Interactive Visualization of Protein RINs using NetworKit in the Cloud

• URL: http://arxiv.org/abs/2203.01263v1
• Date: Wed, 2 Mar 2022 17:41:45 GMT
• Title: Interactive Visualization of Protein RINs using NetworKit in the Cloud
• Authors: Eugenio Angriman, Fabian Brandt-Tumescheit, Leon Franke, Alexander van der Grinten, Henning Meyerhenke
• Abstract summary: In this paper, we consider an example from protein dynamics, specifically residue interaction networks (RINs) We use NetworKit to build a cloud-based environment that enables domain scientists to run their visualization and analysis on large compute servers. To demonstrate the versatility of this approach, we use it to build a custom Jupyter-based widget for RIN visualization.
• Score: 57.780880387925954
• License: http://arxiv.org/licenses/nonexclusive-distrib/1.0/
• 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).

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