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MarieLynneBlock

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• 304 skills
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1. ▌
   Citation Management · marielynneblock bundle

   Comprehensive citation management for academic research. Search Google Scholar and PubMed for papers, extract accurate metadata, validate citations, and generate properly formatted BibTeX entries. This skill should be used when you need to find papers, verify citation information, convert DOIs to BibTeX, or ensure reference accuracy in scientific writing.
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   Timesfm Forecasting · marielynneblock bundle

   Zero-shot time series forecasting with Google's TimesFM foundation model. Use for any univariate time series (sales, sensors, energy, vitals, weather) without training a custom model. Supports CSV/DataFrame/array inputs with point forecasts and prediction intervals. Includes a preflight system checker script to verify RAM/GPU before first use.
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   Asset Frontmatter Check · marielynneblock

   Validate YAML frontmatter of Copilot customisation assets in this lab (SKILL.md, WORKFLOW.md, *.agent.md, *.instructions.md, *.prompt.md). Use when adding, reviewing, or fixing an asset's frontmatter, or when asked to check whether an asset follows repository conventions.
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   Prd · marielynneblock

   Generate high-quality Product Requirements Documents (PRDs) for software systems and AI-powered features. Includes executive summaries, user stories, technical specifications, and risk analysis.
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   Dashboard Beautify · marielynneblock bundle

   Design and build production-grade dashboards and infographics with Dash and Plotly Python: layout strategy, colour semantics, accessibility, and pre-ship validation. Use when creating or beautifying a dashboard, KPI panel, or data infographic.
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   Csharp Nunit · marielynneblock

   Get best practices for NUnit unit testing, including data-driven tests
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   Csharp Tunit · marielynneblock

   Get best practices for TUnit unit testing, including data-driven tests
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   Csharp Xunit · marielynneblock

   Get best practices for XUnit unit testing, including data-driven tests
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   SQL Code Review · marielynneblock

   Universal SQL code review assistant that performs comprehensive security, maintainability, and code quality analysis across all SQL databases (MySQL, PostgreSQL, SQL Server, Oracle). Focuses on SQL injection prevention, access control, code standards, and anti-pattern detection. Complements SQL optimisation prompt for complete development coverage.
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    Finnish Humanizer · marielynneblock bundle

    Detect and remove AI-generated markers from Finnish text, making it sound like a native Finnish speaker wrote it. Use when asked to "humanize", "naturalize", or "remove AI feel" from Finnish text, or when editing .md/.txt files containing Finnish content. Identifies 26 patterns (12 Finnish-specific + 14 universal) and 4 style markers.
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    Dnanexus Integration · marielynneblock bundle

    DNAnexus cloud genomics platform. Build apps/applets, manage data (upload/download), dxpy Python SDK, run workflows, FASTQ/BAM/VCF, for genomics pipeline development and execution.
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    Imaging Data Commons · marielynneblock bundle

    Query and download public cancer imaging data from NCI Imaging Data Commons using idc-index. Use for accessing large-scale radiology (CT, MR, PET) and pathology datasets for AI training or research. No authentication required. Query by metadata, visualise in browser, check licenses.
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    Latchbio Integration · marielynneblock bundle

    Latch platform for bioinformatics workflows. Build pipelines with Latch SDK, @workflow/@task decorators, deploy serverless workflows, LatchFile/LatchDir, Nextflow/Snakemake integration.
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    Neuropixels Analysis · marielynneblock bundle

    Neuropixels neural recording analysis. Load SpikeGLX/OpenEphys data, preprocess, motion correction, Kilosort4 spike sorting, quality metrics, Allen/IBL curation, AI-assisted visual analysis, for Neuropixels 1.0/2.0 extracellular electrophysiology. Use when working with neural recordings, spike sorting, extracellular electrophysiology, or when the user mentions Neuropixels, SpikeGLX, Open Ephys, Kilosort, quality metrics, or unit curation.
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    Opentargets Database · marielynneblock bundle

