A network approach to genetic circuit designs

Abstract

Visualising the complex information captured by synthetic biology designs is still a major challenge. The popular glyph approach where each genetic part is displayed on a linear sequence allows researchers to generate diagrams and visualise abstract designs, but only represents a single, static representation that results in visualisation that is not specific to the requirements of a user resulting in a one-size-fits-all visualisation. We developed a network visualisation technique that automatically turns all design information into a graph, displaying otherwise hidden data. The structure of the resulting graphs can be dynamically adjusted according to specific visualisation requirements, such as highlighting proteins, interactions or hierarchy. Since biological systems have an inherent affinity with network visualisation, we advocate for adopting this approach to standardise and automate the representation of complex information.

Overview of methods for characterization and visualization of a protein–protein interaction network in a multi-omics integration context

“…Visual representation allows to understanding PPIs and to analyze networks ( Iranzo, Krupovic and Koonin, 2016 ; Armanious et al, 2020 ; Schneider et al, 2021 ; Sejdiu and Tieleman, 2021 ). However, due to complexity of proteomes of different organisms, visualization is a challenge ( Crowther, Wipat and Goñi-Moreno, 2021 ). Moreover, the density of the graph representing the proportion of interactions in the network compared to the total number of possible interactions makes representation more difficult ( Ren et al, 2013 ; Franzese et al, 2019 ; Wu et al, 2019 ).…”