Visualizing metagenomic and metatranscriptomic data: A comprehensive review.

The fields of Metagenomics and Metatranscriptomics involve the examination of complete nucleotide sequences, gene identification, and analysis of potential biological functions within diverse organisms or environmental samples. Despite the vast opportunities for discovery in metagenomics, the sheer volume and complexity of sequence data often present challenges in processing analysis and visualization. This article highlights the critical role of advanced visualization tools in enabling effective exploration, querying, and analysis of these complex datasets. Emphasizing the importance of accessibility, the article categorizes various visualizers based on their intended applications and highlights their utility in empowering bioinformaticians and non-bioinformaticians to interpret and derive insights from meta-omics data effectively.

Four-Year Overview of Winter Colony Losses in Greece: Citizen Science Evidence That Transitioning to Organic Beekeeping Practices Reduces Colony Losses.

The honey bee is one of the most important pollinators with a close relationship to humans. The questionnaire from the non-governmental association "COLOSS", answered by beekeepers around the world, is a valuable tool for monitoring and analyzing factors involved in overwintering losses, as well as for understanding the evolution of the beekeeping sector over the years. Between 2018-2021, Greece's participation in this survey involved collecting data from 752 beekeepers and 81,903 hives, from almost the whole country, with a stable balance between professional/non-professional participants and hives, providing a solid representation of the beekeeping practices and winter losses during this period. The results of this study identify a transition towards more natural beekeeping practices concomitant with a significant decrease in winter losses (average losses in 2018: 22.3% and 2019: 24%, dropped in 2020: 14.4% and 2021: 15.3%). Indeed, some factors, such as the increased use of natural landscapes for honey production (from 66.7% usage in 2018 to 76.3% in 2021) and the reduction in the exclusive use of synthetic acaricides (from 24.7% usage in 2018 to 6.7% in 2021) seem to have a significant impact on hive survival. Although these correlations remain to be confirmed experimentally, our study shows that Greek beekeepers follow recommendations and policies toward more sustainable practices. In the future, these trends could be further analyzed and integrated into training programs to strengthen the cooperation and information exchange between citizens and science.

Arena3Dweb: interactive 3D visualization of multilayered networks supporting multiple directional information channels, clustering analysis and application integration.

Arena3Dweb is an interactive web tool that visualizes multi-layered networks in 3D space. In this update, Arena3Dweb supports directed networks as well as up to nine different types of connections between pairs of nodes with the use of Bézier curves. It comes with different color schemes (light/gray/dark mode), custom channel coloring, four node clustering algorithms which one can run on-the-fly, visualization in VR mode and predefined layer layouts (zig-zag, star and cube). This update also includes enhanced navigation controls (mouse orbit controls, layer dragging and layer/node selection), while its newly developed API allows integration with external applications as well as saving and loading of sessions in JSON format. Finally, a dedicated Cytoscape app has been developed, through which users can automatically send their 2D networks from Cytoscape to Arena3Dweb for 3D multi-layer visualization. Arena3Dweb is accessible at http://arena3d.pavlopouloslab.info or http://arena3d.org.