Results for “mongodb-atlas”

MongoDB - NoSQL document database with flexible schema design, aggregation pipelines, indexing strategies, and Spring Data integration

Streams change data capture from MongoDB into Redpanda or Kafka using Redpanda Connect's mongodb_cdc input, covering Change Streams, snapshots, document modes, and resume-token checkpointing.

Installs the official MongoDB Node.js driver and verifies package integrity for building MongoDB-backed applications.

MySQL relational database. Covers queries, indexes, and optimization. Use when working with MySQL databases. USE WHEN: user mentions "mysql", "mariadb", asks about "AUTO_INCREMENT", "ON DUPLICATE KEY UPDATE", "GROUP_CONCAT", "mysql specific syntax" DO NOT USE FOR: PostgreSQL - use `postgresql` instead, MongoDB - use `mongodb` instead, Oracle - use `oracle` instead, SQL Server - use `sqlserver` instead

Perform create, read, update, and delete operations in MongoDB, covering query and update operators, atomic operations, and bulk writes.

Manages AlloyDB for PostgreSQL clusters, instances, and backups using gcloud CLI commands.

Computes mass-spectral similarity and identifies compounds for metabolomics with matchms — comparing mass spectra, scoring similarity (cosine, modified cosine), and searching spectral libraries to annotate unknowns. Use when matching MS/MS spectra, identifying metabolites, or library searching; for full LC-MS/MS proteomics pipelines use pyopenms. Part of the AlterLab Academic Skills suite.

Access the Human Metabolome Database (HMDB, 220K+ metabolites), searching by name, HMDB ID, or structure to retrieve chemical properties, biomarker data, NMR/MS reference spectra, and associated pathways. Use when identifying a human metabolite, looking up its biomarker or disease associations, matching NMR/MS spectra, or running metabolomics annotation. Part of the AlterLab Academic Skills suite.

Runs NCBI BLAST+ 2.17.0 sequence searches from the command line: makeblastdb (with -parse_seqids), blastn/blastp/blastx/tblastn with tabular -outfmt 6/7 for parsing, correct -task choice (megablast vs blastn vs blastn-short), -taxids/-negative_taxids taxonomic scoping, and -mt_mode multithreading; plus a DIAMOND blastp --ultra-sensitive path for large protein searches. Warns that -max_target_seqs is a heuristic keep-count, not a top-N best-hits filter. Use when the user wants command-line BLAST, makeblastdb, a local BLAST database, blastn/blastp/blastx/tblastn searches, or DIAMOND protein search. For the Bio.Blast web NCBIWWW API prefer alterlab-biopython; for quick one-liner database lookups prefer alterlab-gget. Part of the AlterLab Academic Skills suite.

Reads from, writes to, and manages relational databases using MATLAB Database Toolbox. Use when connecting to databases, reading data with sqlread or fetch, filtering with rowfilter, writing with sqlwrite, updating with sqlupdate, executing SQL statements, managing transactions with commit and rollback, mapping MATLAB classes to tables with ORM (Mappable, ormread, ormwrite, ormupdate), or performing any database operation from MATLAB. Triggers on: database, SQL, sqlread, sqlwrite, sqlupdate, fetch, execute, rowfilter, RowFilter, ORM, Mappable, ormread, ormwrite, ormupdate, orm2sql, transaction, commit, rollback, Database Toolbox, PostgreSQL, MySQL, SQLite, SQL Server, Oracle, database connection, database table, query database, insert data, update rows, delete rows, stored procedure, prepared statement, odbc, databaseConnectionOptions, datasource, data source, DSN, connection string, multithreaded, parallel.

Detect and exploit NoSQL injection vulnerabilities in MongoDB, CouchDB, and other NoSQL databases to demonstrate authentication bypass, data extraction, and unauthorized access risks.

NoSQL injection playbook. Use when MongoDB-style operators, JSON query objects, flexible search filters, or backend query DSLs may allow data or logic abuse.

