Checks whether the uv Python package manager is installed and installs it if missing. Ensures uv is on PATH. Use when another skill requires uv as a prerequisite.
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See how to installReview the instructions the agent will receive before you install.
uv is a fast Python package manager used by Science Skills to run their Python
CLI scripts. Many skills depend on uv being installed and on
PATH.
Ensure uv is available before running any skill that depends on it.
Check if uv is already available: uv --version (or & uv --version in
PowerShell). If this succeeds, uv is ready — skip the remaining steps.
Check whether uv is installed at its default location but not on PATH:
"$HOME/.local/bin/uv" --version& "$HOME\.local\bin\uv.exe" --versionIf either succeeds, skip to step 4.
If uv is not installed do these steps in order:
(a) Tell the user that uv is a tool for creating a consistent and reliable Python environment used for running the Science Skills, and that you need to install it now.
(b) Install uv:
- **Unix/macOS**: `curl -LsSf https://astral.sh/uv/install.sh | sh`
- **Windows (PowerShell)**: `powershell -ExecutionPolicy ByPass -c
"irm https://astral.sh/uv/install.ps1 | iex"`
Add uv to PATH and verify (run as a single command):
export PATH="$HOME/.local/bin:$PATH" && uv --version$env:PATH = "$HOME\.local\bin;" + $env:PATH; uv --versionAfter setup, bare uv commands should work without repeating the export.
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Retrieve and analyze AlphaFold predicted structures for a protein. Use when the user provides a specific UniProt Accession ID and wants structural confidence metrics (pLDDT), domain boundary analysis, or disorder assessment. Do not use if the user only has a protein name, gene name, or amino acid sequence — ask for a UniProt ID first.
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Constructs deep-links and URLs for the AlphaGenome Atlas website. Supports generating single-variant exploration links (1-based chr:pos:ref>alt), genomic locus views (1-based closed chr:start-end), candidate summary tables, and AlphaGenome reference vs. alternate predictions. Use whenever visualizing, exploring, charting, or linking genetic variants and genomic loci on the AlphaGenome Atlas, or when asked to inspect, view, or link predictions for a genomic variant.
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Analyzes genetic variant effects on gene expression (RNA-seq), chromatin accessibility (DNASE), histone marks (ChIP), and transcription factors using the AlphaGenome API. Use when the user asks about non-coding variant effects, pathogenicity, clinical significance, disease associations, functional effects, gene expression changes, splicing disruption, or regulatory effects in promoters and enhancers. Also use for resolving biological terms to tissue/cell-type ontologies (UBERON/CL) or analyzing variants in chr:pos:ref>alt format.
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Score, annotate, and analyze the functional impact of genetic variants using AlphaGenome Variant Impact (AVI) scores. Query variants in chr:pos:ref>alt format, annotate VCF/tabular callsets, perform saturation mutagenesis window scans (1-based closed chr:start-end), and extract GENCODE v46 GTF gene/exon/junction coordinates all via the AlphaGenome Atlas API.
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Query the ChEMBL database for bioactive molecules, drug targets, bioactivity data, approved drugs, and chemical structures. Use when the user asks about compounds, targets, IC50/Ki values, drug mechanisms, or structure searches.
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Query ClinicalTrials.gov via APIv2. Use when you want to search for trials by condition, drug, location, status, or phase; retrieve trial details by NCT ID; check eligibility/inclusion criteria; count trials across conditions or time periods; identify a sponsor's trial portfolio; find recruiting trials for patient matching.
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