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Weekly Recap (May 2025, part 2)
Comprehensive evolutionary modeling of human gene function, an AI reasoning model for rare disease diagnosis, an AI agent for scRNA-seq data…
May 15
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Weekly Recap (May 2025, part 2)
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uv, part 3: Python in R with reticulate
Two demos using Python in R via reticulate+uv: (1) Hugging Face transformers for sentiment analysis, (2) pyBigWig to query a BigWig file and visualize…
May 6
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Stephen Turner
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uv, part 3: Python in R with reticulate
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Weekly Recap (May 2025, part 1)
Methods in genetic epidemiology, privacy-preserving methods for QTL and GWAS analysis, family-based GWAS, lots of Nextflow for PGS construction…
May 2
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Weekly Recap (May 2025, part 1)
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April 2025
Listen to papers, PDFs, and articles with ElevenReader
ElevenReader (free for iOS/Android) will read articles and PDFs in realistic voices. Example clips here with Burt Reynolds, Maya Angelou, and Richard…
Apr 25
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Stephen Turner
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Listen to papers, PDFs, and articles with ElevenReader
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Weekly Recap (April 2025, part 2)
Effector genes at GWAS hits, protein evolution, regulatory variant prediction, gene/genome duplication analysis, genomic foundation models, Nextflow…
Apr 24
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Stephen Turner
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Weekly Recap (April 2025, part 2)
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R 4.5.0 and Bioconductor 3.21
Faster package installation, import only the functions you want with use(), built-in Palmer penguins data, grep values shortcut, and lots of new…
Apr 17
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Stephen Turner
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R 4.5.0 and Bioconductor 3.21
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Weekly Recap (April 2025, part 1)
Evo2, genomic foundationless models, the ggalign R package, ancestral reconstruction for ancient DNA, biodiversity genomics reviews, structural…
Apr 11
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Weekly Recap (April 2025, part 1)
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Build a local RAG application with Open WebUI to chat with your Zotero library
Demonstration using Mistral and Nomic Embed with Ollama and Open WebUI
Apr 5
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Stephen Turner
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Build a local RAG application with Open WebUI to chat with your Zotero library
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March 2025
Weekly Recap (March 2025, part 2)
AI agents for biomedical reasoning, species tree inference, a spatial transcriptomics foundation model, biomedical research with LLMs, mapping cells…
Mar 28
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Weekly Recap (March 2025, part 2)
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uv, part 2: building and publishing packages
Using uv to create, manage, build, and publish a Python package to PyPI
Mar 24
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Stephen Turner
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uv, part 2: building and publishing packages
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Weekly Recap (March 2025, part 1)
Heritable polygenic editing, self-supervised learning in single-cell genomics, predictive modeling with tabular foundation models, ESM3, pangenome…
Mar 21
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Weekly Recap (March 2025, part 1)
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GUIs for Local LLMs with RAG
Running local LLMs with Ollama, LMStudio, Open WebUI, and others for private and secure chat, vibe coding, image analysis, and "chat with your…
Mar 14
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Stephen Turner
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GUIs for Local LLMs with RAG
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