Results for “g-suite”

gRPC service development. Protocol Buffers (protobuf), service definitions, streaming (unary, server, client, bidirectional), interceptors, and code generation for Node.js, Go, Java, and Python. USE WHEN: user mentions "gRPC", "protobuf", "Protocol Buffers", ".proto", "grpc-js", "tonic", "grpc-java", "service mesh RPC" DO NOT USE FOR: REST APIs - use `rest-api`; GraphQL - use `graphql`; WebSocket - use real-time skills

Query the NHGRI-EBI GWAS Catalog REST API for SNP-trait associations, retrieving variants by rs ID, disease/trait, or gene along with p-values and summary statistics. Use when investigating genome-wide association study hits, mapping a SNP or rsID to traits, building polygenic risk scores, or doing genetic epidemiology lookups. Part of the AlterLab Academic Skills suite.

Go programming language. Covers goroutines, channels, interfaces, error handling, and modules. Use for building concurrent, high-performance backend services. USE WHEN: user mentions "go", "golang", "goroutines", "channels", asks about "concurrency", "select statement", "interfaces", "error handling", "go modules" DO NOT USE FOR: Gin/Fiber/Echo frameworks - use framework-specific skills DO NOT USE FOR: GORM - use ORM-specific skill DO NOT USE FOR: gRPC - use API design skills

Access the European Nucleotide Archive (ENA) via its API and FTP to retrieve DNA/RNA sequences, raw sequencing reads (FASTQ), and genome assemblies by accession, with support for multiple formats. Use when downloading reads or sequences for a study, run, or sample accession, or when sourcing nucleotide data for genomics and bioinformatics pipelines. Part of the AlterLab Academic Skills suite.

CMake build system for C/C++ projects. Modern CMake (3.20+) with targets, properties, presets (CMakePresets.json), FetchContent, find_package, generator expressions, install rules, vcpkg/Conan integration. USE WHEN: user mentions "CMake", "CMakeLists.txt", "CMakePresets", "find_package", "FetchContent", "target_link_libraries", "vcpkg", "Conan", "C++ build" DO NOT USE FOR: Make, autotools, Bazel, Meson, Visual Studio .vcxproj direct editing

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

Query the GTEx (Genotype-Tissue Expression) portal v2 REST API for tissue-specific gene expression (median TPM across 54 human tissues), expression QTLs (eQTLs), and splicing QTLs (sQTLs). Use when checking which tissues express a gene, finding which gene a non-coding/GWAS variant regulates via eQTLs, or interpreting variant regulatory effects across tissues. NOT for curated trait-variant associations (use alterlab-gwas), population allele frequencies or variant constraint (use alterlab-gnomad), or gene/transcript structure and ID mapping (use alterlab-ensembl). Part of the AlterLab Academic Skills suite.

Query NCBI ClinVar via the E-utilities API or FTP for the clinical significance (pathogenicity) of human germline genetic variants, searching by gene, variant, condition, or genomic position and interpreting ACMG/AMP classifications and review-status star ratings. Use when assessing whether a variant is pathogenic, likely pathogenic, VUS, likely benign, or benign, resolving conflicting interpretations, or annotating a VCF with ClinVar clinical significance. For population allele frequencies by ancestry use alterlab-gnomad; for somatic cancer mutation frequencies use alterlab-cosmic. Part of the AlterLab Academic Skills suite.

Watches a Gmail mailbox for new emails and streams them as NDJSON, with options for Pub/Sub setup, filtering by labels, and output to files.

Subscribes to Google Workspace events and streams them as NDJSON, with options for Pub/Sub setup, polling, and cleanup.

Interact with GitHub via the `gh` CLI. Use for issues (read, comment, file), pull requests (view, comment, check CI status), workflow runs, and `gh api` for queries the subcommands don't cover. Authentication is via the bot's GITHUB_TOKEN (already wired through `gh auth setup-git` at container start).

