Code and derived tables for Information-theoretic Limits on Programmatic Specification of Biological Systems (Kiiskinen, Kivinen & Rivas). https://www.biorxiv.org/content/10.64898/2026.07.27.740886v1
Stochastic-network simulations, the shared entropy estimators, and the C. elegans descriptor ladder are in ensemble_threshold
AlphaFold cross-organism structural accounting is in alphafold_compression
JCVI-syn3A 4D whole-cell analysis is in syn3a_analysis
A cluster-agnostic SLURM job template is in slurm
Extended methods and per-step reproduction commands are in METHODS.md
Input data are not redistributed. AlphaFold proteomes: https://ftp.ebi.ac.uk/pub/databases/alphafold/latest/. JCVI-syn3A 4DWCM: Zenodo record 15579159. Simulation outputs are reproducible from the configs and seeds in ensemble_threshold/configs.
Requires Python ≥ 3.10 with numpy, scipy, pandas, pyarrow, pyyaml, matplotlib, and h5py (syn3A only). MIT licensed.