Interactive Visualization of Protein RINs using NetworKit in the Cloud

TL;DR

This paper presents a cloud-based, customizable, and real-time visualization tool for protein residue interaction networks (RINs) using NetworKit, facilitating easier analysis for domain scientists without extensive programming skills.

Contribution

It introduces a cloud environment with a Jupyter widget for RIN visualization that is customizable, fast, and easily integrated into analysis workflows, advancing existing visualization methods.

Findings

Supports near real-time visualization speeds

Easily customizable through Python code

Integrates seamlessly with analysis pipelines

Abstract

Network analysis has been applied in diverse application domains. In this paper, we consider an example from protein dynamics, specifically residue interaction networks (RINs). In this context, we use NetworKit -- an established package for network analysis -- to build a cloud-based environment that enables domain scientists to run their visualization and analysis workflows on large compute servers, without requiring extensive programming and/or system administration knowledge. To demonstrate the versatility of this approach, we use it to build a custom Jupyter-based widget for RIN visualization. In contrast to existing RIN visualization approaches, our widget can easily be customized through simple modifications of Python code, while both supporting a good feature set and providing near real-time speed. It is also easily integrated into analysis pipelines (e.g., that use Python to feed RIN data into downstream machine learning tasks).