Microck/ordinary-claude-skills Skills

Track complex, multi-session work with dependency graphs using bd (beads) issue tracker. Use when work spans multiple sessions, has complex dependencies, or requires persistent context across compaction cycles. For simple single-session linear tasks, TodoWrite remains appropriate.

This skill should be used when working with annotated data matrices in Python, particularly for single-cell genomics analysis, managing experimental measurements with metadata, or handling large-scale biological datasets. Use when tasks involve AnnData objects, h5ad files, single-cell RNA-seq data, or integration with scanpy/scverse tools.

Optimize AgentDB performance with quantization (4-32x memory reduction), HNSW indexing (150x faster search), caching, and batch operations. Use when optimizing memory usage, improving search speed, or scaling to millions of vectors.

Search arXiv preprint repository for papers in physics, mathematics, computer science, quantitative biology, and related fields

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 regulatory interactions. Supports distributed computation for large-scale datasets.

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.

Define database models with clear naming, appropriate data types, constraints, relationships, and validation at multiple layers. Use this skill when creating or modifying database model files, ORM classes, schema definitions, or data model relationships. Apply when working with model files (e.g., models.py, models/, ActiveRecord classes, Prisma schema, Sequelize models), defining table structures, setting up foreign keys and relationships, configuring cascade behaviors, implementing model validations, adding timestamps, or working with database constraints (NOT NULL, UNIQUE, foreign keys). Use for any task involving data integrity enforcement, relationship definitions, or model-level data validation.

Master Bash Automated Testing System (Bats) for comprehensive shell script testing. Use when writing tests for shell scripts, CI/CD pipelines, or requiring test-driven development of shell utilities.

Master authentication and authorization patterns including JWT, OAuth2, session management, and RBAC to build secure, scalable access control systems. Use when implementing auth systems, securing APIs, or debugging security issues.

Master defensive Bash programming techniques for production-grade scripts. Use when writing robust shell scripts, CI/CD pipelines, or system utilities requiring fault tolerance and safety.

Implement authentication and authorization with Better Auth - a framework-agnostic TypeScript authentication framework. Features include email/password authentication with verification, OAuth providers (Google, GitHub, Discord, etc.), two-factor authentication (TOTP, SMS), passkeys/WebAuthn support, session management, role-based access control (RBAC), rate limiting, and database adapters. Use when adding authentication to applications, implementing OAuth flows, setting up 2FA/MFA, managing user sessions, configuring authorization rules, or building secure authentication systems for web applications.

Efficient database search tool for bioRxiv preprint server. Use this skill when searching for life sciences preprints by keywords, authors, date ranges, or categories, retrieving paper metadata, downloading PDFs, or conducting literature reviews.

AWS Cloud Development Kit (CDK) expert for building cloud infrastructure with TypeScript/Python. Use when creating CDK stacks, defining CDK constructs, implementing infrastructure as code, or when the user mentions CDK, CloudFormation, IaC, cdk synth, cdk deploy, or wants to define AWS infrastructure programmatically. Covers CDK app structure, construct patterns, stack composition, and deployment workflows.

Query CZ CELLxGENE Census (61M+ cells). Filter by cell type/tissue/disease, retrieve expression data, integrate with scanpy/PyTorch, for population-scale single-cell analysis.

Apply strict operational protocols for AI task execution including sequential processing, minimal responses, no destructive operations without confirmation

Collection of AWS development skills covering CDK infrastructure as code, cost optimization, and serverless/event-driven architectures with integrated MCP servers.

Primary Python tool for 40+ bioinformatics services. Preferred for multi-database workflows: UniProt, KEGG, ChEMBL, PubChem, Reactome, QuickGO. Unified API for queries, ID mapping, pathway analysis. For direct REST control, use individual database skills (uniprot-database, kegg-database).

Access RCSB PDB for 3D protein/nucleic acid structures. Search by text/sequence/structure, download coordinates (PDB/mmCIF), retrieve metadata, for structural biology and drug discovery.

Diagnose and troubleshoot bitcoin-auth token generation and verification issues. This skill should be used when users encounter authentication failures, signature verification errors, or integration problems with the bitcoin-auth library.

Use when tests have race conditions, timing dependencies, or inconsistent pass/fail behavior - replaces arbitrary timeouts with condition polling to wait for actual state changes, eliminating flaky tests from timing guesses

Query NCBI ClinVar for variant clinical significance. Search by gene/position, interpret pathogenicity classifications, access via E-utilities API or FTP, annotate VCFs, for genomic medicine.

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.

Optimize cloud costs through resource rightsizing, tagging strategies, reserved instances, and spending analysis. Use when reducing cloud expenses, analyzing infrastructure costs, or implementing cost governance policies.

Add unsigned integer (uint) type support to PyTorch operators by updating AT_DISPATCH macros. Use when adding support for uint16, uint32, uint64 types to operators, kernels, or when user mentions enabling unsigned types, barebones unsigned types, or uint support.