gi-enhancer

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.
version	0.1.0
author	ClawBio + Genomic Intelligence
domain	genomics
license	MIT
tags	["genomics","enhancer","regulatory","cis-regulatory","deepstarr","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, 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."}]
dependencies	{"python":">=3.10","packages":["requests>=2.31"]}
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."}]
endpoints	{"cli":"python skills/gi-enhancer/gi_enhancer.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":["enhancer","enhancer activity","predict enhancer","regulatory element","cis-regulatory","CRE","DeepSTARR","STARR-seq","massively parallel reporter assay","MPRA","gi enhancer","genomic intelligence enhancer"]}}

🎚️ 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 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 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

1. Parse: single-record FASTA.
2. Authenticate: --api-key → GI_API_KEY → hackathon fallback.
3. POST to /v1/tasks/enhancer/predict; the API windows internally.
4. 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

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.