# Gi Enhancer

> 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.

- **Type:** Skill
- **Install:** `agentstack add skill-clawbio-clawbio-gi-enhancer`
- **Verified:** Yes — security-reviewed for prompt injection and unsafe behavior
- **Seller:** [ClawBio](https://agentstack.voostack.com/s/clawbio)
- **Installs:** 0
- **Category:** [Agent Skills](https://agentstack.voostack.com/c/agent-skills)
- **Latest version:** 0.1.0
- **License:** MIT
- **Upstream author:** [ClawBio](https://github.com/ClawBio)
- **Source:** https://github.com/ClawBio/ClawBio/tree/main/skills/gi-enhancer
- **Website:** https://clawbio.github.io/ClawBio/

## Install

```sh
agentstack add skill-clawbio-clawbio-gi-enhancer
```

Requires the [AgentStack CLI](https://agentstack.voostack.com/docs/cli). Works with Claude Code, Cursor, and any MCP-compatible agent.

## About

# 🎚️ 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 . **Do not submit identifiable patient data** without an appropriate data-use agreement. Key setup: see [Authentication](#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

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

```bash
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 ` 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 (50 concurrent / 120 rpm, opt-in only). From wherever the ClawBio files live on your machine:

```bash
# Repo root (git clone) — or ~/.claude/plugins/cache/clawbio/clawbio// 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:

```bash
export GI_API_KEY=gi_yourkeyhere
```

## Demo

```bash
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.

## Source & license

This open-source skill is cataloged on AgentStack and links to its original source — we do not rehost the code.

- **Author:** [ClawBio](https://github.com/ClawBio)
- **Source:** [ClawBio/ClawBio](https://github.com/ClawBio/ClawBio)
- **License:** MIT
- **Homepage:** https://clawbio.github.io/ClawBio/

Install and usage instructions live in the source repository linked above.

## Pricing

- **Free** — Free

## Security capabilities

Automated source analysis of v0.1.0 — what this tool can access:

- **Network access:** no
- **Filesystem access:** no
- **Shell / process execution:** no
- **Environment & secrets:** yes
- **Dynamic code execution:** no

*"Yes" means the capability is present in the source — more access means more to trust, not that it is unsafe.*


## Versions

- **0.1.0** — security scan: passed — Imported from the upstream source.

## Links

- Listing page: https://agentstack.voostack.com/l/skill-clawbio-clawbio-gi-enhancer
- Seller: https://agentstack.voostack.com/s/clawbio
- Browse the marketplace: https://agentstack.voostack.com/browse

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