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概要と使いどころ
KEGG REST API (academic only). Pathways, genes, compounds, enzymes, diseases, drugs via 7 ops (info/list/find/get/conv/link/ddi). ID conversion (NCBI/UniProt/PubChem). Use bioservices for multi-DB Python.
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Query NCBI ClinVar via E-utilities for variant clinical significance, pathogenicity, disease associations. Search by gene/rsID/condition/review status; returns ClinSig, submitter data, conditions, HGVS. For GWAS use gwas-database; for variant consequence prediction use Ensembl VEP.
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gnomAD v4 population variant frequencies via GraphQL API. Allele counts and frequencies stratified by ancestry (AFR, AMR, EAS, NFE, SAS, FIN, ASJ, MID), gene-level constraint (pLI, LOEUF, missense z), and coverage. Identify rare or constrained variants. For clinical pathogenicity use clinvar-database; for GWAS use gwas-database.
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Query CELLxGENE Census (61M+ cells). Search by cell type/tissue/disease/organism; get AnnData, stream out-of-core, train PyTorch models. For your own data use scanpy; for annotated data use anndata.
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Structured ideation methods: SCAMPER, Six Thinking Hats, Morphological Analysis, TRIZ, Biomimicry, plus more. Decision framework for picking methods by challenge type (stuck, improving, systematic exploration, contradiction). Use when generating research ideas or exploring interdisciplinary connections.
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Query ChEMBL (2M+ compounds, 19M+ bioactivity measurements, 13K+ targets) via the public REST/JSON API with plain `requests` — no SDK install required. Search compounds, retrieve IC50/Ki/EC50 bioactivities, find target inhibitors, run SAR, access drug mechanism/indication data.
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scikit-learn compatible Python toolkit for time series ML: classify, cluster, regress, segment, transform with 30+ algorithms (ROCKET, InceptionTime, KNN-DTW, HIVE-COTE, WEASEL). Handles panel, multivariate, and unequal-length series. Maintained successor to sktime. Alternatives: sktime (larger ecosystem), tslearn (fewer algorithms), catch22 (features only).
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NEB-IRC activation energy pipeline for reaction barriers using GFN2-xTB and pysisyphus. Optimize reactant and product geometries, run CI-NEB path search, optimize the transition state with a Hessian, verify with IRC (one imaginary mode, endpoints matching reactant/product, single NEB maximum), and report the electronic and Gibbs barriers. Use when you need a transition state, reaction barrier, activation energy, minimum energy path, or intrinsic reaction coordinate. Covers reactant/product atom-ordering pitfalls, feasibility sizing for single-core runs, and thermochemistry corrections. Renders an IRC energy-profile plot and an animated TS imaginary-mode HTML viewer. For 2D reaction scheme drawing use rdkit-chemdraw-cdxml.
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HuggingFace Transformers with biomedical LMs (BioBERT, PubMedBERT, BioGPT, BioMedLM) for scientific NLP: NER (genes, diseases, chemicals), relation extraction, QA, text classification, abstract summarization. Covers loading, biomedical tokenization, inference pipelines, fine-tuning. Alternatives: spaCy en_core_sci_lg (rule-based NER), Stanza (biomedical models), NLTK.
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API + Python SDK for ordering cell-free protein expression and binding assays. Submit sequences for expression (10–100 µg), measure binding affinity (KD) against targets, track status, and retrieve results programmatically — no wet-lab setup. Built for ML-guided directed evolution and antibody/nanobody optimization. Requires Adaptyv account and API key.
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Python image processing for microscopy and bioimage analysis. Read/write images, filter (Gaussian, median, LoG), segment (thresholding, watershed, active contours), measure region properties, detect features. SciPy/NumPy ecosystem. Use OpenCV for real-time video; CellPose for DL cell segmentation; napari for visualization.
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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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Parse HMDB (Human Metabolome Database) local XML for metabolite info, chemical properties, biological context, disease links, spectra, and cross-DB mapping. No REST API — uses ~6 GB XML download. Use drugbank-database-access for drugs; pubchem-compound-search for live lookups.
