Uncertainty-aware visual analysis of biochemical reaction networks

Abstract

We present a visual analytics system that supports an uncertaintyaware analysis of static and dynamic attributes of biochemical reaction networks (BRNs). These are often described by mathematical models, such as ordinary differential equations (ODEs), which enable the integration of a multitude of different data and data types using parameter estimation. Due to the limited amount of data, parameter estimation does not necessarily yield a single point in parameter space and many attributes of the model remain uncertain. Our system visualizes the model as a graph, where the statistics of the attributes are mapped to the color of edges and vertices. The graph view is combined with several linked views such as lineplots, scatterplots, and correlation matrices, to support the identification of uncertainties and the analysis of their mutual dependencies as well as their time dependencies. To assess the utility of the individual visualization approaches and multiple linked views, a qualitative user study with domain experts was performed. We found that all users were able to process analysis tasks using our system.

iVUN: interactive Visualization of Uncertain biochemical reaction Networks

“…iVUN incorporates animation and linked line plots to visualize attribute dynamics (see Figure 2: dynamics). The animation allows the user to obtain an overview, e.g., to detect drastic changes, and to identify hubs of similar dynamics [6]. Thereby, the time-dependent means or standard deviations of the sample ${MathClass-open\{v^{MathClass-open(\alpha MathClass-close)}MathClass-open(tMathClass-close)MathClass-close\}}_{\alpha =1}^{n_{\text{textsfsans-serifs}}}MathClass-open({MathClass-open\{x^{MathClass-open(\alpha MathClass-close)}MathClass-open(tMathClass-close)MathClass-close\}}_{\alpha =1}^{n_{\text{textsfsans-serifs}}}MathClass-close)$ are mapped to the color of the respective link (node).…”

“…To assess the utility of the individual visualization approaches and multiple linked views of iVUN , a qualitative user study with 10 domain experts was performed. A more detailed description of the design process as well as the design and results of the qualitative user study can be found in our previous work on the uncertainty-aware visual analysis of BRNs [ 6 ].…”

“…iVUN incorporates animation and linked line plots to visualize attribute dynamics (see Figure 2 : dynamics). The animation allows the user to obtain an overview, e.g., to detect drastic changes, and to identify hubs of similar dynamics [ 6 ]. Thereby, the time-dependent means or standard deviations of the sample are mapped to the color of the respective link (node).…”

“…For more details on the visualization tools and the implementation, we refer to the documentation of iVUN ( http://www.vis.uni-stuttgart.de/iVUN ) and our previous publication [ 6 ].…”

“…Furthermore, a multitude of linked views, such as line plots, scatter plots, and correlation matrices, are available to enable the user to explore the BRN model and its uncertainties. We note that this manuscript is based on a conference paper we published at the 2nd IEEE Symposium on Biological Data Visualization [ 6 ] and uses original material thereof. In contrast to this visualization paper, here, we focus on the application to biological data obtained from experiments and included an extensive case study.…”