Skill UI

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.

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.

Matchms is an open-source Python library designed for comprehensive mass spectrometry data processing. It handles spectrum comparison, calculates various similarity scores (like cosine and modified cosine), and aids in identifying unknown compounds. It is highly valuable for metabolomics and spectral library searching pipelines.

A comprehensive guide to MATLAB and GNU Octave, covering core scientific computing tasks. This skill details capabilities in matrix operations, linear algebra, data visualization (2D/3D), statistical analysis, signal processing, and solving differential equations. It is ideal for users requiring complex numerical simulation, data modeling, and scientific scripting.

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.

Medchem is a powerful Python library designed for molecular filtering and prioritization in drug discovery. It allows users to apply rigorous, literature-derived drug-likeness rules (e.g., Lipinski, Veber, CNS), detect structural alerts (PAINS, NIBR), calculate complexity metrics, and combine multiple criteria using a custom query language. It is essential for compound library triage and hit-to-lead optimization.

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.

NetworkX is a powerful Python library used for creating, manipulating, and analyzing complex networks and graphs. It supports graph structures (directed/undirected, multi-edges) and provides extensive algorithms for tasks such as finding shortest paths, calculating centrality measures (e.g., PageRank), detecting communities, and simulating various network types (e.g., scale-free, small-world). Ideal for social science, biology, and transportation network modeling.

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.

This skill provides a comprehensive Python API integration for the OMERO platform, an open-source solution for managing and analyzing large-scale microscopy datasets. Users can programmatically access images, retrieve structured data, analyze raw pixel data, manage complex annotations (ROIs), and execute batch processing workflows essential for high-content screening and advanced biological research.