    Query Open Targets Platform for target-disease associations, drug target discovery, tractability/safety data, genetics/omics evidence, known drugs, for therapeutic target identification.
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    Statistical Analysis · marielynneblock bundle

    Guided statistical analysis with test selection and reporting. Use when you need help choosing appropriate tests for your data, assumption checking, power analysis, and APA-formatted results. Best for academic research reporting, test selection guidance. For implementing specific models programmatically use statsmodels.
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17. ▌
    Diagnose · marielynneblock

    Perform a systematic diagnostic scan of an AI workflow across 5 quality dimensions — prompt quality, context efficiency, tool health, architecture fitness, and safety — producing a scored report with prioritised remediation actions.
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    Refactor · marielynneblock

    Surgical code refactoring to improve maintainability without changing behaviour. Covers extracting functions, renaming variables, breaking down god functions, improving type safety, eliminating code smells, and applying design patterns. Less drastic than repo-rebuilder; use for gradual improvements.
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    SQL Optimisation · marielynneblock

    Universal SQL performance optimisation assistant for comprehensive query tuning, indexing strategies, and database performance analysis across all SQL databases (MySQL, PostgreSQL, SQL Server, Oracle). Provides execution plan analysis, pagination optimisation, batch operations, and performance monitoring guidance.
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    PPTX Posters · marielynneblock bundle

    Create research posters using HTML/CSS that can be exported to PDF or PPTX. Use this skill ONLY when the user explicitly requests PowerPoint/PPTX poster format. For standard research posters, use latex-posters instead. This skill provides modern web-based poster design with responsive layouts and easy visual integration.
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    Benchling Integration · marielynneblock bundle

    Benchling R&D platform integration. Access registry (DNA, proteins), inventory, ELN entries, workflows via API, build Benchling Apps, query Data Warehouse, for lab data management automation.
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    Consciousness Council · marielynneblock bundle

    Run a multi-perspective Mind Council deliberation on any question, decision, or creative challenge. Use this skill whenever the user wants diverse viewpoints, needs help making a tough decision, asks for a council/panel/board discussion, wants to explore a problem from multiple angles, requests devil's advocate analysis, or says things like "what would different experts think about this", "help me think through this from all sides", "council mode", "mind council", or "deliberate on this". Also trigger when the user faces a dilemma, trade-off, or complex choice with no obvious answer.
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23. ▌
    Hypothesis Generation · marielynneblock bundle

    Structured hypothesis formulation from observations. Use when you have experimental observations or data and need to formulate testable hypotheses with predictions, propose mechanisms, and design experiments to test them. Follows scientific method framework. For open-ended ideation use scientific-brainstorming; for automated LLM-driven hypothesis testing on datasets use hypogenic.
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24. ▌
    Opentrons Integration · marielynneblock bundle

    Official Opentrons Protocol API for OT-2 and Flex robots. Use when writing protocols specifically for Opentrons hardware with full access to Protocol API v2 features. Best for production Opentrons protocols, official API compatibility. For multi-vendor automation or broader equipment control use pylabrobot.
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    Scientific Schematics · marielynneblock bundle

    Create publication-quality scientific diagrams using Nano Banana 2 AI with smart iterative refinement. Uses Gemini 3.1 Pro Preview for quality review. Only regenerates if quality is below threshold for your document type. Specialised in neural network architectures, system diagrams, flowcharts, biological pathways, and complex scientific visualisations.
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26. ▌
    Agent Governance Patterns · marielynneblock bundle

    Design and implement governance controls for tool-using and multi-agent AI systems, including policy enforcement, approval gates, audit trails, trust scoring, rate limits, and safe tool execution.
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27. ▌
    Model Recommendation · marielynneblock

    Analyse chatmode or prompt files and recommend optimal AI models based on task complexity, required capabilities, and cost-efficiency
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28. ▌
    Create Pytests · marielynneblock bundle

    Generates pytest test files for a Python codebase (or a targeted scope) that:
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    Latex Posters · marielynneblock bundle

