gdm-science-bundle

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Check before installing. Some of what it can do is expected: a coding skill usually runs build and test commands.

By mkurman/zorai (GitHub) · coding · 327 stars · scanned at commit 8ea1fc3

Vendor of the google-deepmind/science-skills bundle (37 skills for scientific research). Use when a user asks about any of: AlphaGenome single-variant effect analysis (RNA-seq / DNase / ChIP / TF effects, splicing disruption, UBERON/CL ontology resolution for non-coding variants), AlphaFold DB fetch and analyze, ChEMBL bioactivity queries, ClinicalTrials.gov lookups, ClinVar variant interpretation, dbSNP, EMBL-EBI Ontology Lookup Service (OLS4), ENCODE cCREs, Ensembl REST, Foldseek structural s…

Works with any agent that supports SKILL.md skills.

What this skill can do

Downloads and installs other software

The author does not mention this.

Found in 7 places.

skills/scientific-skills-gdm/README.md, line 26npx skills add google-deepmind/science-skills/
skills/scientific-skills-gdm/SKILL.md, line 38bare `python3` or `pip install`.
skills/scientific-skills-gdm/alphagenome_single_variant_analysis/SKILL.md, line 52one-liners. Do not attempt to `pip install` or create new venvs — `uv`

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skills/scientific-skills-gdm/unibind_database/SKILL.md, line 78These commands return large datasets. Use `uvx --from jmespath jp` to extract
skills/scientific-skills-gdm/unibind_database/SKILL.md, line 82uv run <SKILL DIR>/scripts/unibind_api.py list_cell_lines | uvx --from jmespath jp "results[].name"
skills/scientific-skills-gdm/unibind_database/SKILL.md, line 83uv run <SKILL DIR>/scripts/unibind_api.py list_tfs | uvx --from jmespath jp "results[].tf_name"
skills/scientific-skills-gdm/uv/SKILL.md, line 26(b) Install `uv`: `curl -LsSf https://astral.sh/uv/install.sh | sh`

Changes files outside its own folder

The author does not mention this.

Found in 1 place.

skills/scientific-skills-gdm/README.md, line 55`echo "ALPHAGENOME_API_KEY=your_actual_api_key" >> ~/.env`

Runs commands on your computer

This is disclosed by the author in the skill's SKILL.md or README. Expected for a coding skill.

Found in 219 places.

skills/scientific-skills-gdm/alphafold_database_fetch_and_analyze/SKILL.md, line 58uv run scripts/fetch_structure.py P00520 -o /path/to/output/
skills/scientific-skills-gdm/alphafold_database_fetch_and_analyze/SKILL.md, line 74uv run scripts/analyze_plddt.py ./data/AF-P00520-F1-metadata.json
skills/scientific-skills-gdm/alphafold_database_fetch_and_analyze/SKILL.md, line 85uv run scripts/analyze_pae.py ./data/AF-P00520-F1-predicted_aligned_error_v6.json

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skills/scientific-skills-gdm/alphagenome_single_variant_analysis/SKILL.md, line 36printf "Enter AlphaGenome API key (typing hidden): " && read -s key && echo && echo "ALPHAGENOME_API_KEY=$key" >> "ENV_FILE" && echo "Saved."
skills/scientific-skills-gdm/alphagenome_single_variant_analysis/SKILL.md, line 73uv run <script_name> [args...]
skills/scientific-skills-gdm/alphagenome_single_variant_analysis/SKILL.md, line 80uv run --project $SKILL_DIR /tmp/my_analysis.py --arg1 val1
skills/scientific-skills-gdm/chembl_database/SKILL.md, line 42uv run scripts/chembl_api.py <subcommand> --output <file> [options]
skills/scientific-skills-gdm/chembl_database/SKILL.md, line 50uv run scripts/chembl_api.py status --output /tmp/status.json
skills/scientific-skills-gdm/chembl_database/SKILL.md, line 154uv run scripts/chembl_api.py image --id CHEMBL25 --output /tmp/chembl25.svg
skills/scientific-skills-gdm/chembl_database/SKILL.md, line 191uv run scripts/chembl_api.py molecule --limit 2 --offset 0 --output /tmp/page1.json
skills/scientific-skills-gdm/chembl_database/SKILL.md, line 208uv run scripts/chembl_api.py <subcommand> --output <file> [--id ID | --ids ID1;ID2 | --search QUERY] [--limit N] [--offset N] [--filter KEY=VAL ...]
skills/scientific-skills-gdm/clinical_trials_database/SKILL.md, line 100uv run scripts/clinical_trials_api.py search \
skills/scientific-skills-gdm/clinical_trials_database/SKILL.md, line 160uv run scripts/clinical_trials_api.py search \
skills/scientific-skills-gdm/clinical_trials_database/SKILL.md, line 173uv run scripts/clinical_trials_api.py search \
skills/scientific-skills-gdm/clinical_trials_database/SKILL.md, line 188uv run scripts/clinical_trials_api.py get-study \
skills/scientific-skills-gdm/clinical_trials_database/SKILL.md, line 232uv run scripts/clinical_trials_api.py \
skills/scientific-skills-gdm/clinical_trials_database/SKILL.md, line 243uv run scripts/clinical_trials_api.py \
skills/scientific-skills-gdm/clinical_trials_database/SKILL.md, line 254uv run scripts/clinical_trials_api.py count \
skills/scientific-skills-gdm/clinical_trials_database/SKILL.md, line 271uv run scripts/clinical_trials_api.py search \
skills/scientific-skills-gdm/clinical_trials_database/SKILL.md, line 287uv run scripts/clinical_trials_api.py search \

