Volume 19, Issue 2 - Special Issue: Design X Bioinformatics; Guest Editors: Björn Sommer, Daisuke Inoue and Marc Baaden

Bioinformatics applies computer science approaches to the analysis of biological data. It is widely known for its genomics-based analysis approaches that have supported, for example, the 1000 Genomes Project. In addition, bioinformatics relates to many other areas, such as analysis of microscopic images (e.g., organelle localization), molecular modelling (e.g., proteins, biological membranes), and visualization of biological networks (e.g., protein–protein interaction networks, metabolism). Design is a highly interdisciplinary field that incorporates aspects such as aesthetic, economic, functional, philosophical, and/or socio-political considerations into the creative process and is usually determined by context. While visualization plays a critical role in bioinformatics, as reflected in a number of conferences and workshops in the field, design in bioinformatics-related research contexts in particular is not as well studied. With this special issue in conjunction with an international workshop, we aim to bring together bioinformaticians from different fields with designers, design researchers, and medical and scientific illustrators to discuss future challenges in the context of bioinformatics and design.

Data from genomics, proteomics, structural biology and cryo-electron microscopy are integrated into a structural illustration of a cross section through an entire JCVI-syn3.0 minimal cell. The illustration is designed with several goals: to inspire excitement in science, to depict the underlying scientific results accurately, and to be feasible in traditional media. Design choices to achieve these goals include reduction of visual complexity with simplified representations, use of orthographic projection to retain scale relationships, and an approach to color that highlights functional compartments of the cell. Given that this simple cell provides an attractive laboratory for exploring the central processes needed for life, several functional narratives are included in the illustration, including division of the cell and the first depiction of an entire cellular proteome. The illustration lays the foundation for 3D molecular modeling of this cell.

Visual representations are commonly used to explore, analyse, and communicate information and knowledge in systems biology and beyond. Such visualisations not only need to be accurate but should also be aesthetically pleasing and informative. Using the example of the Systems Biology Graphical Notation (SBGN) we will investigate design considerations for graphically presenting information from systems biology, in particular regarding the use of glyphs for types of information, the style of graph layout for network representation, and the concept of bricks for visual network creation.

We discuss how design enriches molecular science, particularly structural biology and bioinformatics. We present two use cases, one in academic practice and the other to design for outreach. The first case targets the representation of ion channels and their dynamic properties. In the second, we document a transition process from a research environment to general-purpose designs. Several testimonials from practitioners are given. By describing the design process of abstracted shapes, exploded views of molecular structures, motion-averaged slices, 360-degree panoramic projections, and experiments with lit sphere shading, we document how designers help make scientific data accessible without betraying its meaning, and how a creative mind adds value over purely data-driven visualizations. A similar conclusion was drawn for public outreach, as we found that comic-book-style drawings are better suited for communicating science to a broad audience.

Among the many properties of proteins, sugars, nucleic acids, membranes and other cellular components, color is not present. At the same time, we humans have a natural ability of recognizing and appreciating colors, and use them generously, with the aim of both delivering information and pleasing the eyes. In this article, I suggest how we can conciliate these two situations, with the contribution of biologists, artists, and computer graphics and perception experts. The concept can be developed in a series of initiatives involving the community, including discussion sessions, technical challenges, experimental studies and outreach activities.

Biomedical illustration and visualization techniques provide a window into complex molecular worlds that are difficult to capture through experimental means alone. Biomedical illustrators frequently employ color to help tell a molecular story, e.g., to identify key molecules in a signaling pathway. Currently, color use for molecules is largely arbitrary and often chosen based on the client, cultural factors, or personal taste. The study of molecular dynamics is relatively young, and some stakeholders argue that color use guidelines would throttle the growth of the field. Instead, content authors have ample creative freedom to choose an aesthetic that, e.g., supports the story they want to tell. However, such creative freedom comes at a price. The color design process is challenging, particularly for those without a background in color theory. The result is a semantically inconsistent color space that reduces the interpretability and effectiveness of molecular visualizations as a whole. Our contribution in this paper is threefold. We first discuss some of the factors that contribute to this array of color palettes. Second, we provide a brief sampling of color palettes used in both industry and research sectors. Lastly, we suggest considerations for developing best practices around color palettes applied to molecular visualization.