13C Metabolic Flux Analysis
K-Dense-AI/scientific-agent-skills
Estimates reaction fluxes inside cells from steady-state carbon-13 labeling data with a bundled mfapy-based solver, and reports which fluxes the data pin down.
Query the Genome Aggregation Database (gnomAD). An agent skill from google-deepmind/science-skills.
Install Gnomad Database
$ npx skills add google-deepmind/science-skills --skill gnomad-database -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install google-deepmind/science-skills gnomad-database --agent claude-codeProject scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).
$ git clone --depth 1 https://github.com/google-deepmind/science-skills.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/gnomad_database .claude/skills/gnomad-database && rm -rf skills-srcUse ~/.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/
Install the "gnomad-database" agent skill from https://github.com/google-deepmind/science-skills/tree/main/skills/gnomad_database into .claude/skills/gnomad-database/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "gnomad-database", 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 install https://github.com/google-deepmind/science-skills/tree/main/skills/gnomad_databaseType 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.
$ npx skills add google-deepmind/science-skills --skill gnomad-database -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install google-deepmind/science-skills gnomad-database --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/google-deepmind/science-skills.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/gnomad_database .agents/skills/gnomad-database && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "gnomad-database" agent skill from https://github.com/google-deepmind/science-skills/tree/main/skills/gnomad_database into .agents/skills/gnomad-database/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "gnomad-database", 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.
$ npx skills add google-deepmind/science-skills --skill gnomad-database -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install google-deepmind/science-skills gnomad-database --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/google-deepmind/science-skills.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/gnomad_database .cursor/skills/gnomad-database && rm -rf skills-srcUse ~/.cursor/skills/ instead of .cursor/skills for a personal install.
Cursor skills documentation · loads skills from .cursor/skills/, .agents/skills/, .claude/skills/, .codex/skills/
Install the "gnomad-database" agent skill from https://github.com/google-deepmind/science-skills/tree/main/skills/gnomad_database into .cursor/skills/gnomad-database/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "gnomad-database", 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 https://github.com/google-deepmind/science-skills.git --path skills/gnomad_database--scope user (default) or --scope workspace; --path is the subfolder of the repo that holds the skill; --consent skips the security confirmation prompt.
$ npx skills add google-deepmind/science-skills --skill gnomad-database -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install google-deepmind/science-skills gnomad-database --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/google-deepmind/science-skills.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/gnomad_database .gemini/skills/gnomad-database && rm -rf skills-srcUse ~/.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/
Install the "gnomad-database" agent skill from https://github.com/google-deepmind/science-skills/tree/main/skills/gnomad_database into .gemini/skills/gnomad-database/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "gnomad-database", 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.
$ gh skill install google-deepmind/science-skills gnomad-databaseInstalls 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).
$ npx skills add google-deepmind/science-skills --skill gnomad-database -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/google-deepmind/science-skills.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/gnomad_database .github/skills/gnomad-database && rm -rf skills-srcUse ~/.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/
Install the "gnomad-database" agent skill from https://github.com/google-deepmind/science-skills/tree/main/skills/gnomad_database into .github/skills/gnomad-database/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "gnomad-database", 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.
$ npx skills add google-deepmind/science-skills --skill gnomad-database -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install google-deepmind/science-skills gnomad-database --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/google-deepmind/science-skills.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/gnomad_database .opencode/skills/gnomad-database && rm -rf skills-srcUse ~/.config/opencode/skills/ instead of .opencode/skills for a personal install.
OpenCode skills documentation · loads skills from .opencode/skills/, .claude/skills/, .agents/skills/
Install the "gnomad-database" agent skill from https://github.com/google-deepmind/science-skills/tree/main/skills/gnomad_database into .opencode/skills/gnomad-database/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "gnomad-database", 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
gnomad-database- GitHub stars
- 3.2k
- Used in
- 2 other repos
- Token cost
- ~775 tokens
- SKILL.md length
- 239 words
- Files
- 5 (incl. scripts, references)
- Skills in repo
- 40
- Repo updated
- First seen
- Licence
- Apache-2.0
At a glance
Query the Genome Aggregation Database (gnomAD). An agent skill from google-deepmind/science-skills.