and 199 more places

Reads your saved credentials, such as SSH keys or .env files

This is disclosed by the author in the skill's SKILL.md or README.

Found in 15 places.

skills/scientific-skills-gdm/alphagenome_single_variant_analysis/scripts/analyze_ism.py, line 274dotenv.load_dotenv(os.path.expanduser('~/.env'))
skills/scientific-skills-gdm/alphagenome_single_variant_analysis/scripts/generate_ontology_mapping.py, line 163dotenv.load_dotenv(os.path.expanduser('~/.env'))
skills/scientific-skills-gdm/alphagenome_single_variant_analysis/scripts/interpret_splicing.py, line 271dotenv.load_dotenv(os.path.expanduser('~/.env'))

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skills/scientific-skills-gdm/alphagenome_single_variant_analysis/scripts/lookup_gene_info.py, line 265dotenv.load_dotenv(os.path.expanduser('~/.env'))
skills/scientific-skills-gdm/alphagenome_single_variant_analysis/scripts/resolve_ontology_terms.py, line 106dotenv.load_dotenv(os.path.expanduser("~/.env"))
skills/scientific-skills-gdm/alphagenome_single_variant_analysis/scripts/visualize_genome_tracks.py, line 348dotenv.load_dotenv(os.path.expanduser('~/.env'))
skills/scientific-skills-gdm/alphagenome_single_variant_analysis/scripts/visualize_variant_effects.py, line 1134dotenv.load_dotenv(os.path.expanduser('~/.env'))
skills/scientific-skills-gdm/clinvar_database/scripts/clinvar_api.py, line 615dotenv.load_dotenv(os.path.expanduser('~/.env'))
skills/scientific-skills-gdm/dbsnp_database/scripts/dbsnp_cli.py, line 513dotenv.load_dotenv(os.path.expanduser("~/.env"))
skills/scientific-skills-gdm/literature_search_openalex/scripts/openalex_cli.py, line 526dotenv.load_dotenv(os.path.expanduser("~/.env"))
skills/scientific-skills-gdm/ncbi_sequence_fetch/scripts/ncbi_fetch.py, line 1076dotenv.load_dotenv(os.path.expanduser('~/.env'))
skills/scientific-skills-gdm/openfda_database/scripts/openfda_query.py, line 496dotenv.load_dotenv(os.path.expanduser("~/.env"))
skills/scientific-skills-gdm/protein_sequence_msa/scripts/msa_align.py, line 152dotenv.load_dotenv(os.path.expanduser("~/.env"))
skills/scientific-skills-gdm/protein_sequence_similarity_search/scripts/uniprot_blast.py, line 274dotenv.load_dotenv(os.path.expanduser("~/.env"))
skills/scientific-skills-gdm/pubmed_database/scripts/pubmed_api.py, line 638dotenv.load_dotenv(os.path.expanduser("~/.env"))

Connects to the internet

The author does not mention this.

