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Agent skill

Gi Enhancer

by ClawBio in ClawBio/ClawBio

Predict enhancer activity in DNA sequences using the Genomic Intelligence G0 DeepSTARR model, via the hosted /v1/tasks/enhancer/predict API.

MITAuto-check: notesResearch & Science

Install Gi Enhancer

skills CLI
$ npx skills add ClawBio/ClawBio --skill gi-enhancer -a claude-code

Project install by default; add -g for ~/.claude/skills/.

GitHub CLI
$ gh skill install ClawBio/ClawBio gi-enhancer --agent claude-code

Project scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).

Manual copy
$ git clone --depth 1 https://github.com/ClawBio/ClawBio.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/gi-enhancer .claude/skills/gi-enhancer && rm -rf skills-src

Use ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.

Claude Code skills documentation · loads skills from .claude/skills/

Facts

Skill name
gi-enhancer
GitHub stars
1.2k
Token cost
~1.8k tokens
SKILL.md length
615 words
Files
6
Skills in repo
104
Repo updated
First seen
Licence
MIT

At a glance

Predict enhancer activity in DNA sequences using the Genomic Intelligence G0 DeepSTARR model, via the hosted /v1/tasks/enhancer/predict API.

  • Works in 3 steps: Parse: single-record FASTA. → POST to /v1/tasks/enhancer/predict; the… → Render: report.md + result.json +…
  • Tasks that involve Bioinformatics
  • SKILL.md covers Trigger, Why This Exists, API Backed and Workflow, plus 7 more sections
  • Runs Python scripts from its folder; calls python; reaches api.genomicintelligence.ai; needs GI_API_KEY

What it does

Gi Enhancer is an agent skill from ClawBio/ClawBio. 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.

Its SKILL.md is about 1.8k tokens, which your agent loads only when the skill is triggered. The skill folder holds 7 other files (for example `api.py`, `gi_enhancer.py` and `tests/__init__.py`).

It sits in Research & Science, covering Bioinformatics. The repository describes itself as: 🦖 ClawBio - The first bioinformatics-native AI agent skill library. Local-first. Reproducible. Open. Free. The licence is MIT.

When your agent uses it

  • Tasks that involve Bioinformatics

Example prompts

  • “/gi-enhancer”

Requirements

  • Python 3
  • A credential in GI_API_KEY

Workflow steps

3 steps, taken from the first numbered list in SKILL.md.

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

What it can do on your machine

Read from SKILL.md and the folder at commit 5e045e3. It shows what the files ask for, not the result of running them.

  • Tool permissions

    Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.

    From allowed-tools in the SKILL.md frontmatter.

  • Runs code

    Ships script files (Python), which the agent can run.

    Shell commands in SKILL.md call:

    • python

    From the folder's file list and the shell code blocks in SKILL.md.

  • Network

    Hosts in commands or code, which the agent is likely to contact:

    • api.genomicintelligence.ai

    Also links to:

    • genomicintelligence.ai

    From URLs in SKILL.md, links to its own repository left out.

  • Credentials

    Names these keys or tokens, usually read from environment variables:

    • GI_API_KEY

    From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.

Context cost

Gi Enhancer loads about 1.8k tokens when it runs. Until then it costs about 47 tokens; SKILL.md has 615 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it
~47
When it runs · the whole SKILL.md, loaded when a task matches
~1.8k

Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.

Safety

Auto-check: notes

The automated check noted patterns worth knowing about, such as sudo or a known installer.

  • NoteMentions a .env fileSKILL.md:138
    cp .env.example .env
  • NoteMentions a .env fileSKILL.md:139
    set -a && source .env && set +a

Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); files beside SKILL.md are not scanned.

SKILL.md

The full file from ClawBio/ClawBio at commit 5e045e3, republished under its MIT licence (© ClawBio). 615 words, ~1,842 tokens.

Download SKILL.mdSave it as .claude/skills/gi-enhancer/SKILL.md (or your agent's skills folder). This skill also uses 5 other files; get the full folder from GitHub.
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.author
ClawBio + Genomic Intelligence
metadata.domain
genomics
metadata.tags
genomics, enhancer, regulatory, cis-regulatory, deepstarr, dna-lm, gi-api
metadata.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

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 <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:

bash
# Repo root (git clone) — or ~/.claude/plugins/cache/clawbio/clawbio/<version>/ for plugin installs
cp .env.example .env
set -a && source .env && set +a
Show full SKILL.md (247 more words)Show less
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; 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.

