KBase offers a comprehensive suite of tools for generating and refining metabolic models. Modeling researchers have observed that genome-scale metabolic models (GEMs) generated from automated reconstruction pipelines often lack accuracy in energy biosynthesis. It is therefore often useful to construct a simplified version of a GEM: a core metabolic model (CMM) that is comprised of only the high-confidence central pathways and electron transport chains. This newly published chapter in Springer’s Reconstruction and Analysis of Central Metabolism in Microbes describes how to use KBase to build and simulate core metabolic models (CMM) based on genome annotations. For more information, see http://kbase.us/core-models/, which includes a link to a Narrative that you can copy and run yourself.
Edirisinghe J.N., Faria J.P., Harris N.L., Allen B.H., Henry C.S. (2018) Reconstruction and Analysis of Central Metabolism in Microbes. In: Fondi M. (eds) Metabolic Network Reconstruction and Modeling. Methods in Molecular Biology, vol 1716. Humana Press, New York, NY