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概要と使いどころ
Cloud quantum chemistry platform with Python SDK. Run geometry optimization, conformer generation, torsional scans, and energy minimization (DFT/semiempirical), and retrieve properties (dipole, partial charges, frontier orbitals) — no local QC software or HPC needed.
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Constraint-based (COBRA) analysis of genome-scale metabolic models: FBA, FVA, knockouts, flux sampling, production envelopes, gapfilling, media optimization. Use for strain design, essential gene ID, flux analysis. For kinetic modeling use tellurium; for visualization use Escher.
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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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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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MATLAB/GNU Octave numerical computing: matrices, linear algebra, ODEs, signal processing, optimization, statistics, scientific visualization. MATLAB-syntax examples run on both. For Python use numpy/scipy; for statistical modeling use statsmodels.
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Interactive viewer for microscopy. Displays 2D/3D/4D arrays as Image, Labels, Points, Shapes, Tracks layers; supports annotation, plugin analysis, headless screenshots. Core visualization for Python bioimage workflows. Use ImageJ/FIJI for macro processing; napari for Python-native interactive visualization and DL segmentation review.
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Guide for choosing and creating scientific visualizations for publications and talks. Covers chart-type selection by data structure, color theory for accessibility/print, figure composition, journal formatting (Nature, Cell, ACS), and common pitfalls. Consult when visualizing data or preparing submission figures.
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3Dmol.js WebGL molecular visualization emitted as self-contained HTML. Render structures (PDB/SDF/XYZ/MOL2/cube) with stick, sphere, cartoon, line, and surface styles; animate trajectories with a frame-delay (interval, ms) control; and animate vibrational normal modes via vibrate() from per-atom dx/dy/dz displacements or from precomputed frames. Output standalone HTML that loads 3Dmol from a CDN, with optional play/pause and speed controls. Use for transition-state imaginary-mode animations, MD or reaction-path playback, docking poses, and orbital/density isosurfaces. For static 2D chemical structure drawings use rdkit-chemdraw-cdxml; for 2D statistical plots use matplotlib or plotly.
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Multi-repository coordination, synchronization, and architecture management with AI swarm orchestration
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CLI modernization and hooks system enhancement for claude-flow v3. Implements interactive prompts, command decomposition, enhanced hooks integration, and intelligent workflow automation.
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Achieve aggressive v3 performance targets: 2.49x-7.47x Flash Attention speedup, 150x-12,500x search improvements, 50-75% memory reduction. Comprehensive benchmarking and optimization suite.
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Optimize AgentDB performance with quantization (4-32x memory reduction), HNSW indexing (150x faster search), caching, and batch operations. Use when optimizing memory usage, improving search speed, or scaling to millions of vectors.
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Provides AWS CloudFormation patterns for Lambda functions, layers, API Gateway integration, event sources, cold start optimization, monitoring, logging, template validation, and deployment workflows. Use when creating Lambda functions with CloudFormation, configuring event sources, implementing cold start optimization, managing layers, integrating with API Gateway, and deploying Lambda infrastructure.
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Provides patterns for unit testing Spring Security with `@PreAuthorize`, `@Secured`, `@RolesAllowed`. Validates role-based access control and authorization policies. Use when testing security configurations and access control logic.
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Provides JWT authentication and authorization patterns for Spring Boot 3.5.x covering token generation with JJWT, Bearer/cookie authentication, database/OAuth2 integration, and RBAC/permission-based access control using Spring Security 6.x. Use when implementing authentication or authorization in Spring Boot applications.
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Assess company readiness for construction industry uberization. Analyze data transparency, process automation, and competitive positioning against open data platforms.
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Create visualizations for construction data. Generate charts, graphs, heatmaps, and interactive dashboards using Matplotlib, Seaborn, and Plotly for project analysis and reporting.
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BigQuery/Snowflake接続、EDA、可視化、Marimoノートブック作成を行うサブエージェント。 データ分析関連の4つのルール（data_analysis, visualization, notebook, marimo_variable_naming）を統合。 「データ分析して」「BigQueryに接続」「EDAを実行」「Marimoで分析」等のリクエストで発動。
Builds estimates, quotes, and bids for trades and field-service businesses (HVAC, plumbing, electrical, roofing, landscaping, painting, cleaning, remodeling, general contracting, IT/AV installs). Turns a scope into line items with waste factors, burdened labor, materials, equipment, subs, permits, mobilization, contingency, overhead, profit, and tax, then writes a client-ready xlsx (live formulas) and PDF plus an internal cost sheet, with good/better/best options, add-ons, a payment schedule, exclusions, and assumptions. Use whenever someone asks for a quote, estimate, bid, proposal price, or job price, asks "how much should I charge for this job", wants to check a price or margin on a job, or is confused about markup vs margin. Computes deterministically with a script instead of mental math, because models routinely treat a 30% markup as a 30% margin and drop labor burden, waste, and mobilization.
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Pre-tax vs Roth analysis, charitable giving optimization, capital gains timing, deduction maximization. Not a substitute for CPA.
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Profiles Python code for performance bottlenecks and memory issues. Use when Python code is slow or when profiling for optimization before a release.
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Designs memory palace structures with spatial layouts and domain organization. Use when creating a new palace or planning knowledge architecture by hand.
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Analyzes changesets with risk scoring, categorization by type and impact, and release note preparation. Use when extracting insights from raw change data.
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Guides TensorFlow Fast Style Transfer training, image stylization, and video stylization workflows from checkpoints, VGG/COCO assets, and script-oriented CLIs.
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