MarieLynneBlock

@marielynneblock source repo

304 skills
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8 hours ago last updated

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Sympy · marielynneblock bundle
Use this skill when working with symbolic mathematics in Python. This skill should be used for symbolic computation tasks including solving equations algebraically, performing calculus operations (derivatives, integrals, limits), manipulating algebraic expressions, working with matrices symbolically, physics calculations, number theory problems, geometry computations, and generating executable code from mathematical expressions. Apply this skill when the user needs exact symbolic results rather than numerical approximations, or when working with mathematical formulas that contain variables and parameters.

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MCP CLI · marielynneblock
Interface for MCP (Model Context Protocol) servers via CLI. Use when you need to interact with external tools, APIs, or data sources through MCP servers, list available MCP servers/tools, or call MCP tools from command line.

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PDF · marielynneblock bundle
Use this skill whenever the user wants to do anything with PDF files. This includes reading or extracting text/tables from PDFs, combining or merging multiple PDFs into one, splitting PDFs apart, rotating pages, adding watermarks, creating new PDFs, filling PDF forms, encrypting/decrypting PDFs, extracting images, and OCR on scanned PDFs to make them searchable. If the user mentions a .pdf file or asks to produce one, use this skill.

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Security Review · marielynneblock bundle
AI-powered codebase security scanner that reasons about code like a security researcher — tracing data flows, understanding component interactions, and catching vulnerabilities that pattern-matching tools miss. Use this skill when asked to scan code for security vulnerabilities, find bugs, check for SQL injection, XSS, command injection, exposed API keys, hardcoded secrets, insecure dependencies, access control issues, or any request like "is my code secure?", "review for security issues", "audit this codebase", or "check for vulnerabilities". Covers injection flaws, authentication and access control bugs, secrets exposure, weak cryptography, insecure dependencies, and business logic issues across JavaScript, TypeScript, Python, Java, PHP, Go, Ruby, and Rust.

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Gh CLI · marielynneblock
GitHub CLI (gh) comprehensive reference for repositories, issues, pull requests, Actions, projects, releases, gists, codespaces, organisations, extensions, and all GitHub operations from the command line.

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Pdftk Server · marielynneblock bundle
Skill for using the command-line tool pdftk (PDFtk Server) for working with PDF files. Use when asked to merge PDFs, split PDFs, rotate pages, encrypt or decrypt PDFs, fill PDF forms, apply watermarks, stamp overlays, extract metadata, burst documents into pages, repair corrupted PDFs, attach or extract files, or perform any PDF manipulation from the command line.

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Drawio · marielynneblock bundle
Generate draw.io diagrams as .drawio files and export to PNG/SVG/PDF with embedded XML

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Remember Interactive Programming · marielynneblock
Micro-skill that reminds the agent to use an available REPL or live runtime as the source of truth during interactive programming tasks.

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Java MCP Server Generator · marielynneblock
Generate a complete Model Context Protocol server project in Java using the official MCP Java SDK with reactive streams and optional Spring Boot integration.

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Javax To Jakarta Migration · marielynneblock
Migrate Java code from javax.* to jakarta.* namespace. Use when upgrading to Tomcat 11, Jakarta EE 10, or when javax imports are detected in the codebase.

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Breakdown Epic Pm · marielynneblock
Prompt for creating an Epic Product Requirements Document (PRD) for a new epic. This PRD will be used as input for generating a technical architecture specification.

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Python Pypi Package Builder · marielynneblock bundle
End-to-end skill for building, testing, linting, versioning, and publishing a production-grade Python library to PyPI. Covers all four build backends (setuptools+setuptools_scm, hatchling, flit, poetry), PEP 440 versioning, semantic versioning, dynamic git-tag versioning, OOP/SOLID design, type hints (PEP 484/526/544/561), Trusted Publishing (OIDC), and the full PyPA packaging flow. Use for: creating Python packages, pip-installable SDKs, CLI tools, framework plugins, pyproject.toml setup, py.typed, setuptools_scm, semver, mypy, pre-commit, GitHub Actions CI/CD, or PyPI publishing.

