strmt7/ai_skills_collection_benchmarked - Page 12

docker-patterns

Docker and Docker Compose patterns for local development, container security, networking, volume strategies, and multi-service orchestration.

docs-knowledge-maintainer

Keep repository documentation accurate when behavior, topology, env contracts, or troubleshooting procedures change.

documentation-lookup

Use current official documentation and release notes for OMERO, Django, Docker, Python, PostgreSQL, monitoring tools, and AI harnesses instead of memory.

documentation-lookup

Use up-to-date library and framework docs via Context7 MCP instead of training data. Activates for setup questions, API references, code examples, or when the user names a framework (e.g. React, Next.js, Prisma).

env-contract-reviewer

Review environment-driven configuration changes so they stay template-backed, typed, documented, and free of hard-coded runtime values.

frontend-preview

Preview HTML/CSS/JS changes in Django plugin templates with the pinned host-side Vite/Vitest toolchain, then validate live in OMERO.web.

omero-runtime-verifier

Safe runtime-debugging workflow for OMERO Docker Extended, including Loki-first log triage, container venv discovery, and correct OMERO service-user usage.

plugin-regression-triager

Map changed files to the correct split pytest suites and fast regression checks for this repository.

postgres-patterns

PostgreSQL guidance for the main OMERO database, plugin database, migrations, indexes, and maintenance contracts.

postgres-patterns

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

python-patterns

Python patterns for this repo's helpers, plugins, services, startup tooling, and environment-driven contracts.

python-patterns

Pythonic idioms, PEP 8 standards, type hints, and best practices for building robust, efficient, and maintainable Python applications.

python-testing

Python testing guidance for split pytest lanes, contract tests, shell checks, and syntax-only fallbacks in this repo.

python-testing

Python testing strategies using pytest, TDD methodology, fixtures, mocking, parametrization, and coverage requirements.

search-first

Research-before-coding workflow for OMERO Docker Extended. Check the repo, tests, official upstream docs, and release notes before writing new code.

search-first

Research-before-coding workflow. Search for existing tools, libraries, and patterns before writing custom code. Invokes the researcher agent.

security-finding-triager

Triage code-scanning findings using the repo's live runbook, closed-history ledger, and canonical prevention playbook before editing security-sensitive code.

security-review

Security review for uploads, filesystem paths, SQL, responses, subprocesses, Docker, workflows, and secrets in this repo.

security-review

Use this skill when adding authentication, handling user input, working with secrets, creating API endpoints, or implementing payment/sensitive features. Provides comprehensive security checklist and patterns.

site-extract

Extract the smallest useful amount of text or structured data from a known public page before falling back to full browser automation.

source-audit

Verify public-web findings with source quality, dates, and second-source checks before turning them into advice or claims.

tdd-workflow

TDD guidance for repo changes using narrow regression tests, split pytest lanes, and docs updates as part of done-ness.

tdd-workflow

Use this skill when writing new features, fixing bugs, or refactoring code. Enforces test-driven development with 80%+ coverage including unit, integration, and E2E tests.

verification-loop

Repository-specific verification flow for OMERO Docker Extended. Runs docs validation, Ruff, split pytest suites, and targeted fallback checks without overstating coverage.

verification-loop

A comprehensive verification system for Claude Code sessions.

web-discovery

Plan and run current public-web discovery for docs, releases, issues, and community evidence without guessing or over-browsing.

adaptyv

How to use the Adaptyv Bio Foundry API and Python SDK for protein experiment design, submission, and results retrieval. Use this skill whenever the user mentions Adaptyv, Foundry API, protein binding assays, protein screening experiments, BLI/SPR assays,…

aeon

This skill should be used for time series machine learning tasks including classification, regression, clustering, forecasting, anomaly detection, segmentation, and similarity search. Use when working with temporal data, sequential patterns, or time-indexed…

anndata

Data structure for annotated matrices in single-cell analysis. Use when working with .h5ad files or integrating with the scverse ecosystem. This is the data format skill—for analysis workflows use scanpy; for probabilistic models use scvi-tools; for…

arboreto

Infer gene regulatory networks (GRNs) from gene expression data using scalable algorithms (GRNBoost2, GENIE3). Use when analyzing transcriptomics data (bulk RNA-seq, single-cell RNA-seq) to identify transcription factor-target gene relationships and…

astropy

Comprehensive Python library for astronomy and astrophysics. This skill should be used when working with astronomical data including celestial coordinates, physical units, FITS files, cosmological calculations, time systems, tables, world coordinate systems…

benchling-integration

Benchling R&D platform integration. Access registry (DNA, proteins), inventory, ELN entries, workflows via API, build Benchling Apps, query Data Warehouse, for lab data management automation.

bgpt-paper-search

Search scientific papers and retrieve structured experimental data extracted from full-text studies via the BGPT MCP server. Returns 25+ fields per paper including methods, results, sample sizes, quality scores, and conclusions. Use for literature reviews,…

biopython

Comprehensive molecular biology toolkit. Use for sequence manipulation, file parsing (FASTA/GenBank/PDB), phylogenetics, and programmatic NCBI/PubMed access (Bio.Entrez). Best for batch processing, custom bioinformatics pipelines, BLAST automation. For quick…

bioservices

Unified Python interface to 40+ bioinformatics services. Use when querying multiple databases (UniProt, KEGG, ChEMBL, Reactome) in a single workflow with consistent API. Best for cross-database analysis, ID mapping across services. For quick single-database…

cellxgene-census

Query the CELLxGENE Census (61M+ cells) programmatically. Use when you need expression data across tissues, diseases, or cell types from the largest curated single-cell atlas. Best for population-scale queries, reference atlas comparisons. For analyzing your…

cirq

Google quantum computing framework. Use when targeting Google Quantum AI hardware, designing noise-aware circuits, or running quantum characterization experiments. Best for Google hardware, noise modeling, and low-level circuit design. For IBM hardware use…

citation-management

Comprehensive citation management for academic research. Search Google Scholar and PubMed for papers, extract accurate metadata, validate citations, and generate properly formatted BibTeX entries. This skill should be used when you need to find papers, verify…

clinical-decision-support

Generate professional clinical decision support (CDS) documents for pharmaceutical and clinical research settings, including patient cohort analyses (biomarker-stratified with outcomes) and treatment recommendation reports (evidence-based guidelines with…

clinical-reports

Write comprehensive clinical reports including case reports (CARE guidelines), diagnostic reports (radiology/pathology/lab), clinical trial reports (ICH-E3, SAE, CSR), and patient documentation (SOAP, H&P, discharge summaries). Full support with templates,…