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把一句话需求转成可复现、可验收视频工程的乔木智能剪辑导演。Use when the user asks to create, plan, edit, remix, explain, narrate, subtitle, animate, composite, or render a video—including one-line requests such as “制作一个科普视频：介绍 LLM 中的 RL”. Builds English-learning movie mixes, person profiles, explainers, code-drawn motion graphics (UI morph loops, showreels, kinetic-type promos, line-art/pixel/Three.js animation, lyric MVs), product launch videos, cinematic shorts, social clips, course/PPT videos, AI image/video/TTS/music-assisted stories, stock-footage stories, or multi-source montage. Routes across 33台词, ClipSeek/open media, local files, ListenHub, image generation, HTML/SVG/Canvas motion graphics with beat-grid storyboards and determinism probes, Manim, ffmpeg-full, captions, sound design, frame-0 video covers with YouTube thumbnails, and release checks.
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Use when running throughput/latency (serving speed) benchmarks against an already-running model server. Uses sgl_jax.bench_serving to sweep batch-size/concurrency and measure throughput and latency, producing summary.csv and per-point bs_<N>/result.jsonl. Speed only — accuracy/eval belongs to model-accuracy-benchmark. Triggers on throughput, latency, bench_serving, batch-size sweep, tok/s, TTFT, TPOT — not accuracy/eval.
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Provides AWS CloudFormation patterns for IAM roles, policies, managed policies, permission boundaries, and trust relationships. Use when modeling least-privilege access, cross-account assumptions, service roles, or reusable IAM stacks that other CloudFormation templates consume.
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Provides advanced AWS CLI patterns for managing EC2, Lambda, S3, DynamoDB, RDS, VPC, IAM, and CloudWatch. Generates bulk operation scripts, automates cross-service workflows, validates security configurations, and executes JMESPath queries for complex filtering. Triggers on "aws cli help", "aws command line", "aws scripting", "aws automation", "aws batch operations", "aws bulk operations", "aws cli pagination", "aws multi-region", "aws profiles", "aws cli troubleshooting".
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Provides AWS CloudFormation patterns for security infrastructure including KMS encryption, Secrets Manager, IAM security, VPC security, ACM certificates, parameter security, outputs, and secure cross-stack references. Use when implementing security best practices, encrypting data, managing secrets, applying least privilege IAM policies, securing VPC configurations, managing TLS/SSL certificates, and implementing defense in depth strategies.
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How to find and fix performance problems in Shift's desktop app. Use when something is slow, choppy, janky, or laggy (scrubbing, dragging, editing, undo, opening fonts), when profiling or measuring, when adding or reviewing perf tests, and before claiming a change made something faster.
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Canonical rules for preparing, opening, and updating Shift pull requests. Use whenever the user asks to create, open, draft, update, or review a pull request. Enforces issue discovery and linkage, Conventional Commit titles, release-note quality, complete validation evidence, and safe pushing.
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Canonical rules for writing git commits in the Shift codebase. Use whenever the user asks to commit, stage and commit, create a pull request that requires commits, or draft a commit message. Enforces Conventional Commits, release-note quality, concise subjects, and logical commit boundaries.
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Add or revise source-level Rustdoc for Shift Rust APIs. Use before writing or editing documentation comments in `.rs` files, especially for public or crate-visible APIs, domain structures, compiler adapters, persistence boundaries, trait implementations, unsafe code, or any API where ownership, units, coordinate spaces, mutation, I/O, sparse behavior, failure modes, panics, or concurrency are easy to misunderstand.
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Add or revise source-level JSDoc for Shift APIs. Use this skill before writing or editing documentation comments for exported classes, methods, constructors, domain data structures, render frames, reactive state, or any API where caller intent, side effects, lifetime, ownership, or nullability are easy to misunderstand.
日本語の概要は準備中です。原文の説明を表示しています。
When the user needs to decide what to build, cut, and defer for a first release or minimum viable version of a product or feature.
日本語の概要は準備中です。原文の説明を表示しています。