Access NCBI GEO for gene expression/genomics data. Search/download microarray and RNA-seq datasets (GSE, GSM, GPL), retrieve SOFT/Matrix files, for transcriptomics and expression analysis.

Access ClinPGx pharmacogenomics data (successor to PharmGKB). Query gene-drug interactions, CPIC guidelines, allele functions, for precision medicine and genotype-guided dosing decisions.

Query ClinicalTrials.gov via API v2. Search trials by condition, drug, location, status, or phase. Retrieve trial details by NCT ID, export data, for clinical research and patient matching.

Medicinal chemistry filters. Apply drug-likeness rules (Lipinski, Veber), PAINS filters, structural alerts, complexity metrics, for compound prioritization and library filtering.

Differential gene expression analysis (Python DESeq2). Identify DE genes from bulk RNA-seq counts, Wald tests, FDR correction, volcano/MA plots, for RNA-seq analysis.

Parse FCS (Flow Cytometry Standard) files v2.0-3.1. Extract events as NumPy arrays, read metadata/channels, convert to CSV/DataFrame, for flow cytometry data preprocessing.

Constraint-based metabolic modeling (COBRA). FBA, FVA, gene knockouts, flux sampling, SBML models, for systems biology and metabolic engineering analysis.

Plan a huge chunk of work (more than one agent session can hold) as a shared map of decision tickets on your issue tracker, and resolve them one at a time until the way to the destination is clear.

Scan a codebase for deepening opportunities, present them as a visual HTML report, then grill through whichever one you pick.

Guidelines for upgrading Expo SDK versions and fixing dependency issues

Track ML experiments with automatic logging, visualize training in real-time, optimize hyperparameters with sweeps, and manage model registry with W&B - collaborative MLOps platform

Validate an existing Sim webhook trigger against provider API docs and repository conventions

Create, triage, label, assign GitHub issues via gh or REST.

Manim CE animations: 3Blue1Brown math/algo videos.

TRL: SFT, DPO, GRPO, RLOO reward modeling for LLM RLHF.

PostgreSQL database patterns for query optimization, schema design, indexing, and security. Based on Supabase best practices.

Use when writing, restructuring, or reviewing any prose documentation — a tutorial, how-to guide, reference page, or explanation/conceptual doc — for a public docs site (e.g. Mintlify MDX, docs/, README material), a getting-started guide, an API/CLI reference page, or a "why we built it this way" conceptual page. Applies the Diátaxis framework (see https://diataxis.fr/) — every document belongs to exactly one of the four quadrants (tutorial / how-to guide / reference / explanation), and mixing quadrants inside one document is the single most common documentation failure. Covers the four-quadrant compass for picking the right form, per-quadrant structure templates, an anti-pattern list for quadrant drift, and generic voice/craft rules — repo-specific voice and target output format (e.g. Mintlify MDX) are resolved from the repo's docs-manifest (falling back to project-context), never hardcoded here.

Use gh (GitHub CLI) for all GitHub operations — creating PRs, checking status, commenting, and capturing URLs. Prefer gh over GitHub MCP tools to minimize token usage.

Import, merge, or combine repositories into an Nx workspace using nx import. USE WHEN the user asks to adopt Nx across repos, move projects into a monorepo, or bring code/history from another repository.

Import, merge, or combine repositories into an Nx workspace using nx import. USE WHEN the user asks to adopt Nx across repos, move projects into a monorepo, or bring code/history from another repository.