Agent skill

Organ Aging Studio

Interactive Goeminne proteomic aging clock with organ filters and per-protein contribution breakdown (protein NPX × coefficient).

MITAuto-check passedResearch & Science

Install Organ Aging Studio

skills CLI

$ npx skills add ClawBio/ClawBio --skill organ-aging-studio -a claude-code

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

GitHub CLI

$ gh skill install ClawBio/ClawBio organ-aging-studio --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/organ-aging-studio .claude/skills/organ-aging-studio && 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/

Paste into Claude Code

Install the "organ-aging-studio" agent skill from https://github.com/ClawBio/ClawBio/tree/main/skills/organ-aging-studio into .claude/skills/organ-aging-studio/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "organ-aging-studio", then confirm the skill loads.

Claude Code copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

$skill-installer

$skill-installer install https://github.com/ClawBio/ClawBio/tree/main/skills/organ-aging-studio

Type this inside Codex. $skill-installer <name> installs a curated skill from openai/skills. The installer writes to $CODEX_HOME/skills (default ~/.codex/skills). Restart Codex if the skill does not show up.

skills CLI

$ npx skills add ClawBio/ClawBio --skill organ-aging-studio -a codex

Project install goes to .agents/skills/; add -g for ~/.codex/skills/.

GitHub CLI

$ gh skill install ClawBio/ClawBio organ-aging-studio --agent codex

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/ClawBio/ClawBio.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/organ-aging-studio .agents/skills/organ-aging-studio && rm -rf skills-src

Use ~/.agents/skills/ instead of .agents/skills for a personal install.

Codex skills documentation · loads skills from .agents/skills/

Paste into Codex

Install the "organ-aging-studio" agent skill from https://github.com/ClawBio/ClawBio/tree/main/skills/organ-aging-studio into .agents/skills/organ-aging-studio/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "organ-aging-studio", then confirm the skill loads.

Codex copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

skills CLI

$ npx skills add ClawBio/ClawBio --skill organ-aging-studio -a cursor

Project install goes to .agents/skills/; add -g for ~/.cursor/skills/.

GitHub CLI

$ gh skill install ClawBio/ClawBio organ-aging-studio --agent cursor

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/ClawBio/ClawBio.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/organ-aging-studio .cursor/skills/organ-aging-studio && rm -rf skills-src

Use ~/.cursor/skills/ instead of .cursor/skills for a personal install.

Cursor skills documentation · loads skills from .cursor/skills/, .agents/skills/, .claude/skills/, .codex/skills/

Paste into Cursor

Install the "organ-aging-studio" agent skill from https://github.com/ClawBio/ClawBio/tree/main/skills/organ-aging-studio into .cursor/skills/organ-aging-studio/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "organ-aging-studio", then confirm the skill loads.

Cursor copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

gemini skills install

$ gemini skills install https://github.com/ClawBio/ClawBio.git --path skills/organ-aging-studio

--scope user (default) or --scope workspace; --path is the subfolder of the repo that holds the skill; --consent skips the security confirmation prompt.

skills CLI

$ npx skills add ClawBio/ClawBio --skill organ-aging-studio -a gemini-cli

Project install goes to .agents/skills/; add -g for ~/.gemini/skills/.

GitHub CLI

$ gh skill install ClawBio/ClawBio organ-aging-studio --agent gemini-cli

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/ClawBio/ClawBio.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/organ-aging-studio .gemini/skills/organ-aging-studio && rm -rf skills-src

Use ~/.gemini/skills/ instead of .gemini/skills for a personal install, then run /skills reload.

Gemini CLI skills documentation · loads skills from .gemini/skills/, .agents/skills/

Paste into Gemini CLI

Install the "organ-aging-studio" agent skill from https://github.com/ClawBio/ClawBio/tree/main/skills/organ-aging-studio into .gemini/skills/organ-aging-studio/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "organ-aging-studio", then confirm the skill loads.

Gemini CLI copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

GitHub CLI

$ gh skill install ClawBio/ClawBio organ-aging-studio

Installs for Copilot at project scope by default; add --scope user for a personal install. Preview a skill first with gh skill preview. Needs GitHub CLI 2.90.0 or later (public preview).

skills CLI

$ npx skills add ClawBio/ClawBio --skill organ-aging-studio -a github-copilot

Project install goes to .agents/skills/; add -g for ~/.copilot/skills/.

Manual copy

$ git clone --depth 1 https://github.com/ClawBio/ClawBio.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/organ-aging-studio .github/skills/organ-aging-studio && rm -rf skills-src

Use ~/.copilot/skills/ instead of .github/skills for a personal install. Commit .github/skills so cloud agent and code review can use it.

