Skill UI

A systematic tool for scientific inquiry, guiding users through the entire research process. It helps formulate testable, mechanistic hypotheses from raw observations or preliminary data, following the established scientific method. The workflow includes comprehensive literature review, evidence synthesis, generating competing explanations, and designing experiments, all while mandating the creation of scientific schematics for visualization.

This skill provides comprehensive integration with the LabArchives Electronic Lab Notebook (ELN) platform via its REST API. It allows users to programmatically manage notebooks, retrieve user data, automate entry creation, upload diverse attachments (PDF, CSV, images), perform full notebook backups, and generate detailed usage reports. Ideal for automating scientific workflows and integrating ELN data with tools like Jupyter or REDCap.

Latch is a robust Python framework designed for building, deploying, and managing complex, scalable bioinformatics workflows as serverless pipelines. It supports integrating multiple analysis tools (like Nextflow/Snakemake) and handles cloud data management (LatchFile/LatchDir) and detailed resource configuration (GPU, CPU, memory). Ideal for running large-scale analyses such as RNA-seq, AlphaFold, and single-cell analysis in a reproducible, production-ready environment.

This advanced skill generates comprehensive, professional-grade market research reports (50+ pages) modeled after top consulting firm deliverables (McKinsey, BCG). It supports deep data analysis using research-lookup, multi-framework strategic assessment (PESTLE, SWOT, Porter's Five Forces), and extensive visual generation using scientific schematics and image generation tools. The output is in professional LaTeX format, compiled to PDF, suitable for strategic planning, investment decisions, and thought leadership.

MarkItDown is a powerful tool designed to convert a wide array of file types—including PDF, DOCX, images, audio, and structured data (JSON/XML)—into clean, token-efficient Markdown format. It supports advanced features like OCR for scanned documents, transcription for audio, and AI-enhanced descriptions, making diverse content readily consumable and structured for modern Language Models and AI pipelines.

Matplotlib is Python's foundational library for creating highly customizable static, animated, and interactive visualizations. It supports various plot types (line, scatter, heatmap, 3D) and offers both pyplot and object-oriented interfaces. Ideal for generating publication-quality scientific charts, complex multi-panel figures, and integrating into notebooks.

Perform comprehensive molecular dynamics (MD) simulations using high-performance engines like OpenMM and analysis tools like MDAnalysis. This skill allows users to model the time evolution of biological systems, covering system preparation (solvation, force field assignment), energy minimization, NVT equilibration, and advanced analysis (RMSD, free energy surfaces). Ideal for structural biology, drug binding studies, and biophysics research.

NeuroKit2 is a comprehensive Python toolkit designed for processing and analyzing diverse physiological biosignals. It covers multiple domains including cardiovascular (ECG, PPG), neural (EEG), autonomic (EDA), respiratory (RSP), and muscular (EMG) signals. Use this skill for advanced psychophysiology research, complex pattern detection, and real-time clinical monitoring applications.

An end-to-end toolkit designed for analyzing high-density Neuropixels electrophysiology recordings. It implements best practices using SpikeInterface, covering the entire workflow: data loading (SpikeGLX, NWB), preprocessing, motion/drift correction, advanced spike sorting (Kilosort4), quality metric computation, and unit curation (including AI-assisted review). Ideal for neuroscience research.

PathML is a comprehensive Python framework designed for computational pathology workflows. It supports end-to-end analysis of Whole Slide Images (WSI), including loading 160+ proprietary formats, performing advanced stain normalization and tissue segmentation, constructing spatial cell graphs, and training deep learning models (e.g., HoVer-Net) for multiplex immunofluorescence and spatial proteomics. Ideal for large-scale biomedical image analysis.

This comprehensive skill provides a standardized pipeline for reconstructing the evolutionary history of biological sequences (genes, proteins, genomes). It guides users through essential steps, including multiple sequence alignment using MAFFT, maximum likelihood tree inference with IQ-TREE 2, and visualization with ETE3. Ideal for research in viral phylodynamics, molecular clock studies, and large-scale comparative genomics.

Polars is a lightning-fast DataFrame library built on Apache Arrow for Python. It provides an expression-based API, lazy query optimization, and parallel computation capabilities for efficient data manipulation, analytics, and ETL pipelines. It is designed to handle large, memory-intensive datasets, making it an ideal alternative for migrating from pandas or optimizing complex data workflows.