192 件 ・ 関連度順
概要と使いどころ
Annotate bacterial and archaeal genomes and plasmids with Bakta's Prodigal/HMM/diamond pipeline. Identifies CDS, ncRNA, tRNA, rRNA, tmRNA, sORFs, CRISPR arrays, oriC/oriV/oriT, and gaps against a curated UniRef-derived database. Produces NCBI-compatible GFF3, GenBank, EMBL, JSON, FASTA, TSV, and a circular genome plot. Use Prokka for legacy pipelines or non-bacterial kingdoms; PGAP for NCBI GenBank submission.
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ENA REST API for sequences, reads, assemblies, and annotations. Portal API search, Browser API retrieval (XML/FASTA/EMBL), file reports for FASTQ/BAM URLs, taxonomy, cross-refs. For multi-DB Python use bioservices; for NCBI-only use pubmed-database or Biopython Entrez.
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Ultra-fast RNA-seq transcript/gene quantification via quasi-mapping (no BAM). Builds a k-mer index from transcriptome FASTA, quantifies in minutes. Outputs TPM/count tables (quant.sf) with optional GC- and sequence-bias correction. Integrates with tximeta/tximport for DESeq2/edgeR. Use STAR when a genome-aligned BAM is needed.
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Genomic interval ops on BED/BAM/GFF/VCF. Find overlaps, merge intervals, compute coverage, extract FASTA, find nearest features. Core for ChIP-seq peak annotation, region filtering, genome arithmetic. Use tabix for indexed single-region queries; use deeptools for normalized bigWig coverage.
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Read/write SAM/BAM/CRAM, VCF/BCF, FASTA/FASTQ. Region queries, pileup, variant filtering, read groups. Python htslib wrapper exposing samtools/bcftools CLI. Use STAR/BWA for alignment; GATK/DeepVariant for variant calling.
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Query UniProt REST API: search by gene/protein name, fetch FASTA, map IDs (Ensembl, PDB, RefSeq), access Swiss-Prot annotations. Use bioservices for multi-DB access; alphafold-database-access for structures.
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Python library for biology: sequence manipulation (DNA/RNA/protein), pairwise/multiple alignment, phylogenetic trees (NJ, UPGMA), diversity (Shannon, Faith PD, Bray-Curtis, UniFrac), ordination (PCoA, CCA, RDA), stats (PERMANOVA, ANOSIM, Mantel), file I/O (FASTA, FASTQ, Newick, BIOM). Use for microbiome, community ecology, or phylogenetics.
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Search the PRIDE Archive v3 REST API for proteomics datasets: discover projects by keyword + faceted filters (organism, instrument, disease, software), fetch project metadata, list and download RAW/PEAK/RESULT/FASTA files (with FTP/Aspera URLs), look up which projects mention a UniProt accession, and find similar projects. PRIDE v3 no longer exposes peptide/PSM-level identification endpoints — for spectrum-level data download the project's RESULT files. Use uniprot-protein-database for protein sequences; interpro-database for domain architecture.
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Auto-annotate plasmids with features (promoters, terminators, resistance, origins, tags, fluorescent proteins) via BLAST against curated DBs (Addgene, fpbase, SnapGene). FASTA or raw sequence in; annotated GenBank, interactive HTML maps, CSV tables out. Handles circular topology. Use to verify synthetic constructs, prep Addgene submissions, share maps, or batch-annotate cloning libraries.
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Biopython sequence analysis: parse FASTA/FASTQ/GenBank/GFF (SeqIO), NCBI Entrez (esearch/efetch/elink), remote/local BLAST, pairwise/MSA alignment (PairwiseAligner, MUSCLE/ClustalW), phylogenetic trees (Phylo). Use for gene family studies, phylogenomics, comparative genomics, NCBI pipelines. For PCR/restriction/cloning use biopython-molecular-biology; for SAM/BAM use pysam.