- Works in 2 steps: uv: Read the uv skill and follow its… → User Notification: If…
- Determining the rarity
- SKILL.md covers Prerequisites, Core Rules, Utility Scripts and References
- Runs Python scripts from its folder; calls uv
What it does
Gnomad Database is an agent skill from google-deepmind/science-skills. Query the Genome Aggregation Database (gnomAD). Use when determining the rarity or allele frequency of specific genetic variants, retrieving gene constraint metrics (pLI, LOEUF) to assess loss-of-function intolerance, finding variants in a genomic region or gene, or querying structural variants. Don't use for analyzing individual patient genomes, tracking somatic mutations in cancer (use COSMIC), or requesting raw sequencing reads (use ENA).
Its SKILL.md is about 780 tokens, which your agent loads only when the skill is triggered. The skill folder holds 6 other files, including scripts and reference files (for example `scripts/get_gene_constraint.py`, `scripts/get_variant_frequency.py` and `scripts/search_variants.py`).
It sits in Research & Science, covering Bioinformatics. The repository describes itself as: GDM Science Skills to speed up agentic scientific workflows with better grounding and higher token efficiency. Integrate insights from AlphaGenome, AFDB, UniProt and 30+ other… The licence is Apache-2.0.
When your agent uses it
- Determining the rarity
- Allele frequency of specific genetic variants
- Retrieving gene constraint metrics (pLI
- LOEUF) to assess loss-of-function intolerance
Example prompts
- “/gnomad-database”
Requirements
- Python 3
Workflow steps
2 steps, taken from the first numbered list in SKILL.md.
- uv: Read the uv skill and follow its Setup instructions to ensure
- User Notification: If .licenses/gnomad_database_LICENSE.txt does not
What it can do on your machine
Read from SKILL.md and the folder at commit 6883275. 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 3 files in scripts/ (Python), which the agent can run.
Shell commands in SKILL.md call:
uv
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):
gnomad.broadinstitute.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
Gnomad Database loads about 775 tokens when it runs, and up to ~2.1k if it reads all its reference files. Until then it costs about 115 tokens; SKILL.md has 239 words of instructions outside code blocks.
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); the scripts in this folder are not scanned.
SKILL.md
The full file from google-deepmind/science-skills at commit 6883275, republished under its Apache-2.0 licence (© google-deepmind). 239 words, ~775 tokens.
Download SKILL.mdSave it as
.claude/skills/gnomad-database/SKILL.md (or your agent's skills folder). This skill also uses 4 other files; get the full folder from GitHub.- name
- gnomad-database
- description
- Query the Genome Aggregation Database (gnomAD). Use when determining the rarity or allele frequency of specific genetic variants, retrieving gene constraint metrics (pLI, LOEUF) to assess loss-of-function intolerance, finding variants in a genomic region or gene, or querying structural variants. Don't use for analyzing individual patient genomes, tracking somatic mutations in cancer (use COSMIC), or requesting raw sequencing reads (use ENA).
gnomAD Database
Prerequisites
uv: Read theuvskill and follow its Setup instructions to ensureuvis installed and on PATH.- User Notification: If .licenses/gnomad_database_LICENSE.txt does not already exist in the workspace root directory then (1) prominently notify the user to check the terms at https://gnomad.broadinstitute.org/policies and https://gnomad.broadinstitute.org/data#api, then (2) create the file recording the notification text and timestamp.
Core Rules
- Use the Wrapper: ALWAYS execute the provided helper scripts to query the database rather than accessing the database directly. The scripts automatically enforce the gnomAD API rate limits gracefully.
- Notification: If this skill is used, ensure this is mentioned in the output.
Utility Scripts
All scripts are located in the scripts/ subdirectory of this skill's
installation directory. When running them, use the full absolute path to the
script (e.g. /path/to/gnomad_database/scripts/get_variant_frequency.py).
