Claude Skills by stanfish06

Convert files and office documents to Markdown. Supports PDF, DOCX, PPTX, XLSX, images (with OCR), audio (with transcription), HTML, CSV, JSON, XML, ZIP, YouTube URLs, EPubs and more.

Expert-thinking profile for Mass Spectrometrist (clinical / research): Reasons from ion formation, m/z resolution and mass accuracy, fragmentation, and calibrated ion statistics through ESI/APCI/MALDI tuning, CID/HCD/ETD MS/MS, isotope-pattern formula assignment, and spectral libraries (NIST, mzCloud, GNPS) under FDA/ICH M10/MSI tiers, while treating matrix suppression...

Spectral similarity and compound identification for metabolomics. Use for comparing mass spectra, computing similarity scores (cosine, modified cosine), and identifying unknown compounds from spectral libraries. Best for metabolite identification, spectral matching, library searching. For full LC-MS/MS proteomics pipelines use pyopenms.

Expert-thinking profile for Materials Chemist (wet-lab / solid-state & solution synthesis / diffraction & spectroscopy): Reasons from Kröger–Vink defect equilibria, soft-chemistry routes (sol-gel, hydrothermal, ALD), and structure–property links; validates with GSAS-II/TOPAS Rietveld QPA, GIPAW ssNMR, ICSD/COD/Materials Project, and XPS/BET protocols while treating preferred orientation, AdC mis-referencing, degas artifacts, and...

Expert-thinking profile for Materials Physicist (experimental / thin-film & bulk / spectroscopy–transport): Reasons from band structure, defects, strain, and Landau order parameters; integrates HRXRD/RSM, ARPES, TEM/4D-STEM, van der Pauw transport, and SQUID/MOKE with Materials Project/VASP while treating matrix-element ARPES artifacts, substrate-dominated GIXRD, contact-resistance Hall errors, and DFT gap overclaim as...

Expert-thinking profile for Materials Scientist (laboratory / computational / processing–structure–property): Reasons from CALPHAD phase diagrams, Scheil solidification, and Hall–Petch microstructure–property links; validates with XRD Rietveld QPA, EBSD, TEM/STEM, and ASTM mechanical testing while treating preferred orientation, FIB Ga artifacts, EBSD overlap, and Rietveld overfitting as first-class failure modes.

Expert-thinking profile for Mathematical Analyst (proof-theoretic / PDE & functional analysis / harmonic analysis / operator spectral theory / symbolic-numerical (SymPy, FEniCS, Lean)): Reasons from function-space topology, convergence modes, and constant- dependent inequalities (Hölder, Sobolev, Gronwall) through compactness theorems (Rellich-Kondrachov, Banach-Alaoglu), Calderon-Zygmund and Schauder estimates, and Lax-Milgram while treating limit-integral swaps without dominated convergence...

Expert-thinking profile for Mathematical Modeler (mechanistic modeling / ODE-PDE & agent-based / identifiability & UQ / calibration & inverse problems): Reasons from nondimensionalization, conservation/positivity laws, and minimal-viable model structure through mechanistic ODE/PDE, stochastic, and agent-based formulations, profile-likelihood and Fisher-information identifiability, and Sobol/Morris sensitivity analysis, while treating sloppy unidentifiable parameters...

Expert-thinking profile for Mathematical Physicist (theoretical / axiomatic & constructive mathematical physics): Reasons from Hilbert-space domains, Wightman/OS and Haag–Kastler axioms, constructive QFT, Gibbs measures, and spectral/scattering theory; uses Reed–Simon, Glimm–Jaffe, MathSciNet/math-ph, while treating wrong self- adjoint extensions, invalid Wick rotation, limit-order swaps, and lattice-as-continuum claims as...

Expert-thinking profile for Mathematical Statistician (theoretical / computational): Reasons from LAN, empirical processes, and influence functions; proves M/Z-estimator limits, minimax rates (Fano/Le Cam/Assouad), and semiparametric efficiency while validating with ADEMP simulations and treating naive bootstrap, non-Donsker classes, and debiasing sparsity violations as first-class failure modes.

Analyze data using MATLAB. Use when the task involves tables, timetables, time-series data, numeric arrays, sensor matrices, or gridded data — including but not limited to exploring, filtering, sorting, cleaning, transforming, aggregating, smoothing, padding, trimming, and answering questions about data. MATLAB provides extensive, easy-to-use built-in functions for these workflows with no additional products required.

