Interactive Visualization of Protein RINs using NetworKit in the Cloud
This work addresses the problem of accessibility and customization in protein network visualization for domain scientists, though it is incremental as it builds on existing tools like NetworKit.
The paper tackles the challenge of enabling domain scientists to visualize and analyze protein residue interaction networks (RINs) without extensive technical expertise by developing a cloud-based environment using NetworKit, resulting in a customizable Jupyter widget that offers near real-time speed and easy integration into analysis pipelines.
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).