GitHub Copilot skills documentation · loads skills from .github/skills/, .claude/skills/, .agents/skills/

Paste into GitHub Copilot

Install the "organ-aging-studio" agent skill from https://github.com/ClawBio/ClawBio/tree/main/skills/organ-aging-studio into .github/skills/organ-aging-studio/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "organ-aging-studio", then confirm the skill loads.

GitHub Copilot copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

skills CLI

$ npx skills add ClawBio/ClawBio --skill organ-aging-studio -a opencode

OpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.

GitHub CLI

$ gh skill install ClawBio/ClawBio organ-aging-studio --agent opencode

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/ClawBio/ClawBio.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/organ-aging-studio .opencode/skills/organ-aging-studio && rm -rf skills-src

Use ~/.config/opencode/skills/ instead of .opencode/skills for a personal install.

OpenCode skills documentation · loads skills from .opencode/skills/, .claude/skills/, .agents/skills/

Paste into OpenCode

Install the "organ-aging-studio" agent skill from https://github.com/ClawBio/ClawBio/tree/main/skills/organ-aging-studio into .opencode/skills/organ-aging-studio/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "organ-aging-studio", then confirm the skill loads.

OpenCode copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

Facts

Skill name: organ-aging-studio
GitHub stars: 1.2k
Token cost: ~2.1k tokens
SKILL.md length: 677 words
Files: 5
Skills in repo: 104
Repo updated: Oct 8, 2026
First seen: Oct 7, 2026
Licence: MIT

At a glance

Interactive Goeminne proteomic aging clock with organ filters and per-protein contribution breakdown (protein NPX × coefficient).

Works in 4 steps: Multi-organ — any organ supported by… → Gen1 / Gen2 — chronological age models… → Protein filters — --top-n,… → …
Tasks that involve Bioinformatics
SKILL.md covers Trigger, Why This Exists, Core Capabilities and Scope, plus 10 more sections
Runs Python scripts from its folder; calls python, uv and pytest

What it does

Organ Aging Studio is an agent skill from ClawBio/ClawBio. Interactive Goeminne proteomic aging clock with organ filters and per-protein contribution breakdown (protein NPX × coefficient). Agent- and demo-friendly.

Its SKILL.md is about 2.1k tokens, which your agent loads only when the skill is triggered. The skill folder holds 6 other files (for example `data/PROVENANCE.md`, `organ_aging_studio.py` and `tests/test_organ_aging_studio.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

“/organ-aging-studio”

Requirements

Python 3
Node.js

Workflow steps

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

Multi-organ — any organ supported by Goeminne et al. (2025); default demo set Heart, Brain, Liver, Immune, Organismal
Gen1 / Gen2 — chronological age models or mortality hazard → years (Gompertz)
Protein filters — --top-n, --min-abs-coef, single --sample-id
Structured outputs — Markdown report, JSON, contribution table, replay commands.sh

What it can do on your machine

Read from SKILL.md and the folder at commit dece754. 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
- uv
- pytest
From the folder's file list and the shell code blocks in SKILL.md.
Network
Links to these hosts (documentation or services it may open):
- github.com
- doi.org
From URLs in SKILL.md, links to its own repository left out.
Credentials
Names no API keys, tokens, secrets or passwords.
From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.

Context cost

Organ Aging Studio loads about 2.1k tokens when it runs. Until then it costs about 44 tokens; SKILL.md has 677 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it: ~44
When it runs · the whole SKILL.md, loaded when a task matches: ~2.1k

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 passed

The automated check found no risky patterns in SKILL.md.

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 dece754, republished under its MIT licence (© ClawBio). 677 words, ~2,123 tokens.

Download SKILL.mdSave it as .claude/skills/organ-aging-studio/SKILL.md (or your agent's skills folder). This skill also uses 4 other files; get the full folder from GitHub.

name: organ-aging-studio
description: Interactive Goeminne proteomic aging clock with organ filters and per-protein contribution breakdown (protein NPX × coefficient). Agent- and demo-friendly.
license: MIT
metadata.version: 0.1.0
metadata.author: ClawBio hackathon contributor
metadata.domain: proteomics
metadata.tags: aging, longevity, proteomics, biological age, organ clock, Goeminne, interpretability

Organ Aging Studio

You are Organ Aging Studio, a ClawBio skill that makes proteomic biological age clocks inspectable. Every prediction decomposes into:

text

predicted_age = intercept + Σ (protein_NPX × coefficient)

Trigger

Fire this skill when the user says any of:

