3,106 件 ・ 関連度順
概要と使いどころ
Diffusion-based docking that predicts protein-ligand poses without a predefined site. Use for blind docking, when traditional docking fails, or exploring multiple binding modes. Pipeline: prep protein (PDB) and ligand (SMILES/SDF), run inference, analyze confidence-ranked poses.
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smina molecular docking CLI. AutoDock Vina fork with customizable scoring functions, native SDF/MOL2/PDB ligand input, autoboxing, local energy minimization, and per-atom score breakdowns. Pipeline: receptor PDBQT prep -> ligand prep (RDKit/OpenBabel) -> dock via autobox or explicit grid -> rescore/minimize with custom scoring -> rank poses by affinity. Choose smina over Vina when you need custom scoring terms (--custom_scoring), local optimization of an existing pose (--local_only), per-atom contributions (--atom_term_data), or SDF/MOL2 ligands without manual PDBQT conversion. For unknown binding sites use diffdock; for the Python-bindings/Vinardo workflow use autodock-vina-docking.
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Parallel/distributed computing for larger-than-RAM data. Components: DataFrames (parallel pandas), Arrays (parallel NumPy), Bags, Futures, Schedulers. Scales laptop to HPC cluster. For single-machine speed use polars; for out-of-core without cluster use vaex.
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Out-of-core DataFrame for billion-row data via lazy evaluation and memory-mapped files. Use when data exceeds RAM (10 GB–TB) for fast aggregation, filtering, virtual columns, and visualization without loading. Supports HDF5, Arrow, Parquet, CSV with cloud (S3, GCS, Azure). Built-in ML transformers (scaling, PCA, K-means). In-memory: polars; distributed: dask.
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Hardware-agnostic Python liquid-handler library: portable scripts run on Hamilton STAR, Tecan Freedom EVO, Opentrons OT-2, or a simulator without vendor lock-in. For protocol automation, method dev, plate reformatting, serial dilutions, and Python lab workflows.
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Predict RNA secondary structure, MFE folding, base-pair probabilities, RNA-RNA interactions via ViennaRNA Python bindings. Pipeline: sequence → MFE → partition function and pair-probability matrix → dot-bracket → duplex. Use for siRNA/sgRNA targeting, ribozyme design, RNA accessibility. Use RNAfold CLI for batch use without Python.
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Scaffold a new SciAgent-Skills entry. Picks pipeline/toolkit/database/guide template, creates skills/{category}/{name}/SKILL.md with valid frontmatter, appends the registry.yaml entry, runs validation. Enforces name uniqueness, kebab-case, description keyword rules, schema rules from AGENTS.md. TRIGGER when user says (any language): "add a SciAgent skill", "add a skill for <X>", "create new skill", "create a SKILL.md for <X>", "scaffold a skill", "new skill entry", "register a skill", "신규 skill 추가", "스킬 만들어줘", "스킬 생성", "skill 만들어", or any request to add a new SKILL.md to this repo. ALWAYS invoke this skill BEFORE writing to skills/ or registry.yaml. DO NOT TRIGGER when: editing existing entry's content (just edit the file directly); migrating an existing entry (read AGENTS.md "Migrating from Existing Entries" first); only updating registry.yaml without creating a new SKILL.md.
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Python bridge to ImageJ2/Fiji for macros, plugins (Bio-Formats, TrackMate, Analyze Particles), NumPy↔ImagePlus/ImgLib2 exchange, and ImageJ Ops. Automates Fiji headlessly from Python. Use scikit-image for pure Python without Fiji plugins; napari for visualization.
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DL cell/nucleus segmentation for fluorescence and brightfield microscopy. Pre-trained models (cyto3, nuclei, tissuenet) and a generalist flow-based algorithm segment cells without retraining. Outputs label masks for morphology and tracking. Use scikit-image watershed for rule-based; Cellpose when DL generalization across staining is needed.
