Results for “databases”

Read data from Lyrion's SQLite databases — library stats, stored lyrics, album covers, recent plays. Use this whenever a task queries `library.db` or `persist.db`, adds or changes a statistic, or touches `services/database.py`. Covers the read-only connection model (RO open + `ATTACH persist.db`), the key tables, the `play_counts` view over the Alternative Play Count plugin, the single-flight stats cache, and why the app must never write to these DBs. Reach for it before writing any SQL against the Lyrion databases.

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Query protein-protein and gene interaction databases (STRING, BioGRID, IntAct, SIGNOR, Reactome, HuRI, HuMAP, OmniPath, ConsensusPathDB, DIP). Use when building PPI networks, choosing between physical vs functional vs genetic interactions, signed/directed vs undirected, high-throughput vs curated, picking confidence thresholds, aggregating across resources, or navigating license constraints. Encodes the database decision matrix, STRING v12 channel semantics, OmniPath as meta-database, SIGNOR for signed signaling, and per-resource rate limits.

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Resolves rsIDs, navigates RsMergeArch/SNPHistory merge chains, and converts between rsID, SPDI, HGVS, and VCF representations using the dbSNP Build 156 JSON architecture. Use when normalizing variant identifiers, joining variant databases by cluster ID, or tracking deprecated rsIDs through historical merges.

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Prioritizes rare-disease variants from trio/quad WES/WGS with de novo (DeNovoGear, Triodenovo), compound-heterozygous phasing (WhatsHap), mosaic VAF tiering, phenotype-driven ranking (Exomiser, Phen2Gene, AMELIE), ClinGen gene-disease validity gating, and ACMG SF v3.2 secondary findings reporting. Use when running diagnostic exome / genome pipelines, identifying candidate Mendelian disease genes, screening for incidental findings, or auditing VUS reclassification cycles. The ACMG/AMP classification framework (PVS1 decision tree, Pejaver PP3/BP4 calibration, Tavtigian point system) is in clinical-databases/acmg-classification.

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Queries myvariant.info BioThings aggregator for ClinVar, gnomAD, dbSNP, dbNSFP, COSMIC, CADD, and CIViC annotations in batched, version-tracked requests. Use when annotating variant lists from multiple databases simultaneously without managing per-source APIs, and when reproducibility-grade analyses require recording source data versions via _meta.

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Use Neon serverless Postgres with branching, connection pooling, and instant scalability for modern applications with Prisma or Drizzle ORM integration. Use when setting up serverless Postgres databases, implementing database branching for preview environments, configuring connection pooling, optimizing for serverless cold starts, using Prisma with Neon, implementing database migrations, scaling databases automatically, or building applications on Vercel/Netlify with Postgres.

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Query protein-protein and gene interaction databases (STRING, BioGRID, IntAct, SIGNOR, Reactome, HuRI, HuMAP, OmniPath, ConsensusPathDB, DIP). Use when building PPI networks, choosing between physical vs functional vs genetic interactions, signed/directed vs undirected, high-throughput vs curated, picking confidence thresholds, aggregating across resources, or navigating license constraints. Encodes the database decision matrix, STRING v12 channel semantics, OmniPath as meta-database, SIGNOR for signed signaling, and per-resource rate limits.

The English summary is being prepared. Showing the original description.

Queries myvariant.info BioThings aggregator for ClinVar, gnomAD, dbSNP, dbNSFP, COSMIC, CADD, and CIViC annotations in batched, version-tracked requests. Use when annotating variant lists from multiple databases simultaneously without managing per-source APIs, and when reproducibility-grade analyses require recording source data versions via _meta.

The English summary is being prepared. Showing the original description.

Prioritizes rare-disease variants from trio/quad WES/WGS with de novo (DeNovoGear, Triodenovo), compound-heterozygous phasing (WhatsHap), mosaic VAF tiering, phenotype-driven ranking (Exomiser, Phen2Gene, AMELIE), ClinGen gene-disease validity gating, and ACMG SF v3.2 secondary findings reporting. Use when running diagnostic exome / genome pipelines, identifying candidate Mendelian disease genes, screening for incidental findings, or auditing VUS reclassification cycles. The ACMG/AMP classification framework (PVS1 decision tree, Pejaver PP3/BP4 calibration, Tavtigian point system) is in clinical-databases/acmg-classification.

The English summary is being prepared. Showing the original description.

