jkitchin

@jkitchin source repo

43 skills
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16 hours ago last updated

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Crucible 2 · jkitchin
LLM-compiled knowledge base management. Ingests primary sources (papers, notebooks, data), distills them into interlinked org-mode wiki articles, and provides structured search over the wiki graph database. Triggers: "ingest this", "distill", "add to crucible", "crucible ingest", "crucible search", "search the wiki", "what do we know about", "find related", "knowledge base", "distill this source", "add source", "wiki article", "concept article", "what sources", "what links to", "related articles", "undigested sources", "orphan articles", "crucible sync", "update the wiki"

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Variable Aggregation · jkitchin bundle
Use when reducing a discopt nonlinear optimization model with variable aggregation (reduced-space presolve) — substituting variables defined by equality constraints to shrink the model, improve interior-point convergence reliability, or reproduce Naik et al. (arXiv:2502.13869). Covers method choice (ld1/ecd2/ld2/d2/gr/lm), the structure-preserving-vs-Hessian-cost tradeoff, numerical guards, primal/dual recovery, implicit elimination of cyclic blocks, structural diagnostics, and the study/benchmark harnesses. Triggers on the discopt.aggregation package, "aggregate variables", "reduced-space formulation", "presolve substitution", or eliminating intermediates from an NLP/DAE model.

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Course Assessor · jkitchin
Assess a discopt-course lesson - load the rubric, read the student's exercise notebook and (optional) writing response, then produce structured feedback and update progress.yaml. Trigger when the user runs /course:assess or /course:grade-writing, or otherwise asks Claude to grade a lesson.

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Discopt Doe · jkitchin bundle
Design optimal experiments with discopt (requires the discopt-doe plugin) — check identifiability, explore the design space, and recommend D/A/E-optimal conditions for a model with unknown parameters. Supports sequential/active-learning DoE. Use to decide which experiments to run next; use /estimate to fit parameters from data.

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Discopt Mkm · jkitchin
Build and analyze heterogeneous-catalysis microkinetic models — steady-state coverages, turnover frequency, Campbell degree of rate control, apparent reaction orders / activation energy, reaction routes and the overall reaction, lumped (Langmuir-Hinshelwood) rate laws, and HTML reports. Use whenever the user describes a catalytic reaction mechanism, surface kinetics, adsorbates and sites, coverages, rate-determining or rate-controlling steps, or asks to solve or analyze a microkinetic model.

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Jax Ldt · jkitchin bundle
Pure-JAX linear and hyperplane decision trees (port of LLNL's hyperplanetree). Piecewise-linear surrogate modeling with first-class uncertainty quantification (linear-propagation, quadratic-difference, Mondrian leaf conformal), batched active learning (ask/tell + run sugar with campaign persistence), and MIP-friendly export (solver-neutral JSON, hand-built ONNX, optional discopt adapter for direct MINLP embedding without Pyomo).

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Pounce · jkitchin bundle
Inspect and diagnose pounce solve reports via the pounce-studio CLI. Use when the user asks to analyze a pounce.solve-report JSON, diagnose a stuck or non-converging solve, compare two runs, look up a per-iteration column or finding code, pre-flight an AMPL .nl or GAMS .gms file before solving, check or fix a starting point (check-x0), or set up a warm start.

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Scimax · jkitchin bundle
Searches org-mode notes, displays agenda and TODOs, exports org files to HTML/PDF/LaTeX, validates citations, opens journal entries, maintains the org file index, and publishes org projects via the scimax CLI. Also the reference for org-mode syntax and scimax editor features (links, anchors, back-links, source blocks, tables, citations, task dependencies, project management (task tables, Gantt charts, people/assignees), and the entity selector for contacts/locations). Use when the user works with org-mode notes, asks about org syntax, or runs scimax CLI tasks. Triggers: "find notes about", "search my notes", "what's on my agenda", "show my todos", "what's overdue", "export this file", "check my citations", "rebuild my index", "how many notes", "publish my docs", "index my org files", "open my journal", "journal entry", "today's journal", "yesterday's journal", "morning briefing", "what's on my plate", "weekly review", "wrap up", "end of day", "what should I focus on", "follow up", "prep for", "triage", "org-m

