gi-enhancer

name: gi-enhancerdescription: 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: MITmetadata:   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, 50–500,000 bp (whitespace stripped); the 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. 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 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. Omit model and the API resolves the default — a DeepSTARR model trained on Drosophila S2 cells. GET /v1/tasks/enhancer/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/enhancer/predict; the API windows internally.
3. 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:

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-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; read the score from your own run.

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.
• Length bounds are 50–500,000 bp, published as minLength / maxLength on EnhancerPredictRequest 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.
• 50 bp is admission control, not a meaningful enhancer size. It is the strictest floor any enhancer model needs; some models accept less. The models' context window is 249 bp, so 50–248 bp is accepted and scored — against a window padded out to 249 bp. Compare your length against bio_spec.context_window_bp (GET /v1/tasks/enhancer/models) to know whether the model saw real sequence; 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: "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 and development use. Not for clinical or diagnostic decisions.