Skill UI

Run OpenMM-powered molecular dynamics simulations and MDAnalysis trajectory workflows to build protein or small-molecule systems, minimize energy, equilibrate conditions, and characterize RMSD/RMSF, contacts, and free-energy surfaces for structural biology or drug studies.

A comprehensive toolkit for reconstructing and analyzing the evolutionary history of biological sequences (genes, proteins, genomes). The standard workflow includes multiple sequence alignment using MAFFT, robust maximum likelihood tree inference with IQ-TREE 2 and FastTree, and advanced visualization/manipulation using ETE3. This skill is essential for studies in viral phylodynamics, microbial genomics, protein family evolution, and molecular clock dating.

A comprehensive toolkit for running and analyzing molecular dynamics (MD) simulations. This skill covers the entire workflow: system setup, force field definition, energy minimization, and equilibration using industry-standard tools like OpenMM and MDAnalysis. Essential for structural biology, drug binding studies, and biophysics research.

This comprehensive toolkit facilitates the entire phylogenetic analysis workflow, from sequence alignment to tree inference. It integrates industry-standard tools like MAFFT for multiple sequence alignment, TrimAl for alignment trimming, and powerful maximum likelihood methods using IQ-TREE 2 or FastTree. Ideal for molecular genomics, tracing viral phylodynamics, studying protein evolution, or conducting molecular clock analysis. Built using Python for seamless integration.

Rowan is a cloud-native workflow platform providing a unified Python API for complex molecular modeling and medicinal chemistry tasks. It handles property prediction (pKa, descriptors), conformational analysis, molecular docking, and molecular dynamics. Users can run scalable, multi-step drug discovery pipelines and batch screening campaigns without managing local high-performance computing infrastructure.

Generate data analysis reports by exploring database tables, running multidimensional SQL queries, performing deep attribution analysis, and outputting dynamic HTML visual reports with ECharts for business, trend, and KPI scenarios.

A comprehensive skill for creating, editing, and analyzing complex spreadsheets (.xlsx, .csv, etc.). This skill excels in financial modeling, ensuring all calculations are managed via dynamic Excel formulas rather than hardcoded values. It supports data analysis using pandas, rigorous formatting standards, and complex formula integrity checks, making it ideal for financial reporting and data visualization.

This guide provides comprehensive methodological frameworks for designing rigorous empirical studies suitable for top-tier academic journals. It helps researchers match theoretical claims (e.g., causal effects, cross-level dynamics) to appropriate designs (experiments, panel data, qualitative analysis). It details how to proactively address major threats like Common-Method Bias, Endogeneity, and inconsistent levels of analysis, ensuring high internal and external validity.

A comprehensive guide for environmental economists on transforming raw analysis results into publication-grade exhibits suitable for JEEM/Elsevier. Focuses on moving beyond simple regression coefficients to visualize spatial variation (maps), temporal dynamics (event studies), and welfare changes (WTP curves), ensuring the core environmental signal is clearly communicated to referees and readers.

This comprehensive guide provides rigorous methodological guidelines for executing and reporting empirical analysis on cross-national, multi-level, or panel data, specifically tailored for top-tier international business journals. It covers essential checks like measurement invariance (configural to scalar), Common Method Variance (CMV), dynamic endogeneity, and appropriate estimation techniques (e.g., Multilevel SEM, GMM), ensuring research meets the highest academic standards.

A comprehensive skill for Particle Image Velocimetry (PIV) analysis. It processes pairs of images to measure 2D fluid velocity fields. Functions include cross-correlation, vector validation, outlier replacement, and calculating derived metrics like vorticity and strain rate. Essential for experimental fluid dynamics visualization and analysis.

This guide outlines the rigorous analytical methodology required for Operations Research (OR) manuscripts. It instructs users on selecting the appropriate mathematical machinery—such as duality, dynamic programming, convergence analysis, or concentration inequalities—to establish provable guarantees, approximation factors, and algorithmic complexity. It ensures that claims are backed by rigorous proofs, moving beyond mere heuristics.