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Crucible · jkitchin
LLM-compiled knowledge base management. Ingests primary sources (papers, notebooks, data), distills them into interlinked org-mode wiki articles, and provides structured search over the wiki graph database. Triggers: "ingest this", "distill", "add to crucible", "crucible ingest", "crucible search", "search the wiki", "what do we know about", "find related", "knowledge base", "distill this source", "add source", "wiki article", "concept article", "what sources", "what links to", "related articles", "undigested sources", "orphan articles", "crucible sync", "update the wiki"

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Scientific Writing · jkitchin bundle
Comprehensive scientific writing guidance for research papers, grants, and technical documentation. Covers paper structure (IMRAD), methods writing, results presentation, figure/table design, citation formatting, abstract writing, and revision responses. Use when users are writing scientific papers, formatting manuscripts, responding to reviewers, writing grant proposals, or need help with any aspect of scientific communication. Triggers include 'write a paper,' 'scientific writing,' 'format my manuscript,' 'methods section,' 'respond to reviewers,' or any research writing task.

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Materials Properties · jkitchin bundle
Expert assistant for calculating materials properties from first-principles using ASE - structure relaxation, surface energies, adsorption, reaction barriers, phonons, elastic constants, and thermodynamic modeling with proper scientific methodology

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Design Of Experiments · jkitchin bundle
Expert guidance for Design of Experiments (DOE) in Python - interactive goal-driven design selection, classical DOE (factorial, response surface, screening), Bayesian optimization with Gaussian processes, model-driven optimal designs, active learning, and sequential experimentation; includes pyDOE3, pycse, BoTorch, Ax, scikit-optimize, statsmodels

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Opentrons Thermocycler · jkitchin
Opentrons Thermocycler Module - automated PCR thermal cycling with independent block (4-99°C) and lid (37-110°C) temperature control, profile execution, and auto-sealing lid support (GEN2) for high-throughput molecular biology workflows

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Python Best Practices · jkitchin bundle
Expert guidance for writing professional Python code following industry best practices including PEP 8 compliance, testing, type hints, error handling, and modern tooling. Use this skill when writing new Python code, refactoring existing code, setting up Python projects, implementing tests, or ensuring code quality and maintainability. Emphasizes: PEP 8, modularity, DRY principle, TDD, virtual environments (uv), and modern tooling (Ruff, Black, Mypy).

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Opentrons Heater Shaker · jkitchin
Opentrons Heater-Shaker Module - temperature control (37-95°C) with orbital mixing (200-3000 rpm) for cell culture, enzymatic reactions, and sample preparation requiring simultaneous heating and agitation

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Scientific Data Extraction · jkitchin bundle
Extract structured data from scientific literature across multiple formats (PDF, HTML, images, plain text). Auto-detects scientific domain to recommend specialized tools for chemistry/materials when appropriate. Use this skill when: extracting numerical data from papers, digitizing graphs/plots, parsing tables from PDFs, extracting chemical properties or reactions, or converting unstructured scientific text to structured formats. Key capabilities: format detection and routing, domain-specific extraction (chemistry/materials), multi-method validation, table extraction, graph digitization, LLM-enhanced extraction with verification, confidence scoring.

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Opentrons Absorbance Reader · jkitchin
Opentrons Absorbance Plate Reader Module for Flex - on-deck microplate spectrophotometry with single/multi-wavelength reading (380-740nm in 10nm increments), automated lid control, and CSV data export for ELISA, cell growth, and colorimetric assays

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Python Multiobjective Optimization · jkitchin
Expert guidance for multiobjective optimization in Python - Pareto optimality, evolutionary algorithms (NSGA-II, NSGA-III, MOEA/D), scalarization methods, Pareto front analysis, and implementation with pymoo, platypus, and DEAP

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Presentations · jkitchin
Create slide presentations in multiple formats: Marp (Markdown, default), Beamer (LaTeX), Jupyter Notebook slides, and PowerPoint (python-pptx). Supports scientific, business, and developer content with math, code, charts, and tables. Converts existing documents into slides or creates from scratch. Auto-compiles to PDF/HTML/PPTX. Use this skill when the user requests: - Creating a presentation or slide deck - Converting a document, paper, or report into slides - Making conference talk, lecture, or meeting slides - Generating PowerPoint, PDF slides, or HTML slideshows - Beamer, Marp, reveal.js, or notebook slideshow creation

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Python Ase · jkitchin bundle
Expert assistance with the Atomic Simulation Environment (ASE) Python library for atomistic simulations, including structure building, calculator setup, optimization, dynamics, and analysis