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Plantuml Ascii · marielynneblock
Generate ASCII art diagrams using PlantUML text mode. Use when user asks to create ASCII diagrams, text-based diagrams, terminal-friendly diagrams, or mentions plantuml ascii, text diagram, ascii art diagram. Supports: Converting PlantUML diagrams to ASCII art, Creating sequence diagrams, class diagrams, flowcharts in ASCII format, Generating Unicode-enhanced ASCII art with -utxt flag

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MCP Copilot Studio Server Generator · marielynneblock
Generate a complete MCP server implementation optimised for Copilot Studio integration with proper schema constraints and streamable HTTP support

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Draw Io Diagram Generator 2 · marielynneblock bundle
Use when creating, editing, or generating draw.io diagram files (.drawio, .drawio.svg, .drawio.png). Covers mxGraph XML authoring, shape libraries, style strings, flowcharts, system architecture, sequence diagrams, ER diagrams, UML class diagrams, network topology, layout strategy, the hediet.vscode-drawio VS Code extension, and the full agent workflow from request to a ready-to-open file.

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Exploratory Data Analysis · marielynneblock bundle
Perform comprehensive exploratory data analysis on scientific data files across 200+ file formats. This skill should be used when analysing any scientific data file to understand its structure, content, quality, and characteristics. Automatically detects file type and generates detailed markdown reports with format-specific analysis, quality metrics, and downstream analysis recommendations. Covers chemistry, bioinformatics, microscopy, spectroscopy, proteomics, metabolomics, and general scientific data formats.

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Imbalanced Classification · marielynneblock
[TODO] Define the specific workflow this skill standardises, including default libraries, quality checks, and expected deliverables.

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Snowflake Semanticview · marielynneblock
Create, alter, and validate Snowflake semantic views using Snowflake CLI (snow). Use when asked to build or troubleshoot semantic views/semantic layer definitions with CREATE/ALTER SEMANTIC VIEW, to validate semantic-view DDL against Snowflake via CLI, or to guide Snowflake CLI installation and connection setup.

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Napkin · marielynneblock bundle
Visual whiteboard collaboration for Copilot CLI. Creates an interactive whiteboard that opens in your browser — draw, sketch, add sticky notes, then share everything back with Copilot. Copilot sees your drawings and text, and responds with analysis, suggestions, and ideas.

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Architecture Models 4plus1 · marielynneblock bundle
Produce Philippe Kruchten's 4+1 architectural view model for a software system, with rendered diagrams (Mermaid primary, PlantUML fallback for deployment) AND Miro RISEN prompts for each view. Use this skill whenever the user mentions "4+1", "architecture views", "architectural documentation", "logical view", "process view", "development view", "physical view", or "deployment view" — and also whenever the user asks to document system architecture, produce architecture blueprints, generate architecture diagrams, or prepare architecture content for review with non-developer stakeholders, even if they don't say "4+1" explicitly. Works with zero-input (user gives a paragraph, skill drafts a full architecture), interview mode (user has detailed context), or partial mode (user wants only one or two views). Flexes notation to audience — UML-flavoured for dev-only audiences, BPMN-style swimlanes for cross-functional audiences, simplified C4 for executives.

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Scientific Critical Thinking · marielynneblock bundle
Evaluate scientific claims and evidence quality. Use for assessing experimental design validity, identifying biases and confounders, applying evidence grading frameworks (GRADE, Cochrane Risk of Bias), or teaching critical analysis. Best for understanding evidence quality, identifying flaws. For formal peer review writing use peer-review.

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4plus1 Models · marielynneblock bundle
Produce Philippe Kruchten's 4+1 architectural view model for a software system. This is the core method skill: audience routing, concerns, per-view generation, and cross-view consistency. It outputs canonical diagram-as-code (Mermaid / PlantUML) plus view prose, and does not own draw.io or Miro rendering.

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Dotnet Best Practices · marielynneblock
Ensure .NET/C# code meets best practices for the solution/project.

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Game Engine · marielynneblock bundle
Expert skill for building web-based game engines and games using HTML5, Canvas, WebGL, and JavaScript. Use when asked to create games, build game engines, implement game physics, handle collision detection, set up game loops, manage sprites, add game controls, or work with 2D/3D rendering. Covers techniques for platformers, breakout-style games, maze games, tilemaps, audio, multiplayer via WebRTC, and publishing games.

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Repo Story Time · marielynneblock
Generate a comprehensive repository summary and narrative story from commit history

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Readme Blueprint Generator · marielynneblock
Intelligent README.md generation prompt that analyses project documentation structure and creates comprehensive repository documentation. Scans .github/copilot directory files and copilot-instructions.md to extract project information, technology stack, architecture, development workflow, coding standards, and testing approaches while generating well-structured markdown documentation with proper formatting, cross-references, and developer-focused content.