    Create professional research posters in LaTeX using beamerposter, tikzposter, or baposter. Support for conference presentations, academic posters, and scientific communication. Includes layout design, colour schemes, multi-column formats, figure integration, and poster-specific best practices for visual communication.
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30. ▌
    Labarchive Integration · marielynneblock bundle

    Electronic lab notebook API integration. Access notebooks, manage entries/attachments, backup notebooks, integrate with Protocols.io/Jupyter/REDCap, for programmatic ELN workflows.
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31. ▌
    Data Breach Blast Radius · marielynneblock bundle

    Pre-breach impact analysis: inventories sensitive data (PII, PHI, PCI-DSS, credentials), traces data flows, scores exposure vectors, and produces a regulatory blast radius report with fine ranges sourced verbatim from GDPR Art. 83, CCPA § 1798.155(a), and HIPAA 45 CFR § 160.404. Cost benchmarks from IBM Cost of a Data Breach Report (annually updated). All citations in references/sources.md for verification. Use when asked: "assess breach impact", "what data could be exposed", "calculate blast radius", "data exposure analysis", "how bad would a breach be", "quantify data risk", "sensitive data inventory", "data flow security audit", "pre-breach assessment", "worst-case breach scenario", "breach readiness", "data risk report", "/data-breach-blast-radius". For any stack handling user data, health records, or financial information. Output labels law-sourced figures (exact) vs heuristic estimates (planning only). Does not replace legal counsel.
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32. ▌
    Eval Driven Dev · marielynneblock bundle

    Build an automated evaluation pipeline that tests a Python LLM application end-to-end with pixie test — real code paths, real LLM calls, instrumented external data — and scores outputs with evaluators instead of assertions. Use when adding evals to a Python AI app.
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33. ▌
    Nano Banana Pro Openrouter · marielynneblock bundle

    Generate or edit images via OpenRouter with the Gemini 3 Pro Image model. Use for prompt-only image generation, image edits, and multi-image compositing; supports 1K/2K/4K output.
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34. ▌
    Forecastic Evaluation · marielynneblock

    [TODO] Define the specific workflow this skill standardises, including default libraries, quality checks, and expected deliverables.
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35. ▌
    Pandas Data Wrangling · marielynneblock

    [TODO] Define the specific workflow this skill standardises, including default libraries, quality checks, and expected deliverables.
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36. ▌
    Pytest Coverage · marielynneblock

    Run pytest tests with coverage, discover lines missing coverage, and increase coverage to 100%.
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37. ▌
    Documentation Writer · marielynneblock

    Diátaxis Documentation Expert. An expert technical writer specialising in creating high-quality software documentation, guided by the principles and structure of the Diátaxis technical documentation authoring framework.
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38. ▌
    Clinicaltrials Database · marielynneblock bundle

    Query ClinicalTrials.gov via API v2. Search trials by condition, drug, location, status, or phase. Retrieve trial details by NCT ID, export data, for clinical research and patient matching.
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39. ▌
    Get Available Resources · marielynneblock bundle

    This skill should be used at the start of any computationally intensive scientific task to detect and report available system resources (CPU cores, GPUs, memory, disk space). It creates a JSON file with resource information and strategic recommendations that inform computational approach decisions such as whether to use parallel processing (joblib, multiprocessing), out-of-core computing (Dask, Zarr), GPU acceleration (PyTorch, JAX), or memory-efficient strategies. Use this skill before running analyses, training models, processing large datasets, or any task where resource constraints matter.
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    Iso 13485 Certification · marielynneblock bundle

    Comprehensive toolkit for preparing ISO 13485 certification documentation for medical device Quality Management Systems. Use when users need help with ISO 13485 QMS documentation, including (1) conducting gap analysis of existing documentation, (2) creating Quality Manuals, (3) developing required procedures and work instructions, (4) preparing Medical Device Files, (5) understanding ISO 13485 requirements, or (6) identifying missing documentation for medical device certification. Also use when users mention medical device regulations, QMS certification, FDA QMSR, EU MDR, or need help with quality system documentation.
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41. ▌
    Market Research Reports · marielynneblock bundle

