Library of network inference methods and R package for networks analysis.

The main computational goals of AtlantECO for Advances in Systems Ecology were to develop cutting edge network analysis methods, to define an all-Atlantic interactome and ecological niches, and to provide indicators of ecosystem stability and sensitivity to environmental stressors and drivers. Here, we reviewed the literature for ecological network reconstruction methods from several disciplines (microbiology, ecology, bioinformatics). We built a computational pipeline for the inference of species ecological networks from heterogeneous data types, combining statistical and ecological metrics, as well as probabilistic and machine learning algorithms. Reference databases of known ecological interactions obtained from the literature can be used to benchmark and validate inferred networks. This review of network inference algorithms is accompanied by a computational workflow: AtlantEcoNet (publicly available at: https://gitlab.univ-nantes.fr/mbudinich/atlanteconet), which builds upon existing software by integrating a selection of complementary methods for ecological network inference, analysis, and validation. This workflow was used by AtlantECO to build a plankton ecological network from omics data compiled for the Atlantic Ocean.