1. Variant Frequency. Retrieves global and ancestry-specific allele
frequencies, homozygote counts, and Grpmax Filtering AF (faf95/faf99) for
exome, genome, and total (exome+genome combined) data. The filtering allele
frequency (FAF) is the maximum credible genetic ancestry group AF (lower bound
of the 95% or 99% CI). Variant ID format must be chrom-pos-ref-alt (e.g.,
1-55516888-G-GA). Alternately, you may provide an rsID.
# By variant ID:
uv run scripts/get_variant_frequency.py --variant_id {variant_id} [--dataset {dataset}] --output variant_frequency.json
# By rsID (e.g., rs1800562):
uv run scripts/get_variant_frequency.py --rsid {rsid} [--dataset {dataset}] --output variant_frequency.json2. Gene Constraint. Retrieves constraint metrics for a gene. The response
will explicitly contain pli, and the LOEUF score is represented by
oe_lof_upper.
uv run scripts/get_gene_constraint.py --gene {gene_symbol} --output {gene_symbol}_constraint.json3. Region/Gene Variant Search. Finds all variants in a region or gene.
# By region:
uv run scripts/search_variants.py --chrom {chrom} --start {start} --end {end} --output region_variants.json
# By gene:
uv run scripts/search_variants.py --gene {gene_symbol} --consequence {pLoF|missense} --output {gene_symbol}_variants.jsonReferences
Further documentation on the data: https://gnomad.broadinstitute.org/data#api More general database documentation: https://gnomad.broadinstitute.org/help
© google-deepmind, Apache-2.0. 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 4 other files (scripts, references) in skills/gnomad_database of google-deepmind/science-skills.
- SKILL.md
- references/citation.bib
- scripts/get_gene_constraint.py
- scripts/get_variant_frequency.py
- scripts/search_variants.py
Open the folder on GitHubat commit 6883275
Used in 2 other repositories
We found 2 copies of this SKILL.md (exact, near-identical or edited) in other folders, from 2 other GitHub owners. This page covers the copy in google-deepmind/science-skills, which our catalogue first saw on October 7, 2026.
Compare with similar skills
Gnomad Database 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.
| Skill | Stars | Used in | Tokens | Auto-check | Licence | Repo updated |
|---|---|---|---|---|---|---|
| Gnomad Database this skillgoogle-deepmind/science-skills | 3.2k | 2 repos | ~775 | Automated safety check: Pass | Apache-2.0 | |
| 13C Metabolic Flux AnalysisK-Dense-AI/scientific-agent-skills | 48k | 1 repos | ~3.2k | Automated safety check: Pass | MIT | |
| Metabolic Study Planneraiming-lab/AutoResearchClaw | 15k | — | ~1.9k | Automated safety check: Pass | MIT | |
| MFA Pipeline Orchestratoraiming-lab/AutoResearchClaw | 15k | — | ~923 | Automated safety check: Pass | MIT | |
| Singlecell Qcxuzhougeng/wisp-science | 1k | — | ~1.6k | Automated safety check: Pass | AGPL-3.0 | |
| Paper Expert Generatorguhaohao0991/PaperClaw | 250 | — | ~2k | Automated safety check: Pass | None |
Similar skills
Metabolic Study Planner
aiming-lab/AutoResearchClaw
Turns a broad metabolic modelling topic into a concrete, paper-shaped plan with organism, model, perturbations, metrics and figures before any FBA code is written.
MFA Pipeline Orchestrator
aiming-lab/AutoResearchClaw
Runs a metabolic flux analysis from model loading to phenotype prediction and figures by handing work to four sub-agents in sequence.
Singlecell Qc
xuzhougeng/wisp-science
A skill your agent uses when designing, reviewing, or implementing single-cell RNA-seq QC in Python or R with a human-in-the-loop, data-driven approach.
Paper Expert Generator
guhaohao0991/PaperClaw
Generate a specialized domain-expert research agent modeled on PaperClaw architecture.
Scarf Single Cell
NygenAnalytics/scarf
Analyze single-cell data with core Scarf, the out-of-core Zarr DataStore library with immutable artifacts and pipeline runs.
