Gi Chromatin

🧶 gi-chromatin

You are gi-chromatin, a ClawBio agent that calls the Genomic Intelligence chromatin-annotation model (DeepSEA-style, 919 tracks: histone marks + DNase + TF binding across ENCODE cell types).

⚠️ Remote inference — opt-in required. Unlike most ClawBio skills, this skill uploads your FASTA sequence to the hosted Genomic Intelligence API at https://api.genomicintelligence.ai. The same models also run interactively at https://genomicintelligence.ai. Do not submit identifiable patient data without an appropriate data-use agreement. Key setup: see Authentication below.

Trigger

Fire this skill when the user says any of:

• "predict chromatin state for this sequence"
• "histone mark prediction", "DNase prediction", "ATAC prediction"
• "TF binding prediction"
• "DeepSEA"
• "gi-chromatin", "predict epigenome"
• "is this region accessible?"

Do NOT fire when:

• The user asks specifically about enhancer activity → gi-enhancer
• The user asks for promoter prediction → gi-promoter

Why This Exists

• Without it: Running DeepSEA / similar locally needs custom torch envs + weight wrangling.
• With it: One CLI call → 919 track predictions per window, in seconds.
• Why ClawBio: Hosted G0 DeepSEA inference plus ClawBio reproducibility and chaining.

API Backed

POST https://api.genomicintelligence.ai/v1/tasks/chromatin/predict. Omit model and the API resolves the default — a 919-track DeepSEA-style prediction head. GET /v1/tasks/chromatin/models is the current list.

Contract note. The Genomic Intelligence API publishes one operation per task, each with its own request schema: per-task minLength/maxLength on sequence, and a typed, closed options object (an unknown option key is a 422 validation_failed, not a silent ignore). The bounds quoted in this file are the published ones, but the authority is always the served schema: GET https://api.genomicintelligence.ai/v1/openapi.json.

Workflow

1. Parse: single-record FASTA.
2. POST to /v1/tasks/chromatin/predict.
3. Render: report.md (window + total-annotation counts; per-track detail in result.json).

CLI Reference

python skills/gi-chromatin/gi_chromatin.py --demo --output /tmp/gi-chromatin-demo
python skills/gi-chromatin/gi_chromatin.py --input my_region.fa --output report_dir
python clawbio.py run gi-chromatin --demo

Authentication

The skill requires a Genomic Intelligence partner key in GI_API_KEY. Resolution order:

1. --api-key <value> CLI flag (explicit override).
2. GI_API_KEY environment variable.
3. Otherwise: the skill raises a RuntimeError pointing here.

Quick start — ClawBio hackathon key

A shared hackathon-tier key ships in .env.example at the repo root (opt-in only). Caps are per-key and are not published as a fixed number — read RateLimit-Limit / RateLimit-Remaining on any /v1/tasks/ response for the live allowance. The runner keeps them for you: they are in result.json under rate_limit, and a 429 names them on the error line. From wherever the ClawBio files live on your machine:

# Repo root (git clone) — or ~/.claude/plugins/cache/clawbio/clawbio/<version>/ for plugin installs
cp .env.example .env
set -a && source .env && set +a

Production / heavier use

Request an individual key at contact@genomicintelligence.ai, then:

export GI_API_KEY=gi_yourkeyhere

Demo

python clawbio.py run gi-chromatin --demo

Bundled fixture is an active-promoter region from chr19. Expect dense annotation across active-promoter tracks (H3K4me3, H3K27ac, DNase, etc.) and many called windows.

Gotchas

• Big response. 919 tracks × N windows → multi-MB result.json. The report.md summarizes; mine result.json programmatically for specific tracks.
• Track labels are in the response. Do not hardcode track indices — read the names from data.tracks.
• Length bounds are 200–500,000 bp, published as minLength / maxLength on ChromatinPredictRequest and counted after whitespace is stripped. Both ends are a 422 validation_failed (over-max is not a 413 — 413 is the separate 16 MiB raw-body cap). The skill rejects either locally before spending a request.
• 200 bp is admission control, not regime. The model's context window is 1,000 bp (bio_spec.context_window_bp on GET /v1/tasks/chromatin/models), so 200–999 bp is accepted and scored — against a window padded out to 1,000 bp. The skill warns when you are under it.
• Pre-windowing is unnecessary — the API windows and strides internally.
• Hackathon key is shared — GI_API_KEY for heavier use.

Output Structure

output_dir/
├── report.md
├── result.json
└── reproducibility/
    ├── command.sh
    └── environment.json

Integration with Bio Orchestrator

Routes here on: "chromatin", "histone marks", "DNase", "ATAC", "TF binding", "DeepSEA".

Chains with: gi-enhancer (cross-validate enhancer calls against H3K27ac), gi-promoter (active-promoter signature: high H3K4me3 + DNase), variant-annotation (variants in accessible chromatin).

Safety

Research and development use. Not for clinical or diagnostic decisions.