121 K-mers, Sourmash, and Open Source Software - More Conversations with Titus Brown
Micro binfie podcast
by Microbial Bioinformatics
2w ago
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 MinHash How Sourmash handles k-mers for metagenomic comparisons vs. MASH The modhash and bottom sketch approaches used in Sourmash Dealing with sequencing errors and noise in k-mer data Sourmash as a reference-based method, and applications for metagenomics Titus' focus on building reusable libraries and APIs vs one-off tools Recruiting col ..read more
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120 Scaling Metagenomic Search with Sourmash - Conversations with Titus Brown
Micro binfie podcast
by Microbial Bioinformatics
1M ago
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 datasets How the sampling approach enables analyses like containment estimation Exciting capabilities of the Branchwater tool for multi-threaded real-time SRA search Scaling to search across millions of metagenomes in seconds with WebAssembly Potential public health applications for tracking and sourcing pathogens Important caveats around resolution limits and need for follow-up analyses Ongoing work to ch ..read more
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119 The Challenges of Microbial Taxonomy - Conversations with Titus Brown
Micro binfie podcast
by Microbial Bioinformatics
1M ago
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 databases Sourmash as a versatile search tool, not a curated database The need for high confidence in taxonomic assignment in public health Most microbial assignment tools have low specificity or sensitivity Possible ways to achieve perfect species classification (in theory) The challenges around defining species based on small genomic differences Interesting cryptography concept of 'un ..read more
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118 Real bioinformaticians react to Jurassic Park
Micro binfie podcast
by Microbial Bioinformatics
2M ago
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://youtu.be/m1lc8GwBKFE?si=rj7Oiq51l2_dB6ro More information on the secret tattoo here: https://underunderstood.com/podcast/episode/jeff-goldblums-secret-tattoo-jurassic-park-ian-malcolm ..read more
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117 From Math to Metagenomics - Titus Brown on Career Journeys and Software Solutions
Micro binfie podcast
by Microbial Bioinformatics
2M ago
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 biology His transition into bioinformatics to analyze the influx of genomic data in the 1990s Developing early tools for comparative genomics and sequence analysis The philosophy of creating usable software with good documentation Work on transcriptomics, metag ..read more
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116 AI Authorship and Ethics in Academic Publishing for Genomics
Micro binfie podcast
by Microbial Bioinformatics
3M ago
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 articles. He explores the ethical implications and potential biases associated with AI-assisted writing, such as the omission of minority figures and novel discoveries. He emphasizes the importance of transparency when using AI and its potential to ..read more
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115 Write-the: speeding up software development for bioinformatics
Micro binfie podcast
by Microbial Bioinformatics
3M ago
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 into code editors to make coding more efficient and less error-prone. The conversation then shifts to discuss the generation of research papers, specifically software announcements, by leveraging code documentation. The participants believe ChatGPT co ..read more
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114 Write-the: Automating Code Documentation ChatGPT
Micro binfie podcast
by Microbial Bioinformatics
3M ago
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 can play in easing this process. We explore the intersection of ChatGPT's capabilities with Write the Docs, a documentation system widely used by developers. From highlighting ChatGPT's ability to understand and generate code snippets, to demonstratin ..read more
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113 Global Microbial Identifier conference with Ruth Timme
Micro binfie podcast
by Microbial Bioinformatics
5M ago
Lee and Andrew are at the Global Microbial Identifier conference (GMI13) in Vancouver Canada. On day 3 we catch up with Dr Ruth Timme ..read more
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112 Global Microbial Identifier conference with Will Hsiao
Micro binfie podcast
by Microbial Bioinformatics
5M ago
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 ..read more
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