Reference for querying the Atlas knowledge graph through its MCP tools — the SECONDARY enrichment/comparison layer that adds best-practice context to systems you have ALREADY scanned from your real sources (`az`, repos, dirs). Use when you need to look up nodes, edges, kinds, clusters, stats, or wiki pages in Atlas to compare against your real inventory. (atlas graph, query atlas, atlas mcp, search the graph, graph neighbors, atlas record, atlas kinds, enrichment layer)

Add official Railway database services (Postgres, Redis, MySQL, MongoDB). Use when user wants to add a database, says "add postgres", "add redis", "add database", "connect to database", or "wire up the database". For other templates (Ghost, Strapi, n8n), use the railway-templates skill.

Manage biological datasets and models with LaminDB, an open-source lineage-native lakehouse. Covers setup, artifact registration, query/search, lineage tracking, validation, ontology-backed annotation, collections, branches, storage, and workflow integrations.

Documents MariaDB-specific ALTER TABLE syntax and behavior, including online DDL algorithms, lock modes, lock timeouts, idempotent subclauses, system versioning, and partition operations, for writing and reviewing schema migrations.

Access the COSMIC catalogue of somatic mutations in cancer to query somatic mutations, the Cancer Gene Census, mutational signatures, and gene fusions (authentication required). Use when curating known cancer driver genes, looking up recurrent somatic mutations in a gene, or interpreting mutational signatures for cancer research and precision oncology. Not for germline pathogenicity calls (use alterlab-clinvar) or interactive cohort visualization like OncoPrints and survival from study data (use alterlab-cbioportal). Part of the AlterLab Academic Skills suite.

Esta habilidade deve ser usada ao trabalhar com LaminDB, um framework de dados de código aberto para biologia que torna dados consultáveis, rastreáveis, reproduzíveis e FAIR. Use ao gerenciar datasets biológicos (scRNA-seq, espacial, citometria de fluxo, etc.), rastrear workflows computacionais, curar e validar dados com ontologias biológicas, construir data lakehouses, ou garantir linhagem de dados e reprodutibilidade em pesquisa biológica. Aborda gerenciamento de dados, anotação, ontologias (genes, tipos de célula, doenças, tecidos), validação de esquema, integrações com orquestradores de workflow (Nextflow, Snakemake) e plataformas MLOps (W&B, MLflow), e estratégias de deployment.

Use when running analytical SQL over Parquet/CSV/JSON without a warehouse, replacing pandas for data wrangling, joining S3 data in-place, building local data marts, or embedding OLAP into an app. Triggers: read_parquet/read_csv setup, partitioned dataset queries, hive partitioning, glob patterns for S3, COPY TO export, attach Postgres/MySQL, UDFs in Python/R, MotherDuck cloud sync, columnar performance vs row stores. NOT for OLTP workloads (concurrent writes), distributed analytics at petabyte scale (use Spark/Trino), or vector search (use pgvector/Lance).

Add official Railway database services (Postgres, Redis, MySQL, MongoDB). Use when user wants to add a database, says "add postgres", "add redis", "add database", "connect to database", or "wire up the database". For other templates (Ghost, Strapi, n8n), use the railway-templates skill.

Query ChEMBL via the chembl_webresource_client Python client for curated bioactive molecules and drug-like compound libraries at scale — search compounds by structure or physicochemical properties, retrieve bioactivity measurements (IC50, Ki, EC50), and find inhibitors of a target. Use when screening chemical libraries, mining curated bioactivity for a protein, running SAR studies, or sourcing medicinal-chemistry data; for measured protein-ligand binding affinities (Ki/Kd/IC50) prefer alterlab-bindingdb instead. Part of the AlterLab Academic Skills suite.

Creates an integration testing plan for .NET data access artifacts during Oracle-to-PostgreSQL database migrations, analyzing a project to identify repositories, DAOs, and service layers that interact with the database, then producing a structured testing plan.

Guides AI coding assistants to the official NemoClaw documentation via MCP server or Markdown files for installation, configuration, operation, and troubleshooting.