"organ aging studio" or "explain my organ age"
"which proteins drive biological age"
"protein breakdown for Goeminne clock"
"interactive proteomic aging" or "filter proteins by coefficient"

Do NOT fire when:

User only wants batch predictions without breakdown → route to proteomics-clock
User asks about methylation / DNAm clocks → route to methylation-clock
User asks about differential abundance → route to affinity-proteomics

Why This Exists

Without this skill	With this skill
Black-box organ age number	Per-protein contributions ranked by \|coefficient\|
Full model always applied	`--top-n` and `--min-abs-coef` filters for demos
Hard to explain to clinicians / judges	`report.md` + `protein_contributions.csv` + JSON for agents

Built on the same pinned organAging coefficients as proteomics-clock. No invented weights. Downloaded coefficients are cached locally with SHA-256 sidecar hashes so the same file cannot silently change between runs.

Core Capabilities

Multi-organ — any organ supported by Goeminne et al. (2025); default demo set Heart, Brain, Liver, Immune, Organismal
Gen1 / Gen2 — chronological age models or mortality hazard → years (Gompertz)
Protein filters — --top-n, --min-abs-coef, single --sample-id
Structured outputs — Markdown report, JSON, contribution table, replay commands.sh

Scope

One skill, one task. This skill makes Goeminne organ-aging clocks inspectable from Olink NPX input and nothing else. It does not normalise data, do differential abundance, or make clinical claims.

Workflow

Validate the input as an Olink NPX table with sample_id plus protein columns.
Download the pinned organAging coefficients and organ-protein map from GitHub.
Predict organ ages, optionally filtering proteins with --top-n and --min-abs-coef.
Convert Gen2 log-hazards to years via the Gompertz transform when requested.
Write report.md, result.json, protein_contributions.csv, and a replayable commands.sh.

Input Formats

Format	Extension	Required columns
Olink NPX CSV	`.csv`	`sample_id` + protein gene symbols
Olink NPX TSV	`.tsv`	same
Compressed	`.csv.gz`	same

Optional: age (for delta = bio − chrono), sex.

CLI Reference

bash

# Demo — synthetic Olink data (no download)
python skills/organ-aging-studio/organ_aging_studio.py \
  --demo --output /tmp/studio

# One patient, Heart only, top 5 drivers
python skills/organ-aging-studio/organ_aging_studio.py \
  --input my_olink.csv.gz --output /tmp/studio \
  --organs Heart --sample-id PATIENT_001 --top-n 5

# All demo samples, multiple organs
python skills/organ-aging-studio/organ_aging_studio.py \
  --demo --output /tmp/studio \
  --organs Heart,Brain,Immune,Organismal --generation gen1

Flags

Flag	Default	Description
`--demo`	off	Use bundled synthetic Olink table
`--organs`	Heart,Brain,Liver,Immune,Organismal	Comma-separated organ list
`--generation`	gen1	`gen1` = years; `gen2` = hazard → years
`--sample-id`	all rows	Analyse one sample
`--top-n`	all present	Keep top N proteins by \|coef\|
`--min-abs-coef`	0	Drop small coefficients

Show full SKILL.md (308 more words)Show less

Demo

bash

cd ClawBio
uv sync
python skills/organ-aging-studio/organ_aging_studio.py \
  --demo --output /tmp/organ-aging-studio \
  --organs Heart,Brain,Immune,Organismal \
  --sample-id DEMO_000 --top-n 10

Expected outputs in /tmp/organ-aging-studio/:

File	Contents
`report.md`	Per-organ predicted age, raw delta vs chronological age, protein counts
`result.json`	Full nested JSON for agents
`tables/protein_contributions.csv`	Long-format NPX × coef × contribution
`commands.sh`	Replay command

Example summary row (synthetic demo):

Organ	Predicted age	Chronological	Raw delta
Heart	~67 yr	66 yr	+1 yr
Brain	~42 yr	66 yr	−24 yr

Demo NPX is synthetic — do not use it to validate correlation with age. For real Olink data, see data/PROVENANCE.md. The delta column is the raw predicted-minus-chronological gap, not age-residualised acceleration.

Gotchas

Olink NPX is already log2-scaled: Do not log-transform the input again.
Non-Olink data needs rescaling: SomaLogic, mass-spec, and other non-Olink inputs must be standardised and rescaled with the paper's Table S3 standard deviations first.
Filtered predictions are illustrative: --top-n and --min-abs-coef intentionally drop part of the published clock, so the resulting ages and raw deltas are not the validated full-model outputs.
Raw delta is not residualised acceleration: The displayed delta is predicted minus chronological age, so it remains age-biased unless you residualise it separately.
Fold order is 1-based: --fold 1 means the first coefficient row in the pinned organAging CSV, matching the upstream published fold ordering.

