2D, 2.5D, or 3D? An Exploratory Study on Multilayer Network Visualisations in Virtual Reality.

Relational information between different types of entities is often modelled by a multilayer network (MLN) - a network with subnetworks represented by layers. The layers of an MLN can be arranged in different ways in a visual representation, however, the impact of the arrangement on the readability of the network is an open question. Therefore, we studied this impact for several commonly occurring tasks related to MLN analysis. Additionally, layer arrangements with a dimensionality beyond 2D, which are common in this scenario, motivate the use of stereoscopic displays. We ran a human subject study utilising a Virtual Reality headset to evaluate 2D, 2.5D, and 3D layer arrangements. The study employs six analysis tasks that cover the spectrum of an MLN task taxonomy, from path finding and pattern identification to comparisons between and across layers. We found no clear overall winner. However, we explore the task-to-arrangement space and derive empirical-based recommendations on the effective use of 2D, 2.5D, and 3D layer arrangements for MLNs.

Operationalizing anthropological theory: four techniques to simplify networks of co-occurring ethnographic codes.

The use of data and algorithms in the social sciences allows for exciting progress, but also poses epistemological challenges. Operations that appear innocent and purely technical may profoundly influence final results. Researchers working with data can make their process less arbitrary and more accountable by making theoretically grounded methodological choices. We apply this approach to the problem of simplifying networks representing ethnographic corpora, in the interest of visual interpretation. Network nodes represent ethnographic codes, and their edges the co-occurrence of codes in a corpus. We introduce and discuss four techniques to simplify such networks and facilitate visual analysis. We show how the mathematical characteristics of each one are aligned with an identifiable approach in sociology or anthropology: structuralism and post-structuralism; identifying the central concepts in a discourse; and discovering hegemonic and counter-hegemonic clusters of meaning. We then provide an example of how the four techniques complement each other in ethnographic analysis.

Ten simple rules to create biological network figures for communication.

Biological network figures are ubiquitous in the biology and medical literature. On the one hand, a good network figure can quickly provide information about the nature and degree of interactions between items and enable inferences about the reason for those interactions. On the other hand, good network figures are difficult to create. In this paper, we outline 10 simple rules for creating biological network figures for communication, from choosing layouts, to applying color or other channels to show attributes, to the use of layering and separation. These rules are accompanied by illustrative examples. We also provide a concise set of references and additional resources for each rule.

Strategy-Driven Exploration for Rule-Based Models of Biochemical Systems with PORGY.

This chapter presents PORGY-an interactive visual environment for rule-based modelling of biochemical systems. We model molecules and molecule interactions as port graphs and port graph rewrite rules, respectively. We use rewriting strategies to control which rules to apply, and where and when to apply them. Our main contributions to rule-based modelling of biochemical systems lie in the strategy language and the associated visual and interactive features offered by PORGY. These features facilitate an exploratory approach to test different ways of applying the rules while recording the model evolution, and tracking and plotting parameters. We illustrate PORGY's features with a study of the role of a scaffold protein in RAF/MEK/ERK signalling.