Query the EMBL-EBI InterPro REST API for protein family, domain, and functional-site annotations integrated from member databases (Pfam, PANTHER, PRINTS, SMART, SUPERFAMILY, CDD, ProSite, NCBIfam, and others). Use when predicting protein function, analyzing or comparing domain architecture, classifying a protein by family or homologous superfamily, resolving a Pfam/InterPro accession, or mapping a protein's signatures to GO terms. Not for raw UniProt entry/FASTA retrieval or AlphaFold 3D structures. Part of the AlterLab Academic Skills suite.

Provide direct REST API access to KEGG (academic use only) for pathway analysis, gene-to-pathway and compound-to-pathway mapping, metabolic reactions, KEGG Orthology (KO), drug-drug interactions, and ID conversion. Use when querying KEGG pathways, mapping genes/compounds to metabolic maps, or running KEGG pathway enrichment via raw HTTP/REST; for protein-protein interaction networks prefer alterlab-string-db, for protein sequences and annotations prefer alterlab-uniprot, and for Python workflows spanning many databases prefer bioservices instead. Part of the AlterLab Academic Skills suite.

Query the STRING API for protein-protein interactions (59M proteins, 20B interactions across 5000+ species), building interaction networks, discovering functional partners, and running GO/KEGG/Pfam enrichment on protein lists. Use when constructing a protein-protein interaction network, expanding from seed proteins to functional partners, or running PPI-based enrichment for systems biology; for curated metabolic pathway maps and reactions prefer alterlab-kegg, and for protein sequences, annotations, or accession ID mapping prefer alterlab-uniprot instead. Part of the AlterLab Academic Skills suite.

Provide direct REST API access to UniProt (Swiss-Prot/TrEMBL) for protein sequence searches, FASTA retrieval, functional annotations (GO terms, domains), and cross-database ID mapping. Use when looking up a protein entry, fetching a protein FASTA sequence, or mapping accessions between databases over raw HTTP/REST; for EXPERIMENTAL 3D structures prefer alterlab-pdb, for AI-PREDICTED 3D structures prefer alterlab-alphafold-db, for protein-protein interaction networks prefer alterlab-string-db, and for Python workflows spanning many databases prefer bioservices instead. Part of the AlterLab Academic Skills suite.

Turbine — small Kotlin testing library for kotlinx.coroutines Flows. Provides ergonomic API to test Flow emissions deterministically: awaitItem, expectMostRecentItem, awaitComplete, awaitError. Works with StateFlow, SharedFlow, Channel-backed flows, combine/map/debounce. KMP-friendly. USE WHEN: user mentions "Turbine", "app.cash.turbine", ".test {}", "awaitItem", "Flow testing", "StateFlow test", "SharedFlow test", "expectMostRecentItem", "cancelAndIgnoreRemainingEvents" DO NOT USE FOR: Mobile E2E - use `testing/maestro` DO NOT USE FOR: Compose snapshot - use `testing/compose-snapshot` DO NOT USE FOR: Generic Kotlin testing - use `testing/kotest` DO NOT USE FOR: Suspend function (non-Flow) testing - use `kotlinx-coroutines-test` directly

proptest — property-based testing for Rust (Hypothesis-style). Generates thousands of random inputs to find counterexamples to invariants, with shrinking to minimal failing case. Critical for crypto, parsers, state machines, and finance code where edge cases matter. Includes strategies (gen functions), regression tracking, and integration with cargo test. Alternative: quickcheck (simpler API, less powerful). USE WHEN: user mentions "proptest", "property-based test", "proptest!", "Strategy", "Arbitrary", "shrink", "quickcheck", "regression file", "fuzz-light", "proptest-derive" DO NOT USE FOR: Generic Rust unit tests - use `testing/rust-testing` DO NOT USE FOR: Fuzzing with mutator (cargo-fuzz, AFL) - use bitcoin/testing/fuzz DO NOT USE FOR: KMP property testing - use `testing/kotest` (has built-in property)

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.