Interactive Multiresolution Visualization of Cellular Network Processes.

Clicks: 335
ID: 74812
2019
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Abstract
Visualization plays a central role in the analysis of biochemical network models to identify patterns that arise from reaction dynamics and perform model exploratory analysis. To facilitate these analyses, we developed PyViPR, a visualization tool that generates static and dynamic representations of biochemical network processes within a Python-based environment. PyViPR embeds network visualizations within Jupyter notebooks, thus enabling integration with modeling, simulation, and analysis workflows. To present the capabilities of PyViPR, we explore execution mechanisms of extrinsic apoptosis in HeLa cells. We show that community-detection algorithms identify groups of molecular species that capture key biological functions and ease exploration of the apoptosis network. We then show how different kinetic parameter sets that fit the experimental data equally well exhibit significantly different signal-execution dynamics as the system progresses toward mitochondrial outer-membrane permeabilization. Therefore, PyViPR aids the conceptual understanding of dynamic network processes and accelerates hypothesis generation for further testing and validation.
Reference Key
ortega2019interactiveiscience Use this key to autocite in the manuscript while using SciMatic Manuscript Manager or Thesis Manager
Authors Ortega, Oscar O;Lopez, Carlos F;
Journal iScience
Year 2019
DOI
S2589-0042(19)30493-6
URL
Keywords
systems biology bioinformatics integrative aspects of cell biology

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