google-deepmind
- 14 skills
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- 17 hours ago last updated
- ▌ Xmanager Cloud · google-deepmindLaunches, manages, and troubleshoots XManager Cloud (XMC) experiments. A MUST READ before launching any XMC experiment, orchestrating jobs on Kubernetes/GKE, or configuring experiment flags. Don't use for internal corporate launches.
- ▌ Agentic Ecology UI · google-deepmind bundleGuidelines and templates for creating a generic web UI to visualize, rank, filter, and annotate vector databases. The UI has a hierarchical structure covering database selection, label selection/definition, ranking/filtering configuration, and row visualization/annotation. Use when building, serving, or adapting an interactive web UI for Hoplite vector databases.
- ▌ Agentic Ecology Init · google-deepmind bundleInitializes a local uv-managed project directory for agentic ecology workloads. Sets up Python dependencies using reference pyproject.toml and uv.lock, configures workspace rules, and ensures Agentic Ecology skills are discoverable. Use when initializing a new project workspace or bootstrapping a clean environment.
- ▌ Agentic Ecology Bioacoustics · google-deepmind bundleProvides bioacoustic analysis capabilities for ecologists and researchers using the perch-hoplite Python package. A typical use case is to use agile modeling to bootstrap the creation and deployment of a bespoke detector for targeted species on an existing collection of passive acoustic monitoring recordings. Use when processing and annotating audio recordings for bioacoustic applications.
- ▌ Agentic Ecology Camera Traps · google-deepmind bundleProvides capabilities to run SpeciesNet detector and classifier on camera trap images, extract crop-level feature embeddings, and populate a Hoplite vector database for downstream search and agile modeling. Use when ingesting camera trap images, classifying wildlife photos, or indexing camera trap data.
- ▌ Pymol · google-deepmind bundleVisualize, analyze, and render protein and molecular structures using PyMOL. Use when the user wants to create images of protein structures, perform structural alignments or superposition, measure distances or contacts, highlight binding sites or active site residues, color by B-factor/pLDDT, or analyze protein-ligand interactions. Do not use for docking, molecular dynamics, or sequence-only analysis.
- ▌ Credentials · google-deepmindInstructions for handling API keys and credentials safely, verifying their presence, and prompting the user to add them if missing using a safe protocol.
- ▌ Pubmed Database · google-deepmind bundleSearch PubMed for scientific literature, including published clinical trials. Fetch abstracts and full text. Link published research to biological databases (gene, protein, nucleotide, PubChem) to discover associations between papers and specific compounds or genes. Verify medical spelling, match raw citations, and cache result sets for bulk processing. Interfaces NCBI E-utilities and PMC BioC APIs.
- ▌ Ncbi Sequence Fetch · google-deepmind bundleRetrieve protein and nucleotide sequences from NCBI databases using E-utilities. Supports direct accession lookup, CDS translation, gene+organism search, locus lookup, PubMed-linked sequences, patent protein extraction, and organism+length fallback search. Use when you need to fetch biological sequences by accession, gene name, locus tag, PubMed ID, or patent number.
- ▌ Literature Search Biorxiv · google-deepmind bundleBrowse, filter, and download life sciences, biology, and medical preprints from bioRxiv and medRxiv. Supports fetching paper metadata by DOI, and browsing by date range with category and keyword filters. Keyword filtering is local, so date ranges MUST be narrow (1-4 weeks) with a category to prevent timeouts.
- ▌ Alphagenome Atlas Website Links · google-deepmind bundleConstructs 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.
- ▌ Alphagenome Variant Impact Score · google-deepmind bundleScore, 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.
- ▌ Protein Sequence Similarity Search · google-deepmind bundleSearches for homologous protein sequences using MMseqs2 (fast, default) or BLAST (comprehensive, fallback). Trigger this whenever the user provides a protein sequence or FASTA file and asks to find homologues, sequence matches, or wants to infer protein function based on sequence similarity, but not when the user wants to infer protein function based on structural similarity.
- ▌ Alphagenome Single Variant Analysis · google-deepmind bundleAnalyzes 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.