DEMA: a distance-bounded energy-field minimization algorithm to model and layout biomolecular networks with quantitative features.

ABSTRACT:

Summary

In biology, graph layout algorithms can reveal comprehensive biological contexts by visually positioning graph nodes in their relevant neighborhoods. A layout software algorithm/engine commonly takes a set of nodes and edges and produces layout coordinates of nodes according to edge constraints. However, current layout engines normally do not consider node, edge or node-set properties during layout and only curate these properties after the layout is created. Here, we propose a new layout algorithm, distance-bounded energy-field minimization algorithm (DEMA), to natively consider various biological factors, i.e., the strength of gene-to-gene association, the gene's relative contribution weight and the functional groups of genes, to enhance the interpretation of complex netw

SUBMITTER: Weng Z 

PROVIDER: S-EPMC9235497 | biostudies-literature | 2022 Jun

REPOSITORIES: biostudies-literature