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Python Jax · jkitchin
Expert guidance for JAX (Just After eXecution) - high-performance numerical computing with automatic differentiation, JIT compilation, vectorization, and GPU/TPU acceleration; includes transformations (grad, jit, vmap, pmap), sharp bits, gotchas, and differences from NumPy

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Claude Light · jkitchin bundle
Expert assistant for conducting remote experiments with Claude-Light - a web-accessible RGB LED and spectral sensor instrument for statistics, regression, optimization, and design of experiments

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Image Generation · jkitchin bundle
AI-powered image generation and editing using Google Gemini, Google Imagen, and OpenAI models. Generate images from text descriptions, edit existing images, create logos/stickers, apply style transfers, and produce product mockups. Use this skill when the user requests: - Image generation from text descriptions - Image editing or modifications - Logos, stickers, or graphic design assets - Product mockups or visualizations - Style transfers or artistic effects - Iterative image refinement Available models: - Google Gemini: gemini-2.5-flash-image (Nano Banana), gemini-3-pro-image-preview (Nano Banana Pro) - Google Imagen: imagen-4.0-generate-001, imagen-4.0-ultra-generate-001, imagen-4.0-fast-generate-001 - OpenAI: gpt-image-1.5 (recommended), gpt-image-1, dall-e-3, dall-e-2 Inspired by: https://github.com/EveryInc/every-marketplace/tree/main/plugins/compounding-engineering/skills/gemini-imagegen

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Code Reviewer · jkitchin bundle
Comprehensive code review and analysis for software quality assurance. Use when Claude needs to review code in any format including (1) Individual files (Python, R, JavaScript, etc.), (2) Directory structures and project organization, (3) Scripts and automation code, (4) Jupyter notebooks and data analysis workflows, (5) Documentation assessment and improvement suggestions, (6) Bug detection and logic verification, (7) Testing coverage and strategy evaluation, (8) Code consistency and maintainability analysis. Provides actionable improvement recommendations across all aspects of software development.

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Troubleshooting · jkitchin bundle
Systematic debugging and problem diagnosis using structured troubleshooting methodologies applicable to any domain - technical issues, process failures, system problems, or general obstacles. Use when users report errors, describe malfunctions, encounter unexpected behavior, or need help diagnosing root causes. Triggers include 'debug this,' 'troubleshoot,' 'why isn't this working,' 'getting an error,' 'something's wrong with,' 'how do I fix,' or any problem description.

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Literature Review · jkitchin bundle
Conduct systematic scientific literature reviews by integrating multi-source searches, iterative analysis, and synthesis into well-structured reports with proper citations. Use this skill when you need to: synthesize knowledge across multiple research domains, identify research gaps, track the evolution of methodologies, evaluate evidence quality, or write comprehensive literature reviews for academic papers, grant proposals, or research projects. Key capabilities: multi-database search strategies, iterative query refinement, content analysis and summarization, thematic synthesis, citation management, quality assessment, bias detection, and structured report generation with multiple output formats.

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Version Control · jkitchin bundle
Expert guidance for Git version control, trunk-based development workflows, and GitHub best practices. Emphasizes Conventional Commits for clean history, short-lived feature branches, frequent integration, and professional collaboration patterns. Use when users need help with git commands, branching strategies, commit messages, PRs, merge conflicts, or git troubleshooting. Triggers include 'git,' 'commit,' 'branch,' 'merge,' 'rebase,' 'PR,' 'pull request,' or version control questions.

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Python Plotting · jkitchin
Comprehensive plotting and visualization in Python - matplotlib (static publication-quality plots), seaborn (statistical visualization), and plotly (interactive plots); includes plot types, customization, best practices, and library selection guidance

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Materials Databases · jkitchin bundle
Expert assistant for accessing materials databases (AFLOW and Materials Project) - query crystal structures, materials properties, thermodynamic data, and computational results from comprehensive databases

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Scientific Reviewer · jkitchin bundle
Comprehensive scientific document review and analysis. Use when Claude needs to review scientific papers, reports, preprints, or other research documents for: (1) Identifying and evaluating claims and supporting evidence, (2) Assessing logical argumentation and experimental design, (3) Reviewing citation adequacy and suggesting additional references, (4) Determining document type and research contribution, (5) Checking technical accuracy and methodology, (6) Providing constructive feedback on presentation and clarity. Also handles language, grammar, and formatting review separately.

