Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0
Jan Schellenberger,Richard Que,Ronan M. T. Fleming,Ines Thiele,Jeffrey D. Orth,Adam M. Feist,Daniel C. Zielinski,Aarash Bordbar,Nathan E. Lewis,Sorena Rahmanian,Joseph Kang,Daniel R. Hyduke,Bernhard O. Palsson +12 more
TLDR
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.Abstract:
The manner in which microorganisms utilize their metabolic processes can be predicted using constraint-based analysis of genome-scale metabolic networks. Herein, we present the constraint-based reconstruction and analysis toolbox, a software package running in the Matlab environment, which allows for quantitative prediction of cellular behavior using a constraint-based approach. Specifically, this software 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. Functions enabling these calculations are included in the toolbox, allowing a user to input a genome-scale metabolic model distributed in Systems Biology Markup Language format and perform these calculations with just a few lines of code. The results are predictions of cellular behavior that have been verified as accurate in a growing body of research. After software installation, calculation time is minimal, allowing the user to focus on the interpretation of the computational results.read more
Citations
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Shrinking the metabolic solution space using experimental datasets.
TL;DR: This mini-review provides a summary of the data-driven computational approaches that are available for reducing the solution space and thereby improve predictions of intracellular fluxes by constraint-based models.
Journal ArticleDOI
Use of genome-scale metabolic models for understanding microbial physiology.
TL;DR: The requirement for having detailed physiological insight in order to exploit microorganisms for production of fuels, chemicals and pharmaceuticals is discussed and the reconstruction process of genome‐scale metabolic models and different algorithms that can be used to apply these models to gain improved insight into microbial physiology are described.
Journal ArticleDOI
Computational systems biology and in silico modeling of the human microbiome
TL;DR: The pressing need for the development of predictive system- level models and for a system-level understanding of the microbiome is highlighted, and potential computational frameworks for metagenomic-based modeling of the microbiota at the cellular, ecological and supra-organismal level are discussed.
Journal ArticleDOI
Identified metabolic signature for assessing red blood cell unit quality is associated with endothelial damage markers and clinical outcomes.
Aarash Bordbar,Pär I. Johansson,Giuseppe Paglia,Scott James Harrison,Kristine Wichuk,Manuela Magnusdottir,Soley Valgeirsdottir,Mikkel Gybel-Brask,Sisse R. Ostrowski,Sirus Palsson,Ottar Rolfsson,Olafur E. Sigurjonsson,M B Hansen,Sveinn Gudmundsson,Bernhard O. Palsson +14 more
TL;DR: An overlooked but essential issue in assessing RBC unit quality and ultimately designing the necessary clinical trials is a metric for what constitutes an old or fresh RBC units.
Journal ArticleDOI
Standardizing biomass reactions and ensuring complete mass balance in genome-scale metabolic models.
TL;DR: This work introduced a systematic procedure for checking the biomass weight and ensuring complete mass balance of a model and proposes the presented procedure as a standard practice for metabolic reconstructions.
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