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.

This guide provides rigorous guidelines for creating high-quality figures and tables for complex systems manuscripts, especially in agricultural science. It emphasizes shifting focus from single-factor bar charts to systemic visualizations that reveal interactions, trade-offs (e.g., Pareto fronts), model dynamics, resource flows (Sankey diagrams), and model performance (observed-vs-simulated fit). Exhibits must be self-contained, reproducible, and convey uncertainty.

This guide provides a comprehensive framework for understanding the academic peer review process used at AISTATS, covering everything from OpenReview submission workflows and author-reviewer dynamics to advanced decision criteria (correctness, significance, empirical support). It helps researchers strategize their submissions and responses to maximize acceptance chances in statistics and machine learning.

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.

This skill provides a comprehensive pre-submission checklist for manuscripts targeting Atmospheric Chemistry and Physics (ACP), an EGU journal. It details the journal's scope—covering aerosols, clouds, chemistry, and dynamics—and outlines the rigorous standards required, including open-access policies, mandatory FAIR data practices, detailed methodological transparency, and preparation for interactive public peer review. Use this guide to assess the fit and completeness of your scientific work.

This guide provides rigorous guidelines for designing and presenting results in Experimental Economics manuscripts. It emphasizes making the treatment comparison and its uncertainty immediately visible through specific figure types (distributions, dynamics plots) and structured tables, ensuring the findings are self-contained and highly credible for academic review.

A comprehensive guide to the rigorous, multi-stage peer review process for top-tier data engineering conferences like ICDE. It details the two-round structure, area-chair coordination, single-blind dynamics, and the high standards set by 'builder-heavy' reviewers. Use this to strategize paper submission, understand key evaluation dimensions (novelty, soundness, evaluation), and anticipate common review objections.

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.