About this Research Topic

Background

Networks are ever-present in biology. Whether in the interplay of factors influencing gene expression, the balance of consumers and producers in food webs, or the interactions between parts of an enzyme that modulate its activity, hardly anything in biology acts completely independently. Understanding the interdependencies is often critical to understanding the behavior of a system. Unfortunately, few tools exist for computing or visualizing network data that utilize many features common in biological networks. At the same time, there are properties of biological networks that cannot be well-captured by current graphs and network formalisms. This Research Topic will bring together descriptions of the current best practices for visualizing and computing the breath of network types present in biological data, new tools that present unique capabilities for this field, and concise descriptions of outstanding challenges in correctly representing real biological networks as the formal graph/network structures.

This Research Topic intends to provide an analysis of the landscape of network approaches applied to biological data and serve as a sourcebook of best practices for dealing with archetypal data types. It will introduce new tools uniquely suited for the challenges of biological network data and will bring together illustrations of remaining problems (as well as corresponding data sets) in biological networks that are not yet addressed. In addition to other poorly served areas of biological network representations, it will highlight the challenges and potential opportunities that exist in situations such as biological networks that have "natural" node orderings or positionings that are independent of edge weights, networks with conditionally-valued edge weights, and metagraph and hypergraph features within biological networks. By highlighting both the current best practices for biological end-users, and areas where current tools could be improved, this Research Topic aims to improve the utilization of network visualization and analytics in the biological sciences, bring potential areas for new contributions to the attention of the broader graph/network community, and invite improvements from areas such as transportation network graphs that have useful but as-yet unexploited applications to biological data.

This Research Topic accepts - but is not limited to - submissions in any aspect of network or graph visualization or visual-analytic approaches to biological data, such as:

• Reviews detailing current best-practices for specific biological domains for either Exploratory or Explanatory purposes.
• Methods papers introducing new approaches or software tuned to specific biological network-visualization needs in either Exploration or Explanation.
• Research papers comparing or contrasting the performance of different network visualization/analytics approaches to specific biological domain questions and data.
• Position papers illustrating challenges in biological network visualization that are not well-served by current approaches, with corresponding demonstration data sets.

Keywords: Networks, Graphs, Interactions, Dependencies, Non-Linear, Exploration, Analysis

Important note: All contributions to this Research Topic must be within the scope of the section and journal to which they are submitted, as defined in their mission statements. Frontiers reserves the right to guide an out-of-scope manuscript to a more suitable section or journal at any stage of peer review.

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