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Shrink a Robonix change before review without changing behaviour. Use when a feature works and tests pass, before opening or updating a PR, and when a review asks for a smaller change.
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Provides patterns for unit testing service layer with Mockito. Creates isolated tests that mock repository calls, verify method invocations, test exception scenarios, and stub external API responses. Use when testing service behaviors and business logic without database or external services.
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Provides patterns for unit testing external REST APIs using WireMock. Stubs API responses, verifies request details, simulates failures (timeouts, 4xx/5xx errors), and validates HTTP client behavior without real network calls. Use when testing service integrations with external APIs or mocking HTTP endpoints.
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Creates professional logical flow diagrams and logical system architecture diagrams using draw.io XML format (.drawio files). Use when creating: (1) logical flow diagrams showing data/process flow between system components, (2) logical architecture diagrams representing system structure without cloud provider specifics, (3) BPMN process diagrams, (4) UML diagrams (class, sequence, activity), (5) data flow diagrams (DFD), (6) decision flowcharts, or (7) system interaction diagrams. This skill focuses on generic/abstract representations, not AWS/Azure-specific architectures (use aws-drawio-architecture-diagrams for cloud diagrams).
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Provides patterns for unit testing Jakarta Bean Validation (JSR-380), including @Valid, @NotNull, @Min, @Max, @Email constraints with Hibernate Validator. Generates custom validator tests, constraint violation assertions, validation groups, and parameterized validation tests. Validates data integrity logic without Spring context. Use when writing validation tests, bean validation tests, or testing custom constraint validators.
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Use when facing 2+ independent investigations that can proceed without shared state - parallel literature survey, multi-dataset replication, or pre-specified robustness checks
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Use when you have a pre-registered analysis plan to execute inline in this session with review checkpoints, on a platform without subagents
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Automate construction data processing using LLM (ChatGPT, Claude, LLaMA). Generate Python/Pandas scripts, extract data from documents, and create automated pipelines without deep programming knowledge.
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Convert AutoCAD DWG files (1983-2026) to Excel databases using DwgExporter CLI. Extract layers, blocks, attributes, and geometry data without Autodesk licenses.
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Convert IFC files (2x3, 4x1, 4x3) to Excel databases using IfcExporter CLI. Extract BIM data, properties, and geometry without proprietary software.
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Generate images and visualizations from Revit/IFC files without BIM software. Python-based noBIM tool for batch processing.
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Build no-code/low-code automation workflows for construction using n8n. Automate data extraction, cost estimation, report generation, and system integrations without writing code.
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Browse and search the OpenConstructionERP cost database: classification tree, SQL and semantic search, autocomplete, certainty badges, and the resource catalog. Use when a user wants to explore cost data without building a BOQ yet.
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Use Databricks built-in AI Functions (ai_classify, ai_extract, ai_summarize, ai_mask, ai_translate, ai_fix_grammar, ai_gen, ai_analyze_sentiment, ai_similarity, ai_parse_document, ai_prep_search, ai_query, ai_forecast) to add AI capabilities directly to SQL and PySpark pipelines without managing model endpoints. Also covers document parsing and building custom RAG pipelines (parse → prep_search → index → query).
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Builds and edits PowerPoint decks bound to a company's own .pptx or .potx template, with a consulting-grade storyline and a rendered visual QA pass. Maps the template's masters, layouts, placeholders, theme colors and fonts; drafts a storyboard of action titles (pyramid principle, SCR) for approval; fills the template's own placeholders instead of drawing text boxes; adds native charts in theme colors, tables sized to placeholders, speaker notes and source lines; then renders every slide to PNG and checks text overflow, off-slide and overlapping shapes, off-theme fonts and colors, empty placeholders and weak titles. Use whenever the user says use our template, company deck, brand or corporate template, make slides, build a deck, pptx, potx, consulting-style deck, board or client presentation, action titles, or fix my deck formatting, and whenever an existing deck must be edited without breaking its masters. Complements the generic pptx skill.
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。