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Tabular Performance At Scale · marielynneblock
[TODO] Define the specific workflow this skill standardises, including default libraries, quality checks, and expected deliverables.

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Shap And Model Explainability · marielynneblock
[TODO] Define the specific workflow this skill standardises, including default libraries, quality checks, and expected deliverables.

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Dynatrace Observability · marielynneblock bundle
Use when investigating Dynatrace incidents, validating releases, writing DQL, triaging security findings, or operating Dynatrace with dtctl.

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Metabolomics Workbench Database · marielynneblock bundle
Access NIH Metabolomics Workbench via REST API (4,200+ studies). Query metabolites, RefMet nomenclature, MS/NMR data, m/z searches, study metadata, for metabolomics and biomarker discovery.

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Review And Refactor · marielynneblock
Review and refactor code in your project according to defined instructions

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Mentoring Juniors · marielynneblock
Socratic mentoring for junior developers and AI newcomers. Guides through questions, never answers. Triggers: "help me understand", "explain this code", "I'm stuck", "Im stuck", "I'm confused", "Im confused", "I don't understand", "I dont understand", "can you teach me", "teach me", "mentor me", "guide me", "what does this error mean", "why doesn't this work", "why does not this work", "I'm a beginner", "Im a beginner", "I'm learning", "Im learning", "I'm new to this", "Im new to this", "walk me through", "how does this work", "what's wrong with my code", "what's wrong", "can you break this down", "ELI5", "step by step", "where do I start", "what am I missing", "newbie here", "junior dev", "first time using", "how do I", "what is", "is this right", "not sure", "need help", "struggling", "show me", "help me debug", "best practice", "too complex", "overwhelmed", "lost", "debug this", "/socratic", "/hint", "/concept", "/pseudocode". Progressive clue systems, teaching techniques, and success metrics.

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Python MCP Server Generator · marielynneblock
Generate a complete MCP server project in Python with tools, resources, and proper configuration

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Dotnet Design Pattern Review · marielynneblock
Review the C#/.NET code for design pattern implementation and suggest improvements.

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Git Flow Branch Creator · marielynneblock
Intelligent Git Flow branch creator that analyses git status/diff and creates appropriate branches following the nvie Git Flow branching model.

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Miro Diagram Generator · marielynneblock bundle
Generate Miro board prompts for architecture diagrams. Use this skill to produce per-view Miro prompts from canonical 4+1 diagram sources, with RISEN structure, strict scope boundaries, and track-specific validation.

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Create Architectural Decision Record · marielynneblock
Create an Architectural Decision Record (ADR) document for AI-optimised decision documentation.

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Technology Stack Blueprint Generator · marielynneblock
Comprehensive technology stack blueprint generator that analyses codebases to create detailed architectural documentation. Automatically detects technology stacks, programming languages, and implementation patterns across multiple platforms (.NET, Java, JavaScript, React, Python). Generates configurable blueprints with version information, licensing details, usage patterns, coding conventions, and visual diagrams. Provides implementation-ready templates and maintains architectural consistency for guided development.

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Data Validation And Schema Contracts · marielynneblock
[TODO] Define the specific workflow this skill standardises, including default libraries, quality checks, and expected deliverables.

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Hypothesis Testing And Ab Evaluation · marielynneblock
[TODO] Define the specific workflow this skill standardises, including default libraries, quality checks, and expected deliverables.

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Javascript Typescript Jest · marielynneblock
Best practices for writing JavaScript/TypeScript tests using Jest, including mocking strategies, test structure, and common patterns.

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Generate Custom Instructions From Codebase · marielynneblock
Generate GitHub Copilot migration instructions by comparing two project versions and extracting conventions for framework upgrades, refactoring, dependency changes, or technology migrations.

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Model Selections And Cross Validation · marielynneblock
[TODO] Define the specific workflow this skill standardises, including default libraries, quality checks, and expected deliverables.

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Openapi To Application Code · marielynneblock
Generate a complete, production-ready application from an OpenAPI specification

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Feature Engineering And Leakage Checks · marielynneblock
[TODO] Define the specific workflow this skill standardises, including default libraries, quality checks, and expected deliverables.

