#17 · Tools & infrastructure

Network analysis tools shift toward interactive 3D, group-aware and omics-linked graph…

The common thread is interactive, accessible handling of biological networks, delivered as browser-based tools or as R/Bioconductor infrastructure. Arena3D 3.0 is a web server for exploring, analyzing, annotating and sharing multilayered networks in 3D, with imports from STRING and IntAct. NORMA 3.0 is a client-side rewrite for annotated networks, adding group-aware layouts, multi-group node rendering and 21 topological analyses. GraphExperiment differs in kind: an S4 class extending SingleCellExperiment that stores feature- and observation-level igraph networks synchronized with omics data. Its distinguishing contribution is coupling network topology with quantitative measurements in one container. The summaries do not report benchmarks against existing tools, and NORMA's summary does not indicate an omics link.