Resolves rsIDs, navigates RsMergeArch/SNPHistory merge chains, and converts between rsID, SPDI, HGVS, and VCF representations using the dbSNP Build 156 JSON architecture. Use when normalizing variant identifiers, joining variant databases by cluster ID, or tracking deprecated rsIDs through historical merges.

The English summary is being prepared. Showing the original description.

Expert database administrator specializing in modern cloud databases, automation, and reliability engineering. Masters AWS/Azure/GCP database services, Infrastructure as Code, high availability, disaster recovery, performance optimization, and compliance. Handles multi-cloud strategies, container databases, and cost optimization. Use PROACTIVELY for database architecture, operations, or reliability engineering.

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Review Perl code that handles user input, files, external commands, databases, and web output. Use concrete examples and a security checklist to identify unsafe patterns and apply input validation, parameterized queries, and appropriate output encoding.

• Reviewing user input validation in Perl
• Checking file access and external command execution
• Preventing SQL injection in DBI queries

Use the gget command line or Python package to look up genes, retrieve sequences, compare similar sequences, and explore biological database results. Save outputs and query details to support reproducible first-pass bioinformatics research.

• Finding gene identifiers and transcript information
• Retrieving nucleotide or amino-acid sequences
• Running quick BLAST or BLAT sequence searches

Design or refactor services so business rules stay separate from databases, APIs, and frameworks. Uses Ports and Adapters—interfaces and their implementations—to define clear boundaries, test workflows, and migrate existing code one feature at a time.

• Separating business rules from database and API calls
• Sharing application workflows across HTTP, CLI, and workers
• Replacing infrastructure while preserving business rules

Set up reproducible development environments with Flox on macOS and Linux. Define tools, package versions, setup steps, and local services in one configuration, then share it with teammates or add project-specific tools for AI agents.

• Sharing a consistent development setup across a team
• Combining language tools and system dependencies
• Running local PostgreSQL and Redis services

Save, organize, synchronize, and retrieve documents, conversations, and project information across local files, memory tools, knowledge repositories, and databases. Check for duplicates before storing information and choose a suitable home for each type of knowledge.

• Saving documents and conversations to a knowledge base
• Consolidating duplicate notes
• Synchronizing knowledge across storage systems

Record software design decisions as numbered Markdown files, with context, rejected alternatives, benefits, drawbacks, and risks. Maintain an index and consult existing ADRs—architecture decision records—to explain why a framework, database, or design approach was chosen.

• Record reasons for framework or database choices
• Document design alternatives and trade-offs
• Find explanations for past technical decisions

Design a persistent multi-agent workflow in Claude Code, with specialist roles, reusable commands, file-based memory, and scheduled tasks. Keep project context and decisions across sessions using JSON and Markdown files without an external database.

• Coordinate specialist agents for development and writing
• Preserve project context across sessions
• Schedule recurring morning briefings

Support drug discovery research by searching public databases for compound activity, molecular properties, drug interactions, and gene–disease associations. Assess drug-likeness, meaning how molecular properties fit established rules for potential oral medicines.

• Finding active compounds for a biological target
• Assessing molecular properties against oral drug rules
• Reviewing drug interactions and reported adverse events

Set up services such as databases and SMS for a project through Stripe Projects. Sync generated credentials into `.env`, connect supported provider accounts, and manage credential rotation, plan changes, and service removal.

• Set up a Postgres database for a project
• Add an SMS service to an application
• Sync service credentials and rotate keys

Build Python MCP servers that let AI agents use APIs, databases, and file workflows. MCP is a connection standard for agent tools. The skill covers starter templates, local testing, client registration, and deployment as HTTP endpoints.

• Making an existing API available to AI agents
• Exposing read-only SQLite queries
• Providing text-file inspection and search tools

Classify images using written labels without additional training data, or find images that match a text query. This skill provides CLIP workflows for image-text similarity, batch processing, and storing searchable image representations in vector databases.

• Classify photos using written category labels
• Find images by describing their content
• Compare images with candidate descriptions

Guides debugging through reproduction, comparison with working examples, hypothesis testing, and a focused fix. It starts with a repeatable check for the exact symptom and uses regression tests to verify the result.

• Investigating failing tests or builds
• Tracing faults across APIs, services, and databases
• Making intermittent bugs easier to reproduce

Find and fix slow page loads, API responses, and database queries using measurements. Compare results before and after each change, discard changes without clear gains, and add checks or monitoring to catch future slowdowns.

• Investigating slow page loads and sluggish interactions
• Reducing API delays and repeated database queries
• Checking whether a recent change caused a slowdown