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Commit Message Storyteller · marielynneblock bundle
Analyses git diffs or staged changes and generates narrative commit messages that explain WHY a change was made, not just what changed — following Conventional Commits format. Use when asked to "write a commit message", "generate a commit", "describe my changes", "what should I commit this as", "commit this", "summarise my diff", or "help me commit". Works with git diff output, staged files, or plain descriptions of changes.

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Draw Io Diagram Generator · marielynneblock bundle
Use when creating, editing, or generating draw.io diagram files (.drawio, .drawio.svg, .drawio.png). Covers mxGraph XML authoring, shape libraries, style strings, flowcharts, system architecture, sequence diagrams, ER diagrams, UML class diagrams, network topology, layout strategy, the hediet.vscode-drawio VS Code extension, and the full agent workflow from request to a ready-to-open file.

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Performance Review Writer · marielynneblock
Draft performance reviews, self-assessments, peer reviews, and upward feedback in your own voice. Analyses your contributions, emails, and meeting history via WorkIQ, then produces honest, impact-focused drafts using the STAR format. USE FOR: write my performance review, draft self-assessment, peer review, 360 feedback, annual review, mid-year review, upward feedback, write review for colleague, performance appraisal.

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Experiment Tracking And Reproducibility · marielynneblock
[TODO] Define the specific workflow this skill standardises, including default libraries, quality checks, and expected deliverables.

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Impediment Prioritisation · marielynneblock bundle
Ranks any list of impediments and their countermeasures using a value-stream scoring model (ROI, Cost to Implement, Ease of Deployment, Risk Factor) and a fixed prioritisation formula. Use when someone asks to prioritise, rank, sequence, or triage impediments, countermeasures, remediation items, risks, findings, gaps, action items, or backlog entries; or mentions value-stream prioritisation, A3 / lean countermeasure ranking, ROI vs. effort scoring, or building a remediation / improvement backlog. Works with GHQR findings, audit results, retrospective action items, risk registers, architecture review gaps, or any free-form `{impediment, countermeasure}` list.

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Spirograph Python Matplotlib · marielynneblock
Create easy Python scripts that generate beautiful, unique spirograph-style generative art with Matplotlib, support multi-colour or gradient background and main palettes, and always save the result as a PNG. Use when the user asks for creative coding, spirographs, procedural art, or quick art scripts with tunable inputs.

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Power Apps Code App Scaffold · marielynneblock
Scaffold a complete Power Apps Code App project with PAC CLI setup, SDK integration, and connector configuration

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Minecraft Plugin Development · marielynneblock bundle
Use this skill when building or modifying Minecraft server plugins for Paper, Spigot, or Bukkit, including plugin.yml setup, commands, listeners, schedulers, player state, team or arena systems, persistent progression, economy or profile data, configuration files, Adventure text, and version-safe API usage. Trigger for requests like "build a Minecraft plugin", "add a Paper command", "fix a Bukkit listener", "create plugin.yml", "implement a minigame mechanic", "add a perk or quest system", or "debug server plugin behaviour".

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Image Manipulation Image Magick · marielynneblock
Process and manipulate images using ImageMagick. Supports resizing, format conversion, batch processing, and retrieving image metadata. Use when working with images, creating thumbnails, resizing wallpapers, or performing batch image operations.

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Scikit Learn Pipelines And Column Transformers · marielynneblock
[TODO] Define the specific workflow this skill standardises, including default libraries, quality checks, and expected deliverables.

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Excalidraw Diagram Generator · marielynneblock bundle
Generate Excalidraw diagrams from natural language descriptions. Use when asked to "create a diagram", "make a flowchart", "visualise a process", "draw a system architecture", "create a mind map", or "generate an Excalidraw file". Supports flowcharts, relationship diagrams, mind maps, and system architecture diagrams. Outputs .excalidraw JSON files that can be opened directly in Excalidraw.

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Create Github Action Workflow Specification · marielynneblock
Create a formal specification for an existing GitHub Actions CI/CD workflow, optimised for AI consumption and workflow maintenance.

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Write Epic · marielynneblock
Produces a complete epic definition following Atlassian agile guidance. An epic captures a large initiative that is too big for a single sprint and must be decomposed into user stories.

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Mlflow · marielynneblock
[TODO] Define the specific workflow this skill standardises, including default libraries, quality checks, and expected deliverables.

