Agentic Data Science in a Reproducible Marimo Notebook

Eric Ma is a Senior Principal Data Scientist at Moderna, where he leads the Data Science and Artificial Intelligence (Research) team. Previously, he conducted biomedical data science research at the Novartis Institutes for Biomedical Research and earned his doctorate in Biological Engineering from MIT. Eric is also an open-source software developer known for leading pyjanitor and nxviz and contributing to NetworkX and PyMC. Dan and Eric discuss Eric's rapidly changing practice of agentic data science, centered on Marimo Pair and reproducible Python notebooks. Eric demonstrates an analysis of protein activity and stereoselectivity data, explains why canonical sources and inline environment metadata matter, and shows how agents make ambitious custom visualizations more approachable even when a live demo fails. The conversation then turns to design documents, testable specifications, repository conventions, and the attention-management practices Eric uses to keep agent work from becoming a context-switching trap. Full episode notes Transcript Chapters (00:00) - Why Eric's data science workflow changed so quickly (05:49) - Marimo Pair puts agents inside the notebook (07:19) - Reproducing a protein-engineering paper (10:45) - Why enzyme stereoselectivity matters (13:20) - Canonical data sources and portable environments (18:08) - Exploring activity and selectivity with interactive plots (27:47) - Finding promising regions for protein engineering (30:24) - From heat maps to a 3D protein viewer (35:54) - Learning from agent traces and preserving intent (47:13) - Opinionated structure for agent-written code (52:25) - Managing attention across agentic tasks ⠀ Links from the show -------------------- Marimo Marimo Pair OpenCode cmux Machine-Directed Evolution of an Imine Reductase for Activity and Stereoselectivity cloudscraper Polars Plotly PEP 723 uv 3Dmol.js anywidget Protein Data Bank PyMOL The Arrow of Intent Hermes Agent Obsidian ⠀ Guests ------- Eric Ma, Senior Principal Data Scientist, Moderna Website LinkedIn GitHub X ⠀ Follow the podcast ------------------- LinkedIn Threads Instagram TikTok ⠀ Follow Dan Gerlanc ------------------- X LinkedIn Threads Bluesky