Skill UI

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.

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.

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.

Molfeat is a comprehensive Python library designed for molecular featurization. It converts chemical structures (SMILES/RDKit) into numerical feature vectors, supporting over 100 featurizers like ECFP, MACCS, and deep embeddings (ChemBERTa). It unifies featurization pipelines, making it ideal for QSAR modeling, virtual screening, and integrating into deep learning ML workflows.

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.

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.

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.

A systematic framework designed for conducting rigorous peer reviews of scientific manuscripts and grant proposals. It provides a structured, checklist-based evaluation covering methodology rigor, statistical validity, reporting compliance (e.g., CONSORT, STROBE), and assesses all sections from abstract to results. Ideal for academic publishing, research quality assessment, and providing detailed, constructive feedback.

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.