Topological analysis of individual pathway networks and aggregated network with LMME-DM

To allow detailed visual analysis of the overall system and its parts, we used a customised version of our Vanted add-on LMME (Large Metabolic Model Explorer) to construct an overview graph showing one node per pathway and the respective interconnecting species. We performed a comprehensive analysis of node centralities on two levels: on the level of the individual pathways as well as on the level of an aggregated network which is composed of the individual pathways. This allows detailed investigation of the individual pathway topologies, the overall topology, the pathway crosstalks, as well as the node centralities.

Our implementation is based on the biological network analysis tool Vanted (https://doi.org/10.1186/1752-0509-6-139) and the two add-ons SBGN-ED (https://doi.org/10.1093/bioinformatics/btq407) and LMME (https://doi.org/10.1093/bioinformatics/btab335) which support the import and export of several standard formats (such as SBML, and SBGN-ML). LMME (Large Metabolic Model Explorer) is our recently developed add-on that allows the exploration of large metabolic models based on model decompositions. We developed a customised version (called LMME-DM) that can be found on GitHub: https://github.com/LSI-UniKonstanz/lmme-dm.

All code including a description of the scripts and results can be found on GitLab: https://git-r3lab.uni.lu/computational-modelling-and-simulation/graphical-exploration-and-topological-analysis.