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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Journal ArticleDOI
Metabolic changes in Klebsiella oxytoca in response to low oxidoreduction potential, as revealed by comparative proteomic profiling integrated with flux balance analysis.
TL;DR: From the integrated protein expression profiles and flux distributions, a rational analytic framework is constructed that elucidates how (facultative) anaerobes respond to extracellular ORP changes.
Journal ArticleDOI
ORCA: a COBRA toolbox extension for model-driven discovery and analysis
Longfei Mao,Wynand S. Verwoerd +1 more
TL;DR: ORCA is a Matlab package, which extends the scope of established Constraint-Based Reconstruction and Analysis metabolic modelling and includes three unique functionalities: a framework method integrating three analyses of multi-objective optimization, robustness analysis and fractional benefit analysis, and a dynamic flux balance analysis framework incorporating kinetic constraints.
Journal ArticleDOI
ACBM: An Integrated Agent and Constraint Based Modeling Framework for Simulation of Microbial Communities
TL;DR: A new integrated agent and constraint based modeling framework abbreviated ACBM has been proposed that integrates agent-based and constraint-based modeling approaches and shows that a percentage of cells are always subject to starvation in a bioreactor with high volume.
Book ChapterDOI
Reconstructing High-Quality Large-Scale Metabolic Models with merlin.
TL;DR: This tutorial covers each feature of merlin in detail, including the assessment of experimental data for the validation of the model.
Journal ArticleDOI
Predictive potential of flux balance analysis of Saccharomyces cerevisiae using as optimization function combinations of cell compartmental objectives.
TL;DR: The quality of the predictions obtained with the FBA depends greatly on the knowledge of the oxygen uptake rate, and in the case of exponential growth with unknown oxygen exchange flux, the objective function "maximization of growth" gave much more accurate estimations of fluxes than the obtained with any other objective function explored in this study.
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