Real-world data (download separately)

Large cohorts are not bundled. See data/PROVENANCE.md for:

Filbin COVID Olink (real plasma) — Mendeley download + proteomics-clock/examples/fetch_filbin.py
GEO GSE40279 (blood methylation validation) — for methylation-clock, not this skill's input
GEO GSE259312 (paired Olink + methylation) — future cross-omics work

Agent Boundary

May select organs, filters, and explain contributions from result.json
Must not invent coefficients or alter the formula
Must state demo data is synthetic when using --demo
Must refuse clinical diagnosis language

Safety

Educational / research use only — not a medical device
Do not run on identifiable patient data without consent
Do not extrapolate beyond populations represented in clock training (UK Biobank–based models)

Tests

bash

pytest skills/organ-aging-studio/tests/ -q

Citation

Goeminne LJE et al. (2025). Cell Metabolism 37(1):205-222.e6. DOI: 10.1016/j.cmet.2024.10.005

Files

SKILL.md and 4 other files in skills/organ-aging-studio of ClawBio/ClawBio.

SKILL.md
data/PROVENANCE.md
organ_aging_studio.py
requirements.txt
tests/test_organ_aging_studio.py

Open the folder on GitHubat commit dece754

Compare with similar skills

Organ Aging Studio 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.

Organ Aging Studio compared with similar skills
Skill	Stars	Used in	Tokens	Auto-check	Licence	Repo updated
Organ Aging Studio this skillClawBio/ClawBio	1.2k	—	~2.1k	Automated safety check: Pass	MIT	yesterday
Alphagenome Single Variant Analysisgoogle-deepmind/science-skills	3.2k	2 repos	~3k	Automated safety check: Notes	Apache-2.0	24 days ago
13C Metabolic Flux AnalysisK-Dense-AI/scientific-agent-skills	48k	1 repos	~3.2k	Automated safety check: Pass	MIT	4 days ago
Clinvar Databasegoogle-deepmind/science-skills	3.2k	2 repos	~3.9k	Automated safety check: Notes	Apache-2.0	24 days ago
Metabolic Study Planneraiming-lab/AutoResearchClaw	15k	—	~1.9k	Automated safety check: Pass	MIT	1 mo ago
Dbsnp Databasegoogle-deepmind/science-skills	3.2k	2 repos	~3.4k	Automated safety check: Notes	Apache-2.0	24 days ago

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Questions about Organ Aging Studio

What does Organ Aging Studio do?

Interactive Goeminne proteomic aging clock with organ filters and per-protein contribution breakdown (protein NPX × coefficient). Organ Aging Studio is an agent skill from ClawBio/ClawBio. Interactive Goeminne proteomic aging clock with organ filters and per-protein contribution breakdown (protein NPX × coefficient).

When should I use Organ Aging Studio?

Organ Aging Studio fits situations like: tasks that involve Bioinformatics.

How do I install Organ Aging Studio in Claude Code?

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

How do I install Organ Aging Studio in Codex?

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

Can I use Organ Aging Studio 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 organ-aging-studio -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/organ-aging-studio, .gemini/skills/organ-aging-studio, .github/skills/organ-aging-studio and .opencode/skills/organ-aging-studio in your project.

What does Organ Aging Studio need to run?

Going by SKILL.md and its folder, Organ Aging Studio needs Python for the scripts in its folder and the command-line tools its instructions call (python, uv and pytest). Our summary lists: Python 3; Node.js.

Does Organ Aging Studio access the network?

SKILL.md names 2 domains. As links in the text: github.com and doi.org. This is read from the text; nothing was executed.

Is Organ Aging Studio safe to install?

Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. Review the folder before installing.

What licence does Organ Aging Studio use?

Organ Aging Studio 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 Organ Aging Studio use?

About 2.1k tokens (SKILL.md is roughly 8.5k 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 Organ Aging Studio?

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

Who maintains Organ Aging Studio?

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 8, 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.

Install Organ Aging Studio

Facts

At a glance

What it does

When your agent uses it

Example prompts

Requirements

Workflow steps

What it can do on your machine

Tool permissions

Runs code

Network

Credentials

Context cost

Safety

SKILL.md

Organ Aging Studio

Trigger

Why This Exists

Core Capabilities

Scope

Workflow

Input Formats

CLI Reference

Flags

Demo

Gotchas

Real-world data (download separately)

Agent Boundary

Safety

Tests

Citation

Files

Compare with similar skills

Similar skills

More from ClawBio/ClawBio

Related

Questions about Organ Aging Studio