gi-enhancer - SKILL.md Agent Skill

name: gi-enhancer description: Predict enhancer activity in DNA sequences using the Genomic Intelligence G0 DeepSTARR model, via the hosted /v1/tasks/enhancer/predict API. Returns per-window activity scores. license: MIT metadata: openclaw: requires: bins: - python3 env: null config: null always: false emoji: 🎚️ homepage: https://docs.genomicintelligence.ai os: - darwin - linux install: - kind: pip package: requests bins: null trigger_keywords: - enhancer - enhancer activity - predict enhancer - regulatory element - cis-regulatory - CRE - DeepSTARR - STARR-seq - massively parallel reporter assay - MPRA - gi enhancer - genomic intelligence enhancer author: ClawBio + Genomic Intelligence demo_data:

path: example_data/enhancer_eve.fa description: Drosophila eve (even-skipped) developmental-enhancer region (chr2R:9972000-9982000, BDGP6, gene-sense, incl. upstream stripe enhancers) — canonical DeepSTARR benchmark. dependencies: python: '>=3.10' packages:
- requests>=2.31 domain: genomics endpoints: cli: python skills/gi-enhancer/gi_enhancer.py --input {input_file} --output {output_dir} 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, max predicted activity, model + timing.
name: result type: file format: json description: Full {data, meta} response.
name: reproducibility type: directory description: command.sh + environment.json. tags:
genomics
enhancer
regulatory
cis-regulatory
deepstarr
dna-lm
gi-api version: 0.1.0

🎚️ gi-enhancer

You are gi-enhancer, a ClawBio agent that calls the Genomic Intelligence enhancer-activity model. Given a sequence, it returns per-window activity predictions, in ~1 s via the hosted API.

⚠️ 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. Prefer a browser? The same models 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 enhancer activity"
"score this for enhancer / CRE / regulatory function"
"is this an enhancer?"
"DeepSTARR prediction", "STARR-seq prediction"
"gi-enhancer"
"predict cis-regulatory activity"

Do NOT fire when:

The user asks for promoter activity → gi-promoter
The user asks for chromatin state / accessibility → gi-chromatin

Why This Exists

Without it: DeepSTARR-style local inference requires Keras + GPU + tokenization knowhow.
With it: One CLI call → per-window activity scores in ~1 s.
Why ClawBio: Hosted G0 DeepSTARR plus ClawBio reproducibility + orchestrator routing.

API Backed

POST https://api.genomicintelligence.ai/v1/tasks/enhancer/predict — default model g0-deepstarr.

Workflow

Parse: single-record FASTA.
POST to /v1/tasks/enhancer/predict; the API windows internally.
Render: report.md + result.json + reproducibility/.

CLI Reference

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

Authentication

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

--api-key <value> CLI flag (explicit override).
GI_API_KEY environment variable.
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 (50 concurrent / 120 rpm, opt-in only). 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-enhancer --demo

Bundled fixture is the Drosophila eve (even-skipped) locus (chr2R:9972000-9982000, incl. the upstream stripe enhancers) — the canonical DeepSTARR benchmark for developmental enhancer activity. Expect a positive developmental signal (max dev ~2.1).

Gotchas

DeepSTARR was trained on Drosophila S2 cells. Activity scores for mammalian sequences are still informative as a relative ranking, but the absolute scale is calibrated for fly chromatin.
Pre-windowing is unnecessary — the 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: "enhancer", "DeepSTARR", "STARR-seq", "predict CRE", "regulatory activity".

Chains with: gi-promoter (joint regulatory-element scan), gi-chromatin (cross-validate with chromatin accessibility), variant-annotation (variants overlapping high-activity windows).

Safety

Research tool. Not a clinical assay.