    Generate comprehensive market research reports (50+ pages) in the style of top consulting firms (McKinsey, BCG, Gartner). Features professional LaTeX formatting, extensive visual generation with scientific-schematics and generate-image, deep integration with research-lookup for data gathering, and multi-framework strategic analysis including Porter Five Forces, PESTLE, SWOT, TAM/SAM/SOM, and BCG Matrix.
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42. ▌
    Protocolsio Integration · marielynneblock bundle

    Integration with protocols.io API for managing scientific protocols. This skill should be used when working with protocols.io to search, create, update, or publish protocols; manage protocol steps and materials; handle discussions and comments; organise workspaces; upload and manage files; or integrate protocols.io functionality into workflows. Applicable for protocol discovery, collaborative protocol development, experiment tracking, lab protocol management, and scientific documentation.
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43. ▌
    Dora Metrics Analysis · marielynneblock

    Use when calculating, validating, interpreting, or improving DORA software delivery performance metrics from GitHub, GitLab, Jira, incident-management, deployment, or Copilot usage data.
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44. ▌
    Numpy Scipy Statistics · marielynneblock

    [TODO] Define the specific workflow this skill standardises, including default libraries, quality checks, and expected deliverables.
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45. ▌
    Doublecheck · marielynneblock bundle

    Three-layer verification pipeline for AI output. Extracts verifiable claims, finds supporting or contradicting sources via web search, runs adversarial review for hallucination patterns, and produces a structured verification report with source links for human review.
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46. ▌
    Git Commit · marielynneblock

    Execute git commit with conventional commit message analysis, intelligent staging, and message generation. Use when user asks to commit changes, create a git commit, or mentions "/commit". Supports: (1) Auto-detecting type and scope from changes, (2) Generating conventional commit messages from diff, (3) Interactive commit with optional type/scope/description overrides, (4) Intelligent file staging for logical grouping
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47. ▌
    Md To DOCX · marielynneblock bundle

    Convert Markdown files to professionally formatted Word (.docx) documents with embedded PNG images — pure JavaScript, no external tools required
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48. ▌
    PPTX Nord Theme · marielynneblock bundle

    Build PowerPoint (.pptx) slide decks in a Nord-themed house style — Nord palette with a dark theme (default) and a light theme, Consolas mono figures, kicker + title + standfirst anatomy, white-on-dark cards with coloured accent bars, green takeaway banners, facilitation-grade speaker notes. Use this skill whenever the user asks for a deck, slides, a presentation, an onboarding session, an inspiration session, a workshop deck, a kickoff deck, or any .pptx output.
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49. ▌
    Markdown Mermaid Writing · marielynneblock bundle

    Markdown and Mermaid Writing
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50. ▌
    Scientific Brainstorming · marielynneblock bundle

    Creative research ideation and exploration. Use for open-ended brainstorming sessions, exploring interdisciplinary connections, challenging assumptions, or identifying research gaps. Best for early-stage research planning when you do not have specific observations yet. For formulating testable hypotheses from data use hypothesis-generation.
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    Scientific Visualisation · marielynneblock bundle

    Meta-skill for publication-ready figures. Use when creating journal submission figures requiring multi-panel layouts, significance annotations, error bars, colorblind-safe palettes, and specific journal formatting (Nature, Science, Cell). Orchestrates matplotlib/seaborn/plotly with publication styles. For quick exploration use seaborn or plotly directly.
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52. ▌
    Asset Self Containment Check · marielynneblock

    Check that a Copilot customisation asset (skill, workflow, agent, instruction, or prompt folder) stays standalone and copyable, with no runtime dependency on paths outside its own folder. Use when packaging an asset for reuse, reviewing whether an asset can be copied out of this repo, or investigating why a copied asset breaks elsewhere.
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53. ▌
    Statsmodels Time Series · marielynneblock