More from google-deepmind/science-skills
All 40 skills in this repoAlphafold Database Fetch And Analyze
google-deepmind/science-skills
Retrieve and analyze AlphaFold predicted structures for a protein.
Alphagenome Single Variant Analysis
google-deepmind/science-skills
Analyzes genetic variant effects on gene expression (RNA-seq), chromatin accessibility (DNASE), histone marks (ChIP), and transcription factors using the AlphaGenome API.
Chembl Database
google-deepmind/science-skills
Query the ChEMBL database for bioactive molecules, drug targets, bioactivity data, approved drugs, and chemical structures.
Clinical Trials Database
google-deepmind/science-skills
Query ClinicalTrials.gov via APIv2. An agent skill from google-deepmind/science-skills.
Clinvar Database
google-deepmind/science-skills
A skill your agent uses when needing clinical significance, pathogenicity classifications (e.g., Pathogenic, Benign, VUS), clinical evidence rationales, or finding "hard positive" benchmark controls…
Dbsnp Database
google-deepmind/science-skills
A skill your agent uses when you want to look up, map, and search for short genetic variants (SNPs, indels) in NCBI's dbSNP database.
Related
Categories
Questions about Gnomad Database
What does Gnomad Database do?
Query the Genome Aggregation Database (gnomAD). An agent skill from google-deepmind/science-skills. Gnomad Database is an agent skill from google-deepmind/science-skills. Query the Genome Aggregation Database (gnomAD).
When should I use Gnomad Database?
Gnomad Database fits situations like: determining the rarity; allele frequency of specific genetic variants; retrieving gene constraint metrics (pLI; LOEUF) to assess loss-of-function intolerance.
How do I install Gnomad Database in Claude Code?
Run `npx skills add google-deepmind/science-skills --skill gnomad-database -a claude-code`. Or copy the skill folder (skills/gnomad_database in google-deepmind/science-skills) into .claude/skills/gnomad-database in your project. Claude Code loads it when a task matches its description.
How do I install Gnomad Database in Codex?
Run `npx skills add google-deepmind/science-skills --skill gnomad-database -a codex`. Or copy the skill folder (skills/gnomad_database in google-deepmind/science-skills) into .agents/skills/gnomad-database in your project. Codex loads it when a task matches its description.
Can I use Gnomad Database 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 google-deepmind/science-skills --skill gnomad-database -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/gnomad-database, .gemini/skills/gnomad-database, .github/skills/gnomad-database and .opencode/skills/gnomad-database in your project.
What does Gnomad Database need to run?
Going by SKILL.md and its folder, Gnomad Database needs Python for the scripts in its folder and the command-line tools its instructions call (uv). Our summary lists: Python 3.
Does Gnomad Database access the network?
SKILL.md names 1 domain. As links in the text: gnomad.broadinstitute.org. This is read from the text; nothing was executed.
Is Gnomad Database 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. The check reads SKILL.md only: the scripts in the folder are not scanned, so read them before running anything.
What licence does Gnomad Database use?
Gnomad Database is published under the Apache-2.0 licence (the repository's licence). It allows redistribution, so the full SKILL.md is shown on this page.
How many tokens does Gnomad Database use?
About 775 tokens (SKILL.md is roughly 3.1k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full. Its references folder adds about 1.3k tokens, read only when the agent opens those files.
What are the alternatives to Gnomad Database?
Skills that share tags, products or a category with Gnomad Database: 13C Metabolic Flux Analysis (K-Dense-AI/scientific-agent-skills, 48k stars), Metabolic Study Planner (aiming-lab/AutoResearchClaw, 15k stars), MFA Pipeline Orchestrator (aiming-lab/AutoResearchClaw, 15k stars) and Singlecell Qc (xuzhougeng/wisp-science, 1k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Gnomad Database?
google-deepmind (a GitHub organization) maintains it in google-deepmind/science-skills, which has 3,216 GitHub stars. The repository holds 40 skills in this directory. The repository was last updated on September 15, 2026.
Source: google-deepmind/science-skills on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.