Analyze the effective toolbox file set to produce a Dependency Manifest — classify all transitive dependencies as included, product, add-on, or external-unresolved, then present resolution options with tradeoffs. Use after matlab-define-toolbox-api when the spec is approved.

Assess toolbox readiness and suggest improvements — validates help text, tests, coverage, code issues, dependencies, and function signatures. Produces a punch list and can execute fixes via delegate skills on user approval. Use before packaging or when asked to improve a toolbox.

Build MATLAB apps from requirements to working code. Asks discovery questions (or skips them when the path is known), recommends UIFigure or UIHTML path, identifies layout archetype (Dashboard, Explorer, Tabbed, Wizard, Canvas), produces an implementation plan, and executes the build. Use when a user wants to build a MATLAB app, create a GUI, make an interactive tool, build a uifigure app, build a uihtml app, or asks which approach to use. Also use when user describes spatial layout needs: da...

Create and customize MATLAB charts and plots. Plot types (line, scatter, bar, histogram, heatmap, surface), axes configuration, annotations, data tips, interactive plots, animation, multiple axes with tiledlayout, colororder, and performance optimization. Works for standalone figures, Live Scripts, and uifigure apps. Use when plotting data, customizing axes, adding annotations or interactivity, animating charts, or arranging multiple axes. Triggers: plot, chart, graph, axes, uiaxes, annotatio...

Execute the build plan — introspect buildfile.m, run its dependency chain, and produce the .mltbx toolbox package. Mechanical execution with no human checkpoint. Works with any buildplan shape.

Call Python libraries from MATLAB using the py. interface, pyrun, pyrunfile, or pyenv. Use when writing or executing MATLAB code that calls Python functions or passes data between MATLAB and Python. REQUIRED when triaging Python errors from MATLAB (ModuleNotFoundError, ImportError, "Unable to resolve the name 'py.*'"). REQUIRED when setting up Python environments for MATLAB, creating virtual environments, or installing Python packages for use with MATLAB.

Guide users or agents to the correct MATLAB tool for processing large tabular data in file-based formats (CSV, Parquet, delimited text, spreadsheets, MDF) that may not fit in memory. Use when a user or agent mentions large files, big data, out-of-memory errors, OOM, scaling up, tall arrays, datastores, or needs to process multiple tabular files. Covers the decision between datastore + tall, datastore + transform, and parallel execution. Also use when a user or agent has working in-memory code...

Generate a MATLAB buildfile.m with tasks for static analysis, testing, coverage reporting, and packaging. Use after matlab-create-project when the project structure is in place and you need repeatable build automation.

Create, edit, and run plain-text MATLAB live scripts (.m files) with rich text formatting, LaTeX equations, section breaks, and inline figures. Use when generating tutorials, analysis notebooks, reports, documentation, or educational content, when modifying existing live scripts, or when converting existing binary .mlx files to .m for version control. Requires R2025a+.

Creates a MATLAB project for an existing folder of MATLAB files using the matlab.project.* APIs via MCP. Adds all existing files, configures the project path, generates a project name/description, and creates a README.md with a function table. Prompts the user before creating any new folders. Never overwrites existing files. Use when asked: "create a project", "set up a MATLAB project", "initialize project", "make this a MATLAB project", "configure project".

Scan a folder, triage files into include/exclude, identify the public API, and produce a toolboxSpecification.m Interface Spec — all in one pass. Use when turning loose code into a toolbox.

Generates all documentation artifacts for a MATLAB toolbox: README.md, functionSignatures.json, GettingStarted.m, and publishable examples with demos.xml help integration. Follows mathworks/toolboxdesign best practices. Use when asked: "document this toolbox", "create documentation", "add examples", "generate function signatures", "getting started guide", "README", "make this ready to share", "add tab completion".

Analyze a toolbox folder and generate a toolbox.ignore file — detects files that should not ship to end users based on what actually exists in the folder. Only suggests patterns for files found. Advisory: presents suggestions with reasons before writing.

Deterministic workflow to download MATLAB Package Manager (mpm) and install MathWorks products from the OS command line with consistent, repeatable behavior. Use when installing MATLAB, Simulink, toolboxes, or support packages via command line, or setting up scripted installations for CI/CD, containers, or fleet provisioning.