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

    Generate professional clinical decision support (CDS) documents for pharmaceutical and clinical research settings, including patient cohort analyses (biomarker-stratified with outcomes) and treatment recommendation reports (evidence-based guidelines with decision algorithms). Supports GRADE evidence grading, statistical analysis (hazard ratios, survival curves, waterfall plots), biomarker integration, and regulatory compliance. Outputs publication-ready LaTeX/PDF format optimised for drug development, clinical research, and evidence synthesis.
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    Pr Dashboard · marielynneblock bundle

    Open a GitHub PR dashboard in the browser. Use when the user asks to see their pull requests, open the PR dashboard, show PRs for a date range, or check PR status. Trigger phrases include "show my PRs", "open PR dashboard", "pull request dashboard".
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    Scientific Slides · marielynneblock bundle

    Build slide decks and presentations for research talks. Use this for making PowerPoint slides, conference presentations, seminar talks, research presentations, thesis defence slides, or any scientific talk. Provides slide structure, design templates, timing guidance, and visual validation. Works with PowerPoint and LaTeX Beamer.
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57. ▌
    Linkedin Post Formatter · marielynneblock bundle

    Format and draft compelling LinkedIn posts using Unicode bold/italic styling, visual separators, structured sections, and engagement-optimised patterns. USE FOR: draft LinkedIn post, format text for LinkedIn, create social media post, write thought leadership post, convert content to LinkedIn format, LinkedIn carousel text, Unicode bold italic formatting.
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58. ▌
    Esm · marielynneblock bundle

    Comprehensive toolkit for protein language models including ESM3 (generative multimodal protein design across sequence, structure, and function) and ESM C (efficient protein embeddings and representations). Use this skill when working with protein sequences, structures, or function prediction; designing novel proteins; generating protein embeddings; performing inverse folding; or conducting protein engineering tasks. Supports both local model usage and cloud-based Forge API for scalable inference.
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59. ▌
    Aeon · marielynneblock bundle

    This skill should be used for time series machine learning tasks including classification, regression, clustering, forecasting, anomaly detection, segmentation, and similarity search. Use when working with temporal data, sequential patterns, or time-indexed observations requiring specialised algorithms beyond standard ML approaches. Particularly suited for univariate and multivariate time series analysis with scikit-learn compatible APIs.
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60. ▌
    Cirq · marielynneblock bundle

    Google quantum computing framework. Use when targeting Google Quantum AI hardware, designing noise-aware circuits, or running quantum characterisation experiments. Best for Google hardware, noise modelling, and low-level circuit design. For IBM hardware use qiskit; for quantum ML with autodiff use pennylane; for physics simulations use qutip.
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61. ▌
    Gget · marielynneblock bundle

    Fast CLI/Python queries to 20+ bioinformatics databases. Use for quick lookups: gene info, BLAST searches, AlphaFold structures, enrichment analysis. Best for interactive exploration, simple queries. For batch processing or advanced BLAST use biopython; for multi-database Python workflows use bioservices.
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62. ▌
    Vaex · marielynneblock bundle

    Use this skill for processing and analysing large tabular datasets (billions of rows) that exceed available RAM. Vaex excels at out-of-core DataFrame operations, lazy evaluation, fast aggregations, efficient visualisation of big data, and machine learning on large datasets. Apply when users need to work with large CSV/HDF5/Arrow/Parquet files, perform fast statistics on massive datasets, create visualisations of big data, or build ML pipelines that do not fit in memory.
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63. ▌
    XLSX · marielynneblock

    Use this skill any time a spreadsheet file is the primary input or output. This means any task where the user wants to: open, read, edit, or fix an existing .xlsx, .xlsm, .csv, or .tsv file (e.g., adding columns, computing formulas, formatting, charting, cleaning messy data); create a new spreadsheet from scratch or from other data sources; or convert between tabular file formats. Trigger especially when the user references a spreadsheet file by name or path — even casually (like "the xlsx in my downloads") — and wants something done to it or produced from it. Also trigger for cleaning or restructuring messy tabular data files (malformed rows, misplaced headers, junk data) into proper spreadsheets. The deliverable must be a spreadsheet file. Do NOT trigger when the primary deliverable is a Word document, HTML report, standalone Python script, database pipeline, or Google Sheets API integration, even if tabular data is involved.
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64. ▌
    AI Ready · marielynneblock