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Molecular biology toolkit: sequence manipulation, FASTA/GenBank/PDB I/O, NCBI Entrez, BLAST automation, pairwise/MSA alignment, Bio.PDB, phylogenetic trees. Use for batch processing, custom pipelines, format conversion, PubMed/GenBank queries. For quick gene lookups use gget; for multi-service REST APIs use bioservices.
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Provides implementation patterns for Clean Architecture, Hexagonal Architecture (Ports & Adapters), and Domain-Driven Design in Python applications with FastAPI or Flask. Use when designing maintainable backends with separation of concerns, implementing repository patterns, creating entities/value objects/aggregates, or structuring domain logic independent of frameworks for testability.
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Python backend for Databricks Apps — FastAPI (default), Flask, Dash, Streamlit, Gradio, Reflex. **Default for a new Databricks App is `databricks-apps` (AppKit — Node/TypeScript/React) — reach for it first.** Use this skill only when the user asks for a Python backend, extends an existing Python app, or the team is Python-only. Covers OAuth auth, app resources, SQL warehouse and Lakebase connectivity, foundation-model / Vector Search / model-serving APIs (via `databricks-python-sdk`), and deployment via CLI or DABs.
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Use DocArray for multimodal Pydantic-style documents, typed DocList and DocVec batches, serialization and local storage, FastAPI payloads, and vector retrieval indexes.
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Use ColabFold for protein structure prediction workflows: validate FASTA/CSV/A3M inputs, generate MSAs, plan batch predictions, inspect outputs, and troubleshoot optional AlphaFold, MMseqs2, JAX, GPU, and OpenMM dependencies.
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Guides ChatGLM2-6B Transformers inference, local demos, FastAPI/OpenAI-compatible serving, C-Eval evaluation, and P-Tuning v2 fine-tuning.
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Use BiSheng's enterprise LLM application DevOps platform repository, including FastAPI backend, workflow/RAG/Linsight runtimes, permissions, dual React frontends, deployment, and maintainer workflows.
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Modern Python project architecture guide for 2025. Use when creating Python projects (APIs, CLI, data pipelines). Covers uv, Ruff, Pydantic, FastAPI, and async patterns.
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Generate boilerplate code and project templates/skeletons automatically. Use when: (1) Creating new projects from scratch (React app, FastAPI backend, Express API), (2) Generating repetitive code patterns (CRUD endpoints, models, controllers), (3) Scaffolding components, services, or modules, (4) Creating test boilerplate, (5) Setting up monorepo structures. Provides project templates and code generation patterns for common development tasks.
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Deploy ML models with FastAPI, Docker, Kubernetes. Use for serving predictions, containerization, monitoring, drift detection, or encountering latency issues, health check failures, version conflicts.
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Local and self-hosted text-to-speech with Kokoro, the ~82M-parameter open-weight (Apache 2.0) model by hexgrad. Use when synthesizing speech offline, on-device, in the browser, or on your own server without per-character API cost — for high-volume narration, audiobooks, privacy-constrained pipelines, and prototyping. Covers running Kokoro via the Python `kokoro` package, ONNX / kokoro-js in the browser, and the OpenAI-compatible Kokoro-FastAPI wrapper; picking voices and language codes; blending voices; chunking long text; controlling pronunciation via misaki/espeak-ng; and judging when Kokoro is the right tool versus when its lack of voice cloning, narrow emotional range, and weaker non-English quality mean you should reach for a hosted or larger model instead. Not for voice cloning, expressive/emotional character performance, or high-fidelity multilingual work — say so and route elsewhere.
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Convert between sequence file formats (FASTA, FASTQ, GenBank, EMBL) using Biopython Bio.SeqIO. Use when changing file formats or preparing data for different tools.
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Generate consensus FASTA sequences by applying VCF variants to a reference using bcftools consensus. Use when creating sample-specific reference sequences or reconstructing haplotypes.
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Read, write, and convert multiple sequence alignment files using Biopython Bio.AlignIO. Supports Clustal, PHYLIP, Stockholm, FASTA, Nexus, and other alignment formats for phylogenetics and conservation analysis. Use when reading, writing, or converting alignment file formats.
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