Add OpenTelemetry tracing to MATLAB code. Use when the user asks to "add tracing", "instrument with spans", "add OpenTelemetry", "trace my code", "add observability" (when about tracing), or mentions "spans", "distributed tracing", or "OTel tracing" in the context of MATLAB functions. Covers span creation, parent-child context propagation, error handling, attributes, events, and semantic conventions.

Show all installed MATLAB products and support packages for a given MATLAB installation folder. Use when listing, checking, or verifying what products or support packages are in a MATLAB installation.

Modernize deprecated MATLAB functions and patterns. Use when check_matlab_code or checkcode reports "not recommended" or "to be removed" warnings, when migrating legacy code, or when replacing deprecated APIs (trainNetwork, csvread, xlsread, datenum, eval, subplot, guide, optimset, wavread, svmtrain, uicontrol) with current equivalents.

Guides the 7-step MATLAB memory optimization workflow: baseline, profile, identify, optimize, measure, verify, report. Use when asked to reduce MATLAB memory usage, find memory bottlenecks, fix out-of-memory errors, or optimize memory-intensive code.

Version-stamp, re-package, and distribute the .mltbx toolbox. Sets version in ToolboxOptions, re-runs packageToolbox, and guides distribution. Requires explicit user confirmation.

Guides the agent to reference official MathWorks Documentation and Help. Determine correct function syntax and workflows from user guides when deeper context is needed. Minimize iterations and repetitive trial and error. Use this skill to: Identify correct syntax and configuration details. Retrieve relevant, version-specific (or release-specific) information from official documentation. Consult user guides when conceptual or workflow context is needed. Apply best practices.

Review MATLAB code for quality, performance, maintainability, and adherence to MathWorks coding standards. Uses check_matlab_code and matlab_coding_guidelines. Use when reviewing code, checking style, finding code smells, assessing quality, or preparing code for handoff or publication.

Generate and run MATLAB unit tests using matlab.unittest and matlab.uitest. Parameterized tests, fixtures, mocking, coverage analysis, CI/CD with buildtool, app testing with gestures. Use when creating tests, writing test classes, running test suites, checking coverage, testing apps, or validating MATLAB code.

Style MATLAB charts and figures. colororder palettes for chart series colors, colormap selection, brand color organization, and the R2025a Theme API for uifigure apps (dark mode with fliplightness, ThemeChangedFcn, uistyle, component colors). Use when customizing chart colors, applying a color palette, organizing brand colors, implementing dark mode, or importing an external color scheme. Triggers: theme, dark mode, brand colors, colororder, colormap, palette, fliplightness, color scheme, sty...

Upgrade C, C++, and Fortran MEX source files from the Separate Complex (SC) API to the Interleaved Complex (IC) API. Use when converting mxGetPr/mxGetPi to mxGetComplexDoubles, migrating MEX files to -R2018a, adding MX_HAS_INTERLEAVED_COMPLEX guards for SC/IC guarded builds, or modernizing legacy MEX code that uses mxGetData/mxSetData/mxGetImagData/mxSetImagData. Covers C (.c), C++ (.cpp, .cxx), and Fortran (.F, .f90) MEX functions. Triggers on: interleaved complex, IC MEX, mex upgrade, mex m...

Use when writing MATLAB functions with arguments blocks — repeating arguments (arguments (Repeating)), .?ClassName property import in constructors, name-value forwarding with namedargs2cell, or migrating from inputParser or validateattributes. Also when reviewing signatures for implicit-conversion pitfalls (size reshaping, class coercion, computed defaults), or when restricting, constraining, or validating function inputs — scalar vs vector enforcement, type rejection, size checking. Also whe...

Generate or improve MATLAB help text (documentation comments) for a function, class, or script file following MathWorks standards (H1 line, syntax paragraphs, See Also, 75-char lines). Read BEFORE writing MATLAB help — default patterns (Inputs:/Outputs: lists, block comments, uppercase See Also) produce non-conforming output. Use when writing, rewriting, fixing, or reviewing MATLAB help comments or function documentation.

Writes MATLAB performance tests using the matlab.perftest.TestCase framework. Use when asked to write, create, or add performance tests for MATLAB code, benchmark functions, measure execution time with statistical rigor, or use runperf.

Low-level plotting library for full customization. Use when you need fine-grained control over every plot element, creating novel plot types, or integrating with specific scientific workflows. Export to PNG/PDF/SVG for publication. For quick statistical plots use seaborn; for interactive plots use plotly; for publication-ready multi-panel figures with journal styling, use scientific-visualization.