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Opencv · marielynneblock
[TODO] Define the specific workflow this skill standardises, including default libraries, quality checks, and expected deliverables.

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Plotly · marielynneblock bundle
Interactive visualisation library. Use when you need hover info, zoom, pan, or web-embeddable charts. Best for dashboards, exploratory analysis, and presentations. For static publication figures use matplotlib or scientific-visualisation.

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Polars · marielynneblock bundle
Fast in-memory DataFrame library for datasets that fit in RAM. Use when pandas is too slow but data still fits in memory. Lazy evaluation, parallel execution, Apache Arrow backend. Best for 1-100GB datasets, ETL pipelines, faster pandas replacement. For larger-than-RAM data use dask or vaex.

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Arboreto · marielynneblock bundle
Infer gene regulatory networks (GRNs) from gene expression data using scalable algorithms (GRNBoost2, GENIE3). Use when analysing transcriptomics data (bulk RNA-seq, single-cell RNA-seq) to identify transcription factor-target gene relationships and regulatory interactions. Supports distributed computation for large-scale datasets.

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Deepchem · marielynneblock bundle
Molecular ML with diverse featurizers and pre-built datasets. Use for property prediction (ADMET, toxicity) with traditional ML or GNNs when you want extensive featurization options and MoleculeNet benchmarks. Best for quick experiments with pre-trained models, diverse molecular representations. For graph-first PyTorch workflows use torchdrug; for benchmark datasets use pytdc.

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Diffdock · marielynneblock bundle
Diffusion-based molecular docking. Predict protein-ligand binding poses from PDB/SMILES, confidence scores, virtual screening, for structure-based drug design. Not for affinity prediction.

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Fluidsim · marielynneblock bundle
Framework for computational fluid dynamics simulations using Python. Use when running fluid dynamics simulations including Navier-Stokes equations (2D/3D), shallow water equations, stratified flows, or when analysing turbulence, vortex dynamics, or geophysical flows. Provides pseudospectral methods with FFT, HPC support, and comprehensive output analysis.

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Histolab · marielynneblock bundle
Lightweight WSI tile extraction and preprocessing. Use for basic slide processing tissue detection, tile extraction, stain normalisation for H&E images. Best for simple pipelines, dataset preparation, quick tile-based analysis. For advanced spatial proteomics, multiplexed imaging, or deep learning pipelines use pathml.

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Pydeseq2 · marielynneblock bundle
Differential gene expression analysis (Python DESeq2). Identify DE genes from bulk RNA-seq counts, Wald tests, FDR correction, volcano/MA plots, for RNA-seq analysis.

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Pyhealth · marielynneblock bundle
Comprehensive healthcare AI toolkit for developing, testing, and deploying machine learning models with clinical data. This skill should be used when working with electronic health records (EHR), clinical prediction tasks (mortality, readmission, drug recommendation), medical coding systems (ICD, NDC, ATC), physiological signals (EEG, ECG), healthcare datasets (MIMIC-III/IV, eICU, OMOP), or implementing deep learning models for healthcare applications (RETAIN, SafeDrug, Transformer, GNN).

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Pymatgen · marielynneblock bundle
Materials science toolkit. Crystal structures (CIF, POSCAR), phase diagrams, band structure, DOS, Materials Project integration, format conversion, for computational materials science.

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Pyopenms · marielynneblock bundle
Complete mass spectrometry analysis platform. Use for proteomics workflows feature detection, peptide identification, protein quantification, and complex LC-MS/MS pipelines. Supports extensive file formats and algorithms. Best for proteomics, comprehensive MS data processing. For simple spectral comparison and metabolite ID use matchms.

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Pyzotero · marielynneblock bundle
Interact with Zotero reference management libraries using the pyzotero Python client. Retrieve, create, update, and delete items, collections, tags, and attachments via the Zotero Web API v3. Use this skill when working with Zotero libraries programmatically, managing bibliographic references, exporting citations, searching library contents, uploading PDF attachments, or building research automation workflows that integrate with Zotero.

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Agentic Eval · marielynneblock
Use when designing and implementing evaluation loops for AI agents, including reflection, evaluator-optimiser patterns, rubric scoring, LLM-as-judge review, test-driven refinement, convergence checks, and iteration logging.

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Process Map · marielynneblock
Produces a structured process map with swim lanes, task nodes, decision diamonds, and handoff arrows. Output is in **Mermaid** flowchart notation (renderable in GitHub, VS Code, Confluence, and Miro) or **BPMN-lite** text when a formal notation is required.

