gi-chromatin

name	gi-chromatin
description	Predict chromatin state — histone marks, DNase, TF binding — across 919 tracks (DeepSEA-style) for DNA sequences, via the hosted Genomic Intelligence /v1/tasks/chromatin/predict API.
version	0.1.0
author	ClawBio + Genomic Intelligence
domain	genomics
license	MIT
tags	["genomics","chromatin","histone","DNase","ATAC","TF-binding","deepsea","dna-lm","gi-api"]
inputs	[{"name":"input_file","type":"file","format":["fa","fasta","fna"],"description":"Single-record FASTA (any length; API windows automatically).","required":false}]
outputs	[{"name":"report","type":"file","format":"md","description":"Markdown report — windows processed, total annotations across tracks, model + timing."},{"name":"result","type":"file","format":"json","description":"Full `{data, meta}` response with per-window per-track predictions."},{"name":"reproducibility","type":"directory","description":"command.sh + environment.json."}]
dependencies	{"python":">=3.10","packages":["requests>=2.31"]}
demo_data	[{"path":"example_data/chromatin_active_promoter_chr19.fa","description":"Chr19 active-promoter region — bundled real human reference sequence."}]
endpoints	{"cli":"python skills/gi-chromatin/gi_chromatin.py --input {input_file} --output {output_dir}"}
metadata	{"openclaw":{"requires":{"bins":["python3"],"env":[],"config":[]},"always":false,"emoji":"🧶","homepage":"https://docs.genomicintelligence.ai","os":["darwin","linux"],"install":[{"kind":"pip","package":"requests","bins":[]}],"trigger_keywords":["chromatin","chromatin state","chromatin annotation","histone mark","histone modification","DNase","ATAC","TF binding","transcription factor binding","DeepSEA","epigenome","gi chromatin","genomic intelligence 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 skill refuses to run unless GI_API_KEY is set — cp .env.example .env && set -a && source .env && set +a to use the shared ClawBio hackathon key (50 concurrent / 120 rpm), or request an individual key at [e-mail]. Prefer a browser? The same models run interactively at https://genomicintelligence.ai. Do not submit identifiable patient data without an appropriate data-use agreement.

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 — default model g0-deepsea (919-track DeepSEA-style prediction head).

Workflow

1. Parse: single-record FASTA.
2. Authenticate: --api-key → GI_API_KEY → hackathon fallback.
3. POST to /v1/tasks/chromatin/predict.
4. 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

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. Don't hardcode track indices — read the names from data.tracks.
• Pre-windowing is unnecessary — API 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 tool. Not a clinical assay.