© ClawBio, MIT. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file

Files

SKILL.md and 5 other files in skills/gi-enhancer of ClawBio/ClawBio.

  • SKILL.md
  • api.py
  • example_data/enhancer_eve.fa
  • gi_enhancer.py
  • tests/__init__.py
  • tests/test_gi_enhancer.py

Open the folder on GitHubat commit 5e045e3

Compare with similar skills

Gi Enhancer next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.

Gi Enhancer compared with similar skills
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Gi Enhancer this skillClawBio/ClawBio1.2k—~1.8kAutomated safety check: NotesMIT
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Metabolic Study Planneraiming-lab/AutoResearchClaw15k—~1.9kAutomated safety check: PassMIT
13C Metabolic Flux AnalysisK-Dense-AI/scientific-agent-skills48k1 repos~3.2kAutomated safety check: PassMIT
Alphagenome Single Variant Analysisgoogle-deepmind/science-skills3.2k2 repos~3kAutomated safety check: NotesApache-2.0
MFA Pipeline Orchestratoraiming-lab/AutoResearchClaw15k—~923Automated safety check: PassMIT

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Categories

Questions about Gi Enhancer

What does Gi Enhancer do?

Predict enhancer activity in DNA sequences using the Genomic Intelligence G0 DeepSTARR model, via the hosted /v1/tasks/enhancer/predict API. Gi Enhancer is an agent skill from ClawBio/ClawBio. Predict enhancer activity in DNA sequences using the Genomic Intelligence G0 DeepSTARR model, via the hosted /v1/tasks/enhancer/predict API.

When should I use Gi Enhancer?

Gi Enhancer fits situations like: tasks that involve Bioinformatics.

How do I install Gi Enhancer in Claude Code?

Run `npx skills add ClawBio/ClawBio --skill gi-enhancer -a claude-code`. Or copy the skill folder (skills/gi-enhancer in ClawBio/ClawBio) into .claude/skills/gi-enhancer in your project. Claude Code loads it when a task matches its description.

How do I install Gi Enhancer in Codex?

Run `npx skills add ClawBio/ClawBio --skill gi-enhancer -a codex`. Or copy the skill folder (skills/gi-enhancer in ClawBio/ClawBio) into .agents/skills/gi-enhancer in your project. Codex loads it when a task matches its description.

Can I use Gi Enhancer in Cursor, Gemini CLI or GitHub Copilot?

Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add ClawBio/ClawBio --skill gi-enhancer -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/gi-enhancer, .gemini/skills/gi-enhancer, .github/skills/gi-enhancer and .opencode/skills/gi-enhancer in your project.

What does Gi Enhancer need to run?

Going by SKILL.md and its folder, Gi Enhancer needs Python for the scripts in its folder, the command-line tools its instructions call (python) and credentials named GI_API_KEY. Our summary lists: Python 3; A credential in GI_API_KEY.

Does Gi Enhancer access the network?

SKILL.md names 2 domains. In commands or code: api.genomicintelligence.ai; the agent is likely to contact it when it follows the instructions. As links in the text: genomicintelligence.ai. This is read from the text; nothing was executed.

Is Gi Enhancer safe to install?

Our automated static check of SKILL.md found notes only (mentions a .env file), nothing it rates as a warning. It is not a guarantee. Review the folder before installing.

What licence does Gi Enhancer use?

Gi Enhancer is published under the MIT licence (declared in SKILL.md). It allows redistribution, so the full SKILL.md is shown on this page.

How many tokens does Gi Enhancer use?

About 1.8k tokens (SKILL.md is roughly 7.4k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full.

What are the alternatives to Gi Enhancer?

Skills that share tags, products or a category with Gi Enhancer: Dbsnp Database (google-deepmind/science-skills, 3.2k stars), Metabolic Study Planner (aiming-lab/AutoResearchClaw, 15k stars), 13C Metabolic Flux Analysis (K-Dense-AI/scientific-agent-skills, 48k stars) and Alphagenome Single Variant Analysis (google-deepmind/science-skills, 3.2k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Gi Enhancer?

ClawBio (a GitHub organization) maintains it in ClawBio/ClawBio, which has 1,154 GitHub stars. The repository holds 104 skills in this directory. The repository was last updated on October 7, 2026.

Source: ClawBio/ClawBio on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.