    Guide users to review and install the external ai-ready skill from its upstream repository. Use when the user asks to install or try John Papa's ai-ready skill.
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65. ▌
    Remember · marielynneblock

    Transform lessons learned into domain-organised memory instructions for global or workspace scope. Syntax: `/remember [>domain [scope]] lesson clue`.
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66. ▌
    Gtars · marielynneblock bundle

    High-performance toolkit for genomic interval analysis in Rust with Python bindings. Use when working with genomic regions, BED files, coverage tracks, overlap detection, tokenization for ML models, or fragment analysis in computational genomics and machine learning applications.
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67. ▌
    Modal · marielynneblock bundle

    Cloud computing platform for running Python on GPUs and serverless infrastructure. Use when deploying AI/ML models, running GPU-accelerated workloads, serving web endpoints, scheduling batch jobs, or scaling Python code to the cloud. Use this skill whenever the user mentions Modal, serverless GPU compute, deploying ML models to the cloud, serving inference endpoints, running batch processing in the cloud, or needs to scale Python workloads beyond their local machine. Also use when the user wants to run code on H100s, A100s, or other cloud GPUs, or needs to create a web API for a model.
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68. ▌
    Pymoo · marielynneblock bundle

    Multi-objective optimisation framework. NSGA-II, NSGA-III, MOEA/D, Pareto fronts, constraint handling, benchmarks (ZDT, DTLZ), for engineering design and optimisation problems.
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69. ▌
    Pysam · marielynneblock bundle

    Genomic file toolkit. Read/write SAM/BAM/CRAM alignments, VCF/BCF variants, FASTA/FASTQ sequences, extract regions, calculate coverage, for NGS data processing pipelines.
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70. ▌
    Pytdc · marielynneblock bundle

    Therapeutics Data Commons. AI-ready drug discovery datasets (ADME, toxicity, DTI), benchmarks, scaffold splits, molecular oracles, for therapeutic ML and pharmacological prediction.
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71. ▌
    Qutip · marielynneblock bundle

    Quantum physics simulation library for open quantum systems. Use when studying master equations, Lindblad dynamics, decoherence, quantum optics, or cavity QED. Best for physics research, open system dynamics, and educational simulations. NOT for circuit-based quantum computing—use qiskit, cirq, or pennylane for quantum algorithms and hardware execution.
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72. ▌
    Rdkit · marielynneblock bundle

    Cheminformatics toolkit for fine-grained molecular control. SMILES/SDF parsing, descriptors (MW, LogP, TPSA), fingerprints, substructure search, 2D/3D generation, similarity, reactions. For standard workflows with simpler interface, use datamol (wrapper around RDKit). Use rdkit for advanced control, custom sanitization, specialised algorithms.
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73. ▌
    Rowan · marielynneblock bundle

    Cloud-based quantum chemistry platform with Python API. Preferred for computational chemistry workflows including pKa prediction, geometry optimisation, conformer searching, molecular property calculations, protein-ligand docking (AutoDock Vina), and AI protein cofolding (Chai-1, Boltz-1/2). Use when tasks involve quantum chemistry calculations, molecular property prediction, DFT or semiempirical methods, neural network potentials (AIMNet2), protein-ligand binding predictions, or automated computational chemistry pipelines. Provides cloud compute resources with no local setup required.
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74. ▌
    Simpy · marielynneblock bundle

    Process-based discrete-event simulation framework in Python. Use this skill when building simulations of systems with processes, queues, resources, and time-based events such as manufacturing systems, service operations, network traffic, logistics, or any system where entities interact with shared resources over time.
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75. ▌
    First Ask · marielynneblock

    Interactive task-refinement workflow that clarifies scope, deliverables, and constraints before carrying out the task. Uses Joyride input tools when available.
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76. ▌
    Noob Mode · marielynneblock bundle