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Seaborn · marielynneblock bundle
Statistical visualisation with pandas integration. Use for quick exploration of distributions, relationships, and categorical comparisons with attractive defaults. Best for box plots, violin plots, pair plots, heatmaps. Built on matplotlib. For interactive plots use plotly; for publication styling use scientific-visualisation.

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Biopython · marielynneblock bundle
Comprehensive molecular biology toolkit. Use for sequence manipulation, file parsing (FASTA/GenBank/PDB), phylogenetics, and programmatic NCBI/PubMed access (Bio.Entrez). Best for batch processing, custom bioinformatics pipelines, BLAST automation. For quick lookups use gget; for multi-service integration use bioservices.

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Deeptools · marielynneblock bundle
NGS analysis toolkit. BAM to bigWig conversion, QC (correlation, PCA, fingerprints), heatmaps/profiles (TSS, peaks), for ChIP-seq, RNA-seq, ATAC-seq visualisation.

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Geomaster · marielynneblock bundle
Comprehensive geospatial science skill covering remote sensing, GIS, spatial analysis, machine learning for earth observation, and 30+ scientific domains. Supports satellite imagery processing (Sentinel, Landsat, MODIS, SAR, hyperspectral), vector and raster data operations, spatial statistics, point cloud processing, network analysis, cloud-native workflows (STAC, COG, Planetary Computer), and 8 programming languages (Python, R, Julia, JavaScript, C++, Java, Go, Rust) with 500+ code examples. Use for remote sensing workflows, GIS analysis, spatial ML, Earth observation data processing, terrain analysis, hydrological modelling, marine spatial analysis, atmospheric science, and any geospatial computation task.

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Geopandas · marielynneblock bundle
Python library for working with geospatial vector data including shapefiles, GeoJSON, and GeoPackage files. Use when working with geographic data for spatial analysis, geometric operations, coordinate transformations, spatial joins, overlay operations, choropleth mapping, or any task involving reading/writing/analysing vector geographic data. Supports PostGIS databases, interactive maps, and integration with matplotlib/folium/cartopy. Use for tasks like buffer analysis, spatial joins between datasets, dissolving boundaries, clipping data, calculating areas/distances, reprojecting coordinate systems, creating maps, or converting between spatial file formats.

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Hypogenic · marielynneblock bundle
Automated LLM-driven hypothesis generation and testing on tabular datasets. Use when you want to systematically explore hypotheses about patterns in empirical data (e.g., deception detection, content analysis). Combines literature insights with data-driven hypothesis testing. For manual hypothesis formulation use hypothesis-generation; for creative ideation use scientific-brainstorming.

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Neurokit2 · marielynneblock bundle
Comprehensive biosignal processing toolkit for analysing physiological data including ECG, EEG, EDA, RSP, PPG, EMG, and EOG signals. Use this skill when processing cardiovascular signals, brain activity, electrodermal responses, respiratory patterns, muscle activity, or eye movements. Applicable for heart rate variability analysis, event-related potentials, complexity measures, autonomic nervous system assessment, psychophysiology research, and multi-modal physiological signal integration.

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Pennylane · marielynneblock bundle
Hardware-agnostic quantum ML framework with automatic differentiation. Use when training quantum circuits via gradients, building hybrid quantum-classical models, or needing device portability across IBM/Google/Rigetti/IonQ. Best for variational algorithms (VQE, QAOA), quantum neural networks, and integration with PyTorch/JAX/TensorFlow. For hardware-specific optimisations use qiskit (IBM) or cirq (Google); for open quantum systems use qutip.

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Pufferlib · marielynneblock bundle
High-performance reinforcement learning framework optimised for speed and scale. Use when you need fast parallel training, vectorized environments, multi-agent systems, or integration with game environments (Atari, Procgen, NetHack). Achieves 2-10x speedups over standard implementations. For quick prototyping or standard algorithm implementations with extensive documentation, use stable-baselines3 instead.

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Tiledbvcf · marielynneblock
Efficient storage and retrieval of genomic variant data using TileDB. Scalable VCF/BCF ingestion, incremental sample addition, compressed storage, parallel queries, and export capabilities for population genomics.

