Ronan M. T. Fleming

TL;DR: The constraint-based reconstruction and analysis toolbox as discussed by the authors is a software package running in the Matlab environment, which allows for quantitative prediction of cellular behavior using a constraintbased approach and allows predictive computations of both steady-state and dynamic optimal growth behavior, the effects of gene deletions, comprehensive robustness analyses, sampling the range of possible cellular metabolic states and the determination of network modules.

TL;DR: Recon 2, a community-driven, consensus 'metabolic reconstruction', is described, which is the most comprehensive representation of human metabolism that is applicable to computational modeling and has improved topological and functional features.

TL;DR: This review outlines some of the advantages and challenges that may accompany a transition from macroscopic to microfluidic cell culture and focuses on decisive factors that distinguish Macroscopic from microfluidity cell culture to encourage a reconsideration of how macroscopy cell culture principles might apply to micro fluidiccell culture.

TL;DR: This protocol provides an overview of all new features of the COBRA Toolbox and can be adapted to generate and analyze constraint-based models in a wide variety of scenarios.

TL;DR: This work presents AGORA (assembly of gut organisms through reconstruction and analysis), a resource of genome-scale metabolic reconstructions semi-automatically generated for 773 human gut bacteria, and identified a defined growth medium for Bacteroides caccae ATCC 34185.