    Plain-English response style for non-technical Copilot CLI users. Explains approval prompts, errors, command output, and technical choices with clear risk indicators.
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77. ▌
    Use Case · marielynneblock

    Produces a complete use case following the Cockburn/RUP format. A use case describes a goal-directed interaction between an actor and the system — capturing not just the happy path, but the extension flows (error, alternative, and exception paths) that user stories typically omit.
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78. ▌
    Dash · marielynneblock

    [TODO] Define the specific workflow this skill standardises, including default libraries, quality checks, and expected deliverables.
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79. ▌
    Dask · marielynneblock bundle

    Distributed computing for larger-than-RAM pandas/NumPy workflows. Use when you need to scale existing pandas/NumPy code beyond memory or across clusters. Best for parallel file processing, distributed ML, integration with existing pandas code. For out-of-core analytics on single machine use vaex; for in-memory speed use polars.
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80. ▌
    Pymc · marielynneblock bundle

    Bayesian modelling with PyMC. Build hierarchical models, MCMC (NUTS), variational inference, LOO/WAIC comparison, posterior checks, for probabilistic programming and inference.
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81. ▌
    Shap · marielynneblock bundle

    Model interpretability and explainability using SHAP (SHapley Additive exPlanations). Use this skill when explaining machine learning model predictions, computing feature importance, generating SHAP plots (waterfall, beeswarm, bar, scatter, force, heatmap), debugging models, analysing model bias or fairness, comparing models, or implementing explainable AI. Works with tree-based models (XGBoost, LightGBM, Random Forest), deep learning (TensorFlow, PyTorch), linear models, and any black-box model.
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82. ▌
    Depmap · marielynneblock bundle

    Query the Cancer Dependency Map (DepMap) for cancer cell line gene dependency scores (CRISPR Chronos), drug sensitivity data, and gene effect profiles. Use for identifying cancer-specific vulnerabilities, synthetic lethal interactions, and validating oncology drug targets.
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83. ▌
    Flowio · marielynneblock bundle

    Parse FCS (Flow Cytometry Standard) files v2.0-3.1. Extract events as NumPy arrays, read metadata/channels, convert to CSV/DataFrame, for flow cytometry data preprocessing.
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84. ▌
    Geniml · marielynneblock bundle

    This skill should be used when working with genomic interval data (BED files) for machine learning tasks. Use for training region embeddings (Region2Vec, BEDspace), single-cell ATAC-seq analysis (scEmbed), building consensus peaks (universes), or any ML-based analysis of genomic regions. Applies to BED file collections, scATAC-seq data, chromatin accessibility datasets, and region-based genomic feature learning.
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85. ▌
    Matlab · marielynneblock bundle

    MATLAB and GNU Octave numerical computing for matrix operations, data analysis, visualisation, and scientific computing. Use when writing MATLAB/Octave scripts for linear algebra, signal processing, image processing, differential equations, optimisation, statistics, or creating scientific visualisations. Also use when the user needs help with MATLAB syntax, functions, or wants to convert between MATLAB and Python code. Scripts can be executed with MATLAB or the open-source GNU Octave interpreter.
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86. ▌
    Pathml · marielynneblock bundle

    Full-featured computational pathology toolkit. Use for advanced WSI analysis including multiplexed immunofluorescence (CODEX, Vectra), nucleus segmentation, tissue graph construction, and ML model training on pathology data. Supports 160+ slide formats. For simple tile extraction from H&E slides, histolab may be simpler.
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87. ▌
    Qiskit · marielynneblock bundle

    IBM quantum computing framework. Use when targeting IBM Quantum hardware, working with Qiskit Runtime for production workloads, or needing IBM optimisation tools. Best for IBM hardware execution, quantum error mitigation, and enterprise quantum computing. For Google hardware use cirq; for gradient-based quantum ML use pennylane; for open quantum system simulations use qutip.
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88. ▌
    Scanpy · marielynneblock bundle

