150 - Genomicx

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 discuss how existing bioinformatics programs can be compiled to WebAssembly and wrapped with simple browser interfaces so analyses run locally on a user’s machine. This keeps genomic data private while making tools easier to access. The prototype tools discussed in the episode are available here: https://genomicx.github.io/ These examples show how browser-based bioinformatics might work for lightweight tasks such as genome comparisons and basic sequence analysis. Topics Covered * Using AI tools to rapidly prototype bioinformatics software * Compiling genomics programs to WebAssembly * Running analyses locally in the browser * Privacy advantages of keeping genomic data on the user’s computer * Practical limits of browser-based computation Try the tools and let us know what you think using the hashtag #genomicx

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 everything from microscopy image processing to drug discovery, enabling researchers to move from analyzing single images to conducting statistical analysis on massive datasets. 🤖 The LLM Era - Real experiences with generative AI tools like ChatGPT and Claude in research workflows, from accelerating literature reviews to writing thousands of lines of code through prompt engineering rather than manual coding. ⚖️ Finding Balance - When AI is genuinely transformative versus when it's just hype, including practical guidance on choosing between sophisticated transformer models and simpler, more energy-efficient approaches like random forests. 🔒 Safety & Trust Challenges - The "lethal trifecta" of untrusted data, private information, and internet access; reproducibility concerns; and the critical importance of validation in scientific AI applications. 🤝 Building Interdisciplinary Bridges - Honest insights about the mutual trust deficit between biologists and data scientists, the importance of finding a "buddy" in the other discipline, and why starting with the biological problem (not the model) is essential for meaningful results. 💡 Practical Advice for Computer Scientists - What skills and mindsets are needed to successfully apply computational expertise to new domains, from understanding domain-specific language to recognizing the complexity of biological problems. Featured Panelists: Dr. Mark Basham - Science Director for AI and Informatics, Rosalind Franklin Institute Dr. Elisa Pedone - Senior Research Scientist, CellVoyant (AI for cell therapy development) James Thomas - Senior Data Scientist, Jean Golding Institute, University of Bristol Key Themes: AI in drug discovery • machine learning in microscopy • generative AI in research • interdisciplinary collaboration • data quality challenges • environmental impact of AI • the future of computational biology This episode was recorded live at the Bridging AI & Biosciences Workshop in the University of Bristol and is part of AIBio UK's mission to highlight innovative applications of artificial intelligence across the biosciences.

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

143 - where we catch up on our professional lives by Microbial Bioinformatics

The crew talks about the genomeqc ecosystem. Check it out at https://happykhan.github.io/qualibact/ Errata: The project name was chaned to qualibact and is no longer genomeqc as mentioned on the episode.

In this episode of the Podcast, hosts Lee Katz and Andrew Page delve into the intricacies of clinical metagenomics. Joined by experts Torsten Seemann and Finlay Maguire, they explore the challenges and methodologies involved in identifying pathogens in clinical samples when traditional diagnostic methods fail. They discuss the types of samples analyzed, the impact of low DNA concentrations, and the complexities of sequencing data interpretation. The conversation highlights the importance of interdisciplinary collaboration between bioinformaticians and clinicians in managing difficult infections. Despite the hurdles, clinical metagenomics is presented as a complementary tool aiding in diagnosis, emphasizing the need for genomic literacy among healthcare professionals.