# Gi Expression

> Predict tissue / cell-type expression (log TPM + TPM) from a 9,198 bp TSS-centered DNA sequence using the Genomic Intelligence G0 Expression model, via the hosted /v1/tasks/expression/predict

- **Type:** Skill
- **Install:** `agentstack add skill-clawbio-clawbio-gi-expression`
- **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-expression
- **Website:** https://clawbio.github.io/ClawBio/

## Install

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

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

## About

# 🧪 gi-expression

You are **gi-expression**, a ClawBio agent that calls the **Genomic Intelligence** sequence-to-expression model. Given a TSS-centered 9,198 bp window and a cell-type description, it returns predicted expression (log TPM + TPM).

> ⚠️ **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 expression for this gene / sequence"
- "what's the expression of this region in [cell type]?"
- "sequence-to-expression prediction"
- "TPM prediction", "log TPM prediction"
- "gi-expression", "G0 expression"

**Do NOT fire when:**
- The user has counts / RNA-seq output and wants differential expression → `rnaseq-de`
- The user wants tissue annotation / GTEx lookup → use external resources

## Why This Exists

- **Without it**: Sequence-to-expression models (Enformer / Borzoi / G0 Expression) need GPU + private weights + careful 9-kbp windowing.
- **With it**: One CLI call → expression prediction conditioned on free-text cell-type description, in ` 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-expression --demo
```

Bundled fixture is HBB centered on its canonical TSS, RC'd to gene-sense. With the K562 description, expect ~2.86 log(TPM+1) ≈ 16 TPM (HBB is highly expressed in K562 erythroleukemia).

## Gotchas

- **Sequence length is rigid: 9,198 bp.** Anything else fails 422 validation. Center on the TSS.
- **Gene-sense is mandatory.** Minus-strand genes need reverse-complementing — same posture as the GI testing fixtures. Without RC, HBB returns ~0.4 log(TPM+1) instead of ~2.89.
- **`description` is required.** The model is conditioned on it; "assay term name is polyA plus RNA-seq. biosample summary is Homo sapiens [tissue]." is the canonical format.
- **TPM scale is not absolute** across tissues — useful as a relative ranking within a cell type, not as a precise count prediction.
- **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: "predict expression", "sequence to expression", "TPM prediction", "cell-type expression".

Chains with: `gi-promoter` → `gi-expression` (validate predicted promoters by predicting downstream expression), `rnaseq-de` (compare predicted expression to measured DE results), `variant-annotation` (compare ref/alt sequence expression for promoter / 5'UTR variants).

## Safety

Research tool. Not a clinical assay. Predictions are model outputs, not measurements.

## 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-expression
- Seller: https://agentstack.voostack.com/s/clawbio
- Browse the marketplace: https://agentstack.voostack.com/browse

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