ner_rnapii_3d

A standalone 1D loop-extrusion + RNAPII + lesion simulation engine. Given a YAML config it simulates, on a 1D lattice:

• cohesin loop extrusion with CTCF capture/release boundaries,
• RNAPII transcription (load → pre-initiation → elongation → termination, with enhancer–promoter gating and cohesin↔RNAPII steric coupling),
• DNA lesions (gene-body occurrence, pre-recognition / repair kinetics, cohesin and RNAPII blocking),

and writes the trajectory to LEFPositions.h5.

Install / run (uv)

uv sync
uv run ner-sim run path/to/config.yaml --output run_dir/
# -> run_dir/LEFPositions.h5

Generate a ready-to-run config with the bundled generator:

uv run python scripts/gen_realistic_configs_variable_tick.py \
  --chain 40000 --bp-per-site 250 --num-chains 20 --suffix demo \
  --out-dir configs/ --seed 2026 --tick-seconds 2 \
  --trajectory-length 80000 --warmup-steps 40000

Please see the script for the detailed parameter descriptions.

Reproduce the paper results

uv sync
bash run_panels.sh

run_panels.sh regenerates the configs and runs the full pipeline end-to-end — the transcription-on vs -off comparison, transcription and cohesin-barrier QC, and the boundary-strength, Type-A/density, block-probability, repair-timing, and cohesin–CTCF lifetime sweeps — writing everything to results_<suffix>/. Adjust nproc (parallel jobs) and seed at the top of the script; the defaults reproduce the published runs.

Python API

import ner_rnapii_3d as ner

cfg = ner.load_lef_config("config.yaml", output_path="run_dir/")
h5_path = ner.run(cfg)

Layout

ner_rnapii_3d/
  config.py    typed config, plugin resolution
  cli.py       `ner-sim` CLI
  engine/      MT19937 port + Numba dynamics kernels + chunked recording
  plugins/     data classes + Python reference rules (topology, cohesin,
               RNAPII, lesions)

The plugins/ modules hold the Python reference implementation of every per-tick rule; the production loop reimplements that logic in engine/kernel.py, with the reference functions kept as the equivalence oracle.

Tests

uv run pytest