, without requiring command-line installs or servers. Nabil states: “Even if you don’t want to use this technology, you should pay attention - because everyone else will.” They…
Join hosts Kieren Sharma (Artificially Ever After podcast, University of Bristol) and Andrew Page (MicroBinfie podcast, Origin Sciences) for a compelling live panel discussion exploring the dynamic intersection of artificial intelligence and the biosciences. In this episode, our expert panel discusses: 🔬 The AI Revolution in Biology - How machine learning and deep learning have transformed…
Final part of our discussion/debate on NextFlow
Part two of debating NextFlow
Andrew, Nabil, and Lee debate about NextFlow!
Nabil and Lee bring a guest host Clint to talk with some of the people behind Pathoplexus http://pathoplexus.org/ * Dr. Emma Hodcroft - https://pathoplexus.org/about/eb * Dr. Theo Sanderson - https://pathoplexus.org/about/development-team * Mr. Arthur Shem Kasambula - https://pathoplexus.org/about/development-team
Nabil and Lee bring a guest host Clint to talk with some of the people behind Pathoplexus http://pathoplexus.org/ * Dr. Emma Hodcroft - https://pathoplexus.org/about/eb * Dr. Theo Sanderson - https://pathoplexus.org/about/development-team * Mr. Arthur Shem Kasambula - https://pathoplexus.org/about/development-team