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Scientific Workflows · jkitchin bundle
Expert assistant for choosing and implementing scientific workflow tools - from simple joblib caching to complex orchestration with Prefect, Parsl, FireWorks, and quacc. Recommends the simplest solution that meets requirements.

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Eln · jkitchin bundle
Professional scientific documentation in org-mode electronic lab notebooks with date-based organization, comprehensive record-keeping of hypotheses, methods, results, reasoning, and outcomes for reproducible research

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Tdd · jkitchin bundle
Test-Driven Development facilitation using the red-green-refactor cycle. Guides users through writing tests first, implementing minimal code to pass, and refactoring for quality. Use when users want to practice TDD, need help writing tests before code, are developing new features test-first, or want guidance on test structure and implementation. Triggers include 'use TDD,' 'test-driven development,' 'write tests first,' 'red-green-refactor,' or requests to develop functionality with tests.

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Vasp · jkitchin bundle
Expert assistant for VASP (Vienna Ab initio Simulation Package) calculations - input file generation, parameter selection, workflow setup, and best practices for accurate DFT calculations

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Citation Verifier · jkitchin
Verify citations and references in scientific documents to detect hallucinated or invalid sources. Extracts DOIs, URLs, arXiv IDs, PubMed IDs, and ISBNs from Markdown, LaTeX, org-mode, and plain text, then validates them using API lookups and web fetches. Use this skill when: - Reviewing AI-generated content for citation accuracy - Validating references in papers, reports, or documentation - Checking if DOIs/URLs resolve to actual papers - Auditing a document for broken or fake citations

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Idaes · jkitchin bundle
Comprehensive guidance for using IDAES (Institute for the Design of Advanced Energy Systems) for process systems engineering. Covers flowsheet modeling, property packages, unit models, optimization, scaling, initialization, and diagnostics. Use when working with chemical process simulations, energy systems modeling, power plant design, material and energy balances, or process optimization. Triggers include 'IDAES', 'flowsheet', 'process model', 'unit operation', 'process optimization', 'property package', 'energy systems', or process engineering tasks.

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Fairchem · jkitchin bundle
Expert guidance for Meta's FAIRChem library - machine learning methods for materials science and quantum chemistry using pretrained UMA models with ASE integration for fast, accurate predictions

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Pymatgen · jkitchin bundle
Comprehensive guidance for using pymatgen (Python Materials Genomics) for computational materials science. Covers structure creation and manipulation, file I/O (CIF, POSCAR, XYZ), symmetry analysis, Materials Project API integration, phase diagrams, electronic structure analysis, and DFT input generation. Use when working with crystal structures, materials properties, computational chemistry calculations, or materials databases. Triggers include 'pymatgen', 'crystal structure', 'Materials Project', 'CIF file', 'POSCAR', 'band structure', 'phase diagram', or materials analysis tasks.

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Planning · jkitchin bundle
Structured planning and project breakdown using proven methodologies for goals, projects, and strategic initiatives. Use when users need to create plans, break down complex projects, set milestones, estimate timelines, identify dependencies, or develop action plans. Triggers include 'help me plan,' 'create a roadmap for,' 'break down this project,' 'what are the steps to,' or 'how should I approach.'

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Pycalphad · jkitchin bundle
Expert guidance for pycalphad - computational thermodynamics library implementing the CALPHAD method for calculating phase diagrams, phase equilibria, and thermodynamic properties of multicomponent materials systems using thermodynamic databases (TDB files)

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Phd Qualifier · jkitchin bundle
Expert evaluation of Chemical Engineering PhD qualifying exams - review written reports, presentations, and prepare comprehensive questioning sessions to assess student readiness for doctoral research

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Brainstorming · jkitchin bundle
Structured brainstorming and ideation facilitation using proven creativity techniques. Use when users want to generate ideas, explore solutions, break through creative blocks, or need facilitated ideation sessions. Triggers include requests like 'help me brainstorm,' 'generate ideas for,' 'creative solutions to,' or 'think of alternatives.'

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Pycse · jkitchin bundle
Use when performing regression analysis with confidence intervals, solving ODEs, fitting models to experimental data, or caching expensive scientific computations - provides convenient wrappers around scipy that automatically calculate confidence intervals and prediction bounds for linear, nonlinear, and polynomial regression

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43 published skills