Found in 44 places.

skills/scientific-skills-gdm/clinvar_database/scripts/clinvar_api.py, line 91resp = self.client.fetch(full_url)
skills/scientific-skills-gdm/interpro_database/scripts/interpro_client.py, line 119resp = CLIENT.fetch(url, headers=headers)
skills/scientific-skills-gdm/interpro_database/scripts/interpro_client.py, line 315help="Limit the number of results to fetch (highly recommended)",

Show 17 more

skills/scientific-skills-gdm/jaspar_database/scripts/jaspar_api.py, line 31import urllib.request
skills/scientific-skills-gdm/literature_search_openalex/scripts/openalex_cli.py, line 142resp = _PDF_CLIENT.fetch(full_url, max_retries=max_retries)
skills/scientific-skills-gdm/literature_search_openalex/scripts/openalex_cli.py, line 144resp = _API_CLIENT.fetch(full_url, max_retries=max_retries)
skills/scientific-skills-gdm/ncbi_sequence_fetch/scripts/ncbi_fetch.py, line 43import urllib.request
skills/scientific-skills-gdm/openfda_database/scripts/openfda_query.py, line 480help="Max pages to fetch (default 10)",
skills/scientific-skills-gdm/pubchem_database/scripts/pubchem_api.py, line 45resp = _CLIENT.fetch(url)
skills/scientific-skills-gdm/pubmed_database/scripts/pubmed_api.py, line 131resp = get_eutils_client().fetch(url, method="POST", data=data_bytes)
skills/scientific-skills-gdm/pymol/references/PYMOL_REFERENCE.md, line 1403. **`cmd.fetch()` will fail** — there is no network inside the container. Use
skills/scientific-skills-gdm/scienceskillscommon/http_client.py, line 26Transport is `urllib.request` (stdlib) — no third-party dependencies.
skills/scientific-skills-gdm/scienceskillscommon/http_client.py, line 64import http.client
skills/scientific-skills-gdm/scienceskillscommon/http_client.py, line 74import urllib.request
skills/scientific-skills-gdm/scienceskillscommon/http_client.py, line 163response: http.client.HTTPResponse,
skills/scientific-skills-gdm/scienceskillscommon/http_client.py, line 164) -> http.client.HTTPResponse | gzip.GzipFile:
skills/scientific-skills-gdm/scienceskillscommon/http_client.py, line 285headers: Response headers (dict-like or `http.client.HTTPMessage`).
skills/scientific-skills-gdm/scienceskillscommon/http_client.py, line 346Uses `urllib.request` as the transport layer. Handles gzip decompression,
skills/scientific-skills-gdm/scienceskillscommon/http_client.py, line 462) -> urllib.request.Request:
skills/scientific-skills-gdm/scienceskillscommon/http_client.py, line 463"""Build a `urllib.request.Request` from the given parameters."""

and 24 more places

Safer alternatives

Low-risk skills in the same category (coding) that look related. Check that one does what you need.

Install

Paste this into your terminal. It downloads exactly the version we scanned, not whatever is newest.

if [ -e ~/.agents/skills/'gdm-science-bundle' ] || [ -L ~/.agents/skills/'gdm-science-bundle' ]; then echo 'A skill folder named gdm-science-bundle already exists — not replacing it' >&2; false; else d=$(mktemp -d) && git clone --quiet --filter=blob:none --no-checkout 'https://github.com/mkurman/zorai' "$d" && git -C "$d" checkout --quiet '8ea1fc3ae126b6e103b8508bacd8f5aa60b6f4ad' -- 'skills/scientific-skills-gdm' && mkdir -p ~/.agents/skills && cp -R "$d"/'skills/scientific-skills-gdm' ~/.agents/skills/'gdm-science-bundle' && rm -rf "$d"; fi

Codex reads ~/.agents/skills directly. For Claude Code, Cursor, Copilot, Gemini CLI, Antigravity or OpenCode, also link it. For Claude Code: ln -s ~/.agents/skills/'gdm-science-bundle' ~/.claude/skills/'gdm-science-bundle' (other agents: ~/.cursor/skills, ~/.copilot/skills, ~/.gemini/skills, ~/.gemini/config/skills, ~/.config/opencode/skills). Or install through the finder skill, which does both.

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Score history

Date	Version	Score
2026-11-13	`8ea1fc3`	57