AI Scientist: Base Module Report

IGOR; b.next; FindWhatMatters

AI Scientist—Jupyter Environment

This environment is configured for easy browsing of the underlying data for the AI Scientist base PURE optimization. The file tree is laid out as follows:

/
├─ analysis/ - specific custom analysis of data
├─ data/ - underlying raw data and structured workspaces from specific scientist iterations
│  ├─20260217-iteration-initial-results
│  ├─20260302-iteration-0
│  ├─20260312-iteration-1
│  ├─20260320-iteration-2
├─ figures/ - compiled figures
├─ general/ - general assets
├─ orchestrated-research/ - IGOR OR (Orchestrated Research) mechanistic developer notes
│  ├─ iter1/
│  ├─ iter2/
├─ curvenote.yml - developer note configuration
├─ main.md - main article text
├─ README.ipynb - this text

from IPython.display import Image
Image("./thumbnail-2.png")

Abbreviations¶

PURE: Protein synthesis Using Recombinant Elements, our base cytosol for compositional biology.