GoogleCloudPlatform/LifeSciences

alphagenome-avi-interpretation

Comprehensive interpretation framework for AlphaGenome Variant Impact (AVI) scores across 18 modalities, Phred scale tiers, and Atlas links.

acmg-clinvar-gnomad-triage

ACMG/AMP clinical variant interpretation and triage workflow integrating ClinVar assertions and gnomAD v4 population frequency thresholds.

gwas-noncoding-variant-mechanisms

Methodology for prioritizing non-coding GWAS variants, interpreting trait associations, linkage disequilibrium, and causal regulatory mechanisms.

pharmacogenomics-star-allele-review

Pharmacogenomic star-allele curation, CPIC dosing guidelines, and PharmGKB clinical evidence level evaluation for therapeutic response.

job-management

Management, monitoring, quota checks, and safe deletion of FoldRun prediction jobs

job-submission

Submission of protein, RNA, ligand, and multimer predictions via AlphaFold2, AlphaFold3, OpenFold3, and Boltz-2

results-analysis

Quality assessment, confidence scoring (pLDDT, PAE, ipTM), and parallel evaluation of predicted protein structures

artifact-conventions

Standard report format, headings, and linking conventions for all OASE project artifacts.

competitive-differentiation

Interpret competitive landscape and patent search results for a concept.

program-state-management

Maintain the Layer 2 program state for a drug discovery program.

site-generation

Build, post-process, and verify the navigable HTML program website.

target-genetic-evidence

Retrieve human genetic evidence for a gene target — population constraint (gnomAD), disease associations (Open Targets, GWAS Catalog), clinical variant pathogenicity (ClinVar), and whole-blood expression (GTEx). Use when assessing whether a gene has causal or…

admet-property-prediction

Predict ADMET endpoint classifications from molecular descriptors — metabolic stability, CYP inhibition risk, permeability, hERG liability, and solubility. Use when assessing a compound's predicted ADMET profile before in vitro studies: identifying which…

binding-mode-analysis

Score docking poses and classify predicted binding strength — receptor preparation, Vina execution, threshold-based pose classification, and residue-contact verification. Use when scoring how well a ligand fits a pocket, confirming a proposed binding mode,…

bioactivity-landscape

Ingest screening data, assess dose-response quality, and compute selectivity margins — activity cutoffs, 4PL/Hill curve fitting, Z-factor screen quality, bell-shaped curve detection, and selectivity ratio computation with margin classification. Use when…

brain-atlas

Query brain region expression and donor/disease data from the Allen Brain Map -- gene expression across brain structures (human and mouse) and the Aging, Dementia, and TBI donor cohort with Braak staging, DSM-IV diagnoses, and APOE4 status. Use when looking…

citation-resolution

Resolve a cited paper or clinical trial to a real registry record — or determine that no such record exists. Use when verifying that a citation is real before relying on it in a finding, checking whether a trial acronym maps to a unique registry entry, or…

citation-verification

Verify that citations in a document resolve to real records and that claimed titles match. Use before trusting a document's reference list.

compound-identity-resolution

Confirm that a PubChem CID, ChEMBL ID, or compound name resolves to a real compound record — or determine that no such record exists — and retrieve published annotations (synonyms, drug status, mechanism of action) for a resolved compound. Use when verifying…

compound-property-profile

Validate SMILES input, compute molecular descriptors, and screen for structural alerts — drug-likeness rules, PAINS/Brenk/aggregator filters, and multi-fragment handling. Use when profiling a compound's physicochemical properties: checking Lipinski and Veber…

debate-protocol

Self-play debate and adversarial match formats for hypothesis evaluation.

disease-transcriptomics

Discover disease-state transcriptomics datasets and curated differential expression signatures across public repositories -- NCBI GEO (Gene Expression Omnibus) for dataset discovery, DisigNAtlas (Disease Signature Atlas) for pre-computed disease vs. control…

elo-tournament

Rating math, pairing policies, match format, and elo CLI usage for hypothesis tournaments.

evolution-operators

Four evolutionary operators (ground, simplify, combine, oob) for refining hypotheses, plus lineage tracking rules.

hypex-tool-setup

Activate and verify the OASE-provisioned Hypex tools before running a hypothesis-exploration workflow.

hypothesis-entry

Hypothesis entry: how hypotheses enter an OASE science program. Four strategies exist, each producing a Layer 0 artifact under raw/hypotheses/ with its own schema and threshold set. Use this skill when planning or executing hypothesis entry — deciding which…

hypothesis-run-corpus

Ingest and interpret a hypex tournament run — determine whether the ranking produced a clear leader, whether any hypotheses carry phantom citations or integrity violations, and whether the result is admissible for downstream work. This is the hypex-specific…

hypothesis-schema

Hypothesis JSON schema reference, quality bar, and hypex CLI usage for creating and validating hypotheses.

in-vivo-pk-analysis

Compute non-compartmental PK parameters from concentration-time data, project human doses via allometric scaling, and predict drug-drug interactions from in vitro CYP inhibition data. Use when analyzing in vivo PK study results: computing Cmax, AUC,…

literature-search

Search and retrieve scientific literature — PubMed, preprint servers (arXiv, bioRxiv), and PubMed Central full text. Use when discovering what has been published on a topic, gene, compound, or disease, when establishing the volume and recency of literature…

manufacturing-feasibility

Assess whether a concept's modality, delivery assumptions, and entity can be manufactured — production-platform fit, synthetic accessibility heuristics, and biologic feasibility. Use when evaluating whether a proposed intervention has a plausible…

meta-review-protocol

Steering memo format, final report format, and pattern-identification methodology for the meta-review agent.

model-organism-phenotype

Retrieve phenotype annotations for a gene from model organism and human phenotype databases — mouse knockout/knockin phenotypes from MGI (via the Alliance of Genome Resources) and human phenotype term associations from HPO. Use when assessing what happens…

pocket-druggability

Detect ligand-binding pockets in a protein structure and assess druggability — determine whether the structure contains a tractable binding site and, optionally, whether a pocket lines a specific interface. Use when evaluating whether a target has a druggable…

preclinical-safety-assessment

Interpret preclinical toxicology studies, compute therapeutic index and hERG safety margins, and assess genotoxicity batteries — repeat-dose study data, cross-artifact margin calculation, ICH S2(R1) weight-of- evidence genotoxicity assessment, and safety…

protein-structure-confidence

Retrieve protein structures and quantify how far their geometry can be trusted — global and per-residue model confidence, disorder extent, domain boundaries, and coverage of the canonical sequence. Use when any structural claim depends on model reliability:…

regulatory-variant-effect

Score a genomic variant's predicted effect on regulatory tracks — gene expression (RNA-seq, CAGE, PROCAP), chromatin accessibility (ATAC, DNase), histone marks, transcription-factor binding, splicing, and 3D contact maps — predict baseline regulatory activity…

review-rubric

Scoring axes with calibrated anchors, review types, and review output format for hypothesis evaluation.

run-protocol

Supervisor run protocol — state machine, worker lifecycle, budget accounting, convergence detection, and error handling for orchestrating multi-epoch hypothesis exploration runs.

safety-screen

Dual-use biosafety rubric, research integrity screen, quarantine procedure, and safety screening workflow for hypothesis review.