    Standard single-cell RNA-seq analysis pipeline. Use for QC, normalisation, dimensionality reduction (PCA/UMAP/t-SNE), clustering, differential expression, and visualisation. Best for exploratory scRNA-seq analysis with established workflows. For deep learning models use scvi-tools; for data format questions use anndata.
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89. ▌
    Scvelo · marielynneblock bundle

    RNA velocity analysis with scVelo. Estimate cell state transitions from unspliced/spliced mRNA dynamics, infer trajectory directions, compute latent time, and identify driver genes in single-cell RNA-seq data. Complements Scanpy/scVI-tools for trajectory inference.
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90. ▌
    Adaptyv · marielynneblock bundle

    Cloud laboratory platform for automated protein testing and validation. Use when designing proteins and needing experimental validation including binding assays, expression testing, thermostability measurements, enzyme activity assays, or protein sequence optimisation. Also use for submitting experiments via API, tracking experiment status, downloading results, optimising protein sequences for better expression using computational tools (NetSolP, SoluProt, SolubleMPNN, ESM), or managing protein design workflows with wet-lab validation.
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91. ▌
    Anndata · marielynneblock bundle

    Data structure for annotated matrices in single-cell analysis. Use when working with .h5ad files or integrating with the scverse ecosystem. This is the data format skill—for analysis workflows use scanpy; for probabilistic models use scvi-tools; for population-scale queries use cellxgene-census.
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92. ▌
    Astropy · marielynneblock bundle

    Comprehensive Python library for astronomy and astrophysics. This skill should be used when working with astronomical data including celestial coordinates, physical units, FITS files, cosmological calculations, time systems, tables, world coordinate systems (WCS), and astronomical data analysis. Use when tasks involve coordinate transformations, unit conversions, FITS file manipulation, cosmological distance calculations, time scale conversions, or astronomical data processing.
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93. ▌
    Cobrapy · marielynneblock bundle

    Constraint-based metabolic modelling (COBRA). FBA, FVA, gene knockouts, flux sampling, SBML models, for systems biology and metabolic engineering analysis.
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94. ▌
    Datamol · marielynneblock bundle

    Pythonic wrapper around RDKit with simplified interface and sensible defaults. Preferred for standard drug discovery including SMILES parsing, standardisation, descriptors, fingerprints, clustering, 3D conformers, parallel processing. Returns native rdkit.Chem.Mol objects. For advanced control or custom parameters, use rdkit directly.
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95. ▌
    Denario · marielynneblock bundle

    Multiagent AI system for scientific research assistance that automates research workflows from data analysis to publication. This skill should be used when generating research ideas from datasets, developing research methodologies, executing computational experiments, performing literature searches, or generating publication-ready papers in LaTeX format. Supports end-to-end research pipelines with customisable agent orchestration.
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96. ▌
    Lamindb · marielynneblock bundle

    This skill should be used when working with LaminDB, an open-source data framework for biology that makes data queryable, traceable, reproducible, and FAIR. Use when managing biological datasets (scRNA-seq, spatial, flow cytometry, etc.), tracking computational workflows, curating and validating data with biological ontologies, building data lakehouses, or ensuring data lineage and reproducibility in biological research. Covers data management, annotation, ontologies (genes, cell types, diseases, tissues), schema validation, integrations with workflow managers (Nextflow, Snakemake) and MLOps platforms (W&B, MLflow), and deployment strategies.
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97. ▌
    Matchms · marielynneblock bundle

    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.
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98. ▌
    Medchem · marielynneblock bundle

    Medicinal chemistry filters. Apply drug-likeness rules (Lipinski, Veber), PAINS filters, structural alerts, complexity metrics, for compound prioritisation and library filtering.
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99. ▌
    Molfeat · marielynneblock bundle

    Molecular featurization for ML (100+ featurizers). ECFP, MACCS, descriptors, pretrained models (ChemBERTa), convert SMILES to features, for QSAR and molecular ML.
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100. ▌
     Primekg · marielynneblock bundle

     Query the Precision Medicine Knowledge Graph (PrimeKG) for multiscale biological data including genes, drugs, diseases, phenotypes, and more.
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