Scaffolds a Spring Boot Kotlin project with Gradle, WebFlux, R2DBC, Redis, MongoDB, and Testcontainers, including Docker Compose setup.

Manage, annotate, and trace biological data with LaminDB, an open-source FAIR data framework that makes datasets queryable, versioned, and reproducible. Use when registering or querying biological datasets (scRNA-seq, spatial, flow cytometry), validating and curating data against ontologies (genes, cell types, diseases, tissues), tracking data lineage and computational workflows, building data lakehouses, or wiring integrations with Nextflow, Snakemake, W&B, or MLflow. Part of the AlterLab Academic Skills suite.

Manages Google AlloyDB for PostgreSQL clusters and instances via gcloud CLI, covering discovery, instance analysis, query insights, backup configuration, and maintenance windows.

Import Gerber, ODB++, Allegro .brd, .mcm files for PCB boards and IC packages. Inspect nets, layers, shapes, and stackups. TRIGGER: user asks to import, read, or open a PCB layout file. Gerber files use gerberRead or PCBReader; ODB++, Allegro .brd, .mcm, and native formats use pcbFileRead. Also when inspecting nets, layers, components, or stackups from an imported board. Invoke BEFORE writing import code — the query API (cadnet, cadnetList, componentList) is specialized. SKIP: EM analysis or S-parameter extraction (use matlab-analyze-em), PDN/IR-drop analysis (use matlab-analyze-pcb-pdn), building custom geometry (use matlab-assemble-pcb-layout), material/stackup definition only (use matlab-manage-pcb-material).

Mass spectrometry analysis. Process mzML/MGF/MSP, spectral similarity (cosine, modified cosine), metadata harmonization, compound ID, for metabolomics and MS data processing.

Project Lombok for reducing Java boilerplate. Covers annotations for getters, setters, constructors, builders, logging, and more. Based on production patterns from castellino and gestionale-presenze projects. USE WHEN: user mentions "lombok", "@Data", "@Builder", "@Slf4j", asks about "boilerplate reduction", "getters/setters", "@RequiredArgsConstructor", "@Value" DO NOT USE FOR: Java language features - use `java` skill instead DO NOT USE FOR: MapStruct integration - use `mapstruct` skill DO NOT USE FOR: Spring annotations - use `backend-spring-boot` skill

Comprehensive guide to bohb. Master the concepts, implementation, best practices, and real-world applications of bohb in professional environments.

Diagnose monogenic and syndromic obesity in children and adolescents using a structured step-by-step algorithm. Use this skill whenever a clinician suspects a genetic cause of obesity, asks about leptin deficiency, MC4R mutation, POMC deficiency, PCSK1 deficiency, leptin receptor deficiency, Bardet-Biedl syndrome, Prader-Willi syndrome, Alström syndrome, or any case of early-onset severe obesity with hyperphagia. Also trigger for questions about targeted pharmacotherapy including setmelanotide or metreleptin, or when to order a genomic obesity panel. Cross-references the NHS Genomic Test Finder skill to surface the relevant R-code once a diagnosis is reached.

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

Redis in-memory data store. Covers data structures, caching, and pub/sub. Use for caching and real-time features. USE WHEN: user mentions "redis", "caching", "session storage", "rate limiting", "pub/sub", "sorted sets", "in-memory database", "cache invalidation" DO NOT USE FOR: relational data - use `postgresql` or `mysql` instead, document storage - use `mongodb` instead, full-text search - use `elasticsearch` instead

Documents MariaDB-specific UPDATE syntax and behavior, including single-table vs multi-table forms, assignment evaluation order, RETURNING with OLD_VALUE(), temporal tables, and common pitfalls. Use when writing, generating, or reviewing UPDATE statements targeting MariaDB.

Expert guidance for architecting, developing, and operating SurrealDB 3, covering SurrealQL, multi-model data modeling, vector search, security, deployment, performance tuning, SDK integration, and ecosystem tools.