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Torchdrug · marielynneblock bundle
PyTorch-native graph neural networks for molecules and proteins. Use when building custom GNN architectures for drug discovery, protein modelling, or knowledge graph reasoning. Best for custom model development, protein property prediction, retrosynthesis. For pre-trained models and diverse featurizers use deepchem; for benchmark datasets use pytdc.

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Gap Analysis · marielynneblock
Provides a repeatable framework for identifying and prioritising gaps between where things are now and where they need to be.

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Networkx · marielynneblock bundle
Comprehensive toolkit for creating, analysing, and visualising complex networks and graphs in Python. Use when working with network/graph data structures, analysing relationships between entities, computing graph algorithms (shortest paths, centrality, clustering), detecting communities, generating synthetic networks, or visualising network topologies. Applicable to social networks, biological networks, transportation systems, citation networks, and any domain involving pairwise relationships.

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Edgartools · marielynneblock bundle
Python library for accessing, analysing, and extracting data from SEC EDGAR filings. Use when working with SEC filings, financial statements (income statement, balance sheet, cash flow), XBRL financial data, insider trading (Form 4), institutional holdings (13F), company financials, annual/quarterly reports (10-K, 10-Q), proxy statements (DEF 14A), 8-K current events, company screening by ticker/CIK/industry, multi-period financial analysis, or any SEC regulatory filings.

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Etetoolkit · marielynneblock bundle
Phylogenetic tree toolkit (ETE). Tree manipulation (Newick/NHX), evolutionary event detection, orthology/paralogy, NCBI taxonomy, visualisation (PDF/SVG), for phylogenomics.

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Polars Bio · marielynneblock bundle
High-performance genomic interval operations and bioinformatics file I/O on Polars DataFrames. Overlap, nearest, merge, coverage, complement, subtract for BED/VCF/BAM/GFF intervals. Streaming, cloud-native, faster bioframe alternative.

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Pylabrobot · marielynneblock bundle
Vendor-agnostic lab automation framework. Use when controlling multiple equipment types (Hamilton, Tecan, Opentrons, plate readers, pumps) or needing unified programming across different vendors. Best for complex workflows, multi-vendor setups, simulation. For Opentrons-only protocols with official API, opentrons-integration may be simpler.

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Scikit Bio · marielynneblock bundle
Biological data toolkit. Sequence analysis, alignments, phylogenetic trees, diversity metrics (alpha/beta, UniFrac), ordination (PCoA), PERMANOVA, FASTA/Newick I/O, for microbiome analysis.

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Scvi Tools · marielynneblock bundle
Deep generative models for single-cell omics. Use when you need probabilistic batch correction (scVI), transfer learning, differential expression with uncertainty, or multi-modal integration (TOTALVI, MultiVI). Best for advanced modelling, batch effects, multimodal data. For standard analysis pipelines use scanpy.

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Skill Name · marielynneblock
[One sentence — what this skill enables the AI to do. This is used to decide when to load the skill, so be specific.]

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Prompt Builder · marielynneblock
Guide users through creating high-quality GitHub Copilot prompt files with clear structure, appropriate tools, validation criteria, and maintainable instructions.

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Risk Analysis · marielynneblock
Provides a structured framework for risk identification and assessment.

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API Design · marielynneblock
Applies REST and GraphQL design principles to produce or review an API contract.

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Bioservices · marielynneblock bundle
Unified Python interface to 40+ bioinformatics services. Use when querying multiple databases (UniProt, KEGG, ChEMBL, Reactome) in a single workflow with consistent API. Best for cross-database analysis, ID mapping across services. For quick single-database lookups use gget; for sequence/file manipulation use biopython.

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Paper 2 Web · marielynneblock bundle
This skill should be used when converting academic papers into promotional and presentation formats including interactive websites (Paper2Web), presentation videos (Paper2Video), and conference posters (Paper2Poster). Use this skill for tasks involving paper dissemination, conference preparation, creating explorable academic homepages, generating video abstracts, or producing print-ready posters from LaTeX or PDF sources.

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Peer Review · marielynneblock bundle
Structured manuscript/grant review with checklist-based evaluation. Use when writing formal peer reviews with specific criteria methodology assessment, statistical validity, reporting standards compliance (CONSORT/STROBE), and constructive feedback. Best for actual review writing, manuscript revision. For evaluating claims/evidence quality use scientific-critical-thinking; for quantitative scoring frameworks use scholar-evaluation.

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304 published skills · page 1 of 4