Bernhard O. Palsson

TL;DR: This primer covers the theoretical basis of the approach, several practical examples and a software toolbox for performing the calculations.

TL;DR: In GNPS, crowdsourced curation of freely available community-wide reference MS libraries will underpin improved annotations and data-driven social-networking should facilitate identification of spectra and foster collaborations.

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: This protocol provides a helpful manual for all stages of the reconstruction process and presents a comprehensive protocol describing each step necessary to build a high-quality genome-scale metabolic reconstruction.

TL;DR: An updated genome‐scale reconstruction of the metabolic network in Escherichia coli K‐12 MG1655 with increased scope and computational capability is presented, expected to broaden the spectrum of both basic biology and applied systems biology studies of E. coli metabolism.