Expert-thinking profile for Mechanical Design Engineer (CAD / GD&T / tolerance / DFM): Reasons from function, datum reference frames, and tolerance budgets; releases inspectable drawings and MBD through ASME Y14.5 GD&T, WC/RSS/Monte Carlo stack-ups, SAE J1739 DFMEA (Action Priority), and Boothroyd–Dewhurst DFM/DFA—not stress plots alone.

Expert-thinking profile for Mechanical Engineer (design / simulation / prototyping): Reasons from equilibrium, failure physics, and code-backed allowables; designs through requirements, GD&T, DFMEA, and hand/FEA/test validation with explicit governing failure modes.

Expert-thinking profile for Mechatronics Engineer (electromechanical co-design / motion control / FOC drives / fieldbus (EtherCAT, CiA 402) / drive safety (IEC 61800-5-2, ISO 13849)): Reasons from reflected inertia, control bandwidth, sensor physics, and thermal duty cycle through Bode loop-shaping with phase/gain margins, FOC current-velocity-position loops, plant identification, HIL, and IEC 61800-5-2 STO architecture while treating backlash and structural-mode resonance, transport-delay ph...

Medicinal chemistry filters for compound triage. Apply drug-likeness rules (Lipinski, Veber, CNS), structural alert catalogs (PAINS, NIBR, ChEMBL), complexity metrics, and the medchem query language for library filtering.

Expert-thinking profile for Medical Geneticist (clinical / laboratory genetics / genetic counseling): Reasons from pedigree priors, HPO phenotype match, and ACMG/ClinGen variant classification; integrates exome/genome, CMA, RNA splicing, NBS ACT pathways, Tier 3 carrier screening, SF v3.3, and CPIC pharmacogenomics while treating VUS overcall, CPM/NIPT discordance, mtDNA heteroplasmy sampling, and SpliceAI-only...

Expert-thinking profile for Medical Mycologist (clinical / laboratory medical mycology): Reasons from EUCAST/CLSI antifungal susceptibility, culture and MALDI-TOF ID, galactomannan/β-D-glucan assays, and CLSI breakpoints while treating contamination, cryptic species mis-ID, and azole MIC trailing as first-class failure modes.

Expert-thinking profile for Medical Parasitologist (clinical / research): Reasons from specimen-stage fit, exposure-based pretest probability, and antigen-versus-antibody kinetics through thick/thin Giemsa films, formalin-ethyl-acetate concentration with trichrome, multiplex PCR, and EITB serology against CDC DPDx and WHO algorithms, while treating pfhrp2/3-deleted RDT false-negatives...

Expert-thinking profile for Medical Physicist (clinical / diagnostic & nuclear imaging / health physics): Reasons from CTDIvol/SSDE, HU accuracy, ACR/MQSA QA, TG-126 PET/CT, TG-18/TG-270 displays, and NCRP 147 shielding across CT, MRI, mammography, NM/PET, and therapy QA while treating phantom-mismatch dose claims, SUV normalization drift, display washout, and post-upgrade MEE gaps as first-class failure modes.

Expert-thinking profile for Medicinal Chemist (lead optimization / SAR / DMPK & ADME / structure-based design / multiparameter (LLE, Fsp3, TPP)): Reasons from structure- activity relationships, lipophilicity and unbound-fraction physicochemistry, synthetic accessibility, and target-product-profile multiparameter optimization through LLE/Fsp3/QED scoring, FEP+/Glide docking validated against co-crystal and SPR data, ELN-tracked LC-MS/NMR synthesis, and DMPK...

Handles end-to-end meeting scheduling using the Superhuman Mail MCP server — from finding available times to sending the invite or proposing times via email. Use this skill whenever someone asks to \"schedule a meeting with [person]\", \"find a time to meet\", \"book a call\", \"set up a meeting\", \"when am I free to meet with [person]\", \"propose times to [person]\", \"send my availability\", \"create a meeting invite\", \"schedule a 1:1\", \"find overlap in our calendars\", \"reschedule m...

Expert-thinking profile for Membrane Biophysicist (wet-lab / computational membrane biophysics): Reasons from Helfrich elasticity, Lo/Ld phase behavior, and intrinsic curvature; builds GUVs, SLBs, nanodiscs, and BLMs; reads Laurdan GP, FRAP/FCS, aspiration, and electrophysiology while treating multilamellarity, detergent carryover, and probe misinterpretation as first-class failure modes.