Snowflake: visualizing microbiome abundance tables as multivariate bipartite graphs.

Current visualizations in microbiome research rely on aggregations in taxonomic classifications or do not show less abundant taxa. We introduce Snowflake: a new visualization method that creates a clear overview of the microbiome composition in collected samples without losing any information due to classification or neglecting less abundant reads. Snowflake displays every observed OTU/ASV in the microbiome abundance table and provides a solution to include the data's hierarchical structure and additional information obtained from downstream analysis (e.g., alpha- and beta-diversity) and metadata. Based on the value-driven ICE-T evaluation methodology, Snowflake was positively received. Experts in microbiome research found the visualizations to be user-friendly and detailed and liked the possibility of including and relating additional information to the microbiome's composition. Exploring the topological structure of the microbiome abundance table allows them to quickly identify which taxa are unique to specific samples and which are shared among multiple samples (i.e., separating sample-specific taxa from the core microbiome), and see the compositional differences between samples. An R package for constructing and visualizing Snowflake microbiome composition graphs is available at https://gitlab.com/vda-lab/snowflake.

BioMOBS: A multi-omics visual analytics workflow for biomolecular insight generation.

One of the challenges in multi-omics data analysis for precision medicine is the efficient exploration of undiscovered molecular interactions in disease processes. We present BioMOBS, a workflow consisting of two data visualization tools integrated with an open-source molecular information database to perform clinically relevant analyses (https://github.com/driesheylen123/BioMOBS). We performed exploratory pathway analysis with BioMOBS and demonstrate its ability to generate relevant molecular hypotheses, by reproducing recent findings in type 2 diabetes UK biobank data. The central visualisation tool, where data-driven and literature-based findings can be integrated, is available within the github link as well. BioMOBS is a workflow that leverages information from multiple data-driven interactive analyses and visually integrates it with established pathway knowledge. The demonstrated use cases place trust in the usage of BioMOBS as a procedure to offer clinically relevant insights in disease pathway analyses on various types of omics data.

Confirmed COVID-19 Cases per Economic Activity during Autumn Wave in Belgium.

Some occupational sectors, such as human health and care, food service, cultural and sport activities, have been associated with a higher risk of SARS-CoV-2 infection than other sectors. To curb the spread of SARS-CoV-2, it is preferable to apply targeted non-pharmaceutical interventions on selected economic sectors, rather than a full lockdown. However, the effect of these general and sector-specific interventions on the virus circulation has only been sparsely studied. We assess the COVID-19 incidence under different levels of non-pharmaceutical interventions per economic activity during the autumn 2020 wave in Belgium. The 14-day incidence of confirmed COVID-19 cases per the Statistical Classification of Economic Activities in the European Community (NACE-BEL) sector is modelled by a longitudinal Gaussian-Gaussian two-stage approach. This is based on exhaustive data on all employees in all sectors. In the presence of sanitary protocols and minimal non-pharmaceutical interventions, many sectors with close contact with others show considerably higher COVID-19 14-day incidences than other sectors. The effect of stricter non-pharmaceutical interventions in the general population and non-essential sectors is seen in the timing of the peak incidence and the width and height of the post-peak incidence. In most sectors incidences returned to higher levels after the peak than before and this decrease took longer for the health and care sector. Sanitary protocols for close proximity occupations may be sufficient during periods of low-level virus circulation, but progressively less with increasing circulation. Stricter general and sector-specific non-pharmaceutical interventions adequately decrease COVID-19 incidences, even in close proximity in essential sectors under solely sanitary protocols.

Remote Instruction for Data Visualization Design-A Report From the Trenches.

In this article, we report on our experiences of running visual design workshops within the context of a master's level data visualization course, in a remote setting. These workshops aim to teach students to explore visual design space for data by creating and discussing hand-drawn sketches. We describe the technical setup employed, the different parts of the workshop, how the actual sessions were run, and to what extent the remote version can substitute for in-person sessions. In general, the visual designs created by the students as well as the feedback provided by them indicate that the setup described here can be a feasible replacement for in-person visual design workshops.

Exploring the Microbiome Analysis and Visualization Landscape.

Research on the microbiome has boomed recently, which resulted in a wide range of tools, packages, and algorithms to analyze microbiome data. Here we investigate and map currently existing tools that can be used to perform visual analysis on the microbiome, and associate the including methods, visual representations and data features to the research objectives currently of interest in microbiome research. The analysis is based on a combination of a literature review and workshops including a group of domain experts. Both the reviewing process and workshops are based on domain characterization methods to facilitate communication and collaboration between researchers from different disciplines. We identify several research questions related to microbiomes, and describe how different analysis methods and visualizations help in tackling them.