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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Kinetic models of metabolism that consider alternative steady-state solutions of intracellular fluxes and concentrations.
TL;DR: This work integrated the omics data of optimally grown Escherichia coli into a stoichiometric model and constructed populations of non-linear large-scale kinetic models of alternative steady-state solutions consistent with the physiology of the E. coli aerobic metabolism, and performed metabolic control analysis on these models.
Journal ArticleDOI
Benchmarking Procedures for High-Throughput Context Specific Reconstruction Algorithms.
TL;DR: This review describes and analyses common validation methods used for testing model building algorithms and deduce properties of these algorithms that can be compared with future developments.
Journal ArticleDOI
GEMSiRV: A software platform for GEnome-scale Metabolic model Simulation, Reconstruction and Visualization
TL;DR: GEMSiRV is a powerful integrative resource that may facilitate the development of systems biology studies and comes with downloadable, ready-to-use public-domain metabolic models, reference metabolite/reaction databases and metabolic network maps.
Journal ArticleDOI
TrypanoCyc: a community-led biochemical pathways database for Trypanosoma brucei
Sanu Shameer,Flora J. Logan-Klumpler,Florence Vinson,Ludovic Cottret,Benjamin Merlet,Fiona Achcar,Michael Boshart,Matthew Berriman,Rainer Breitling,Frédéric Bringaud,Peter Bütikofer,Amy M. Cattanach,Bridget Bannerman-Chukualim,Darren J. Creek,Kathryn Crouch,Harry P. de Koning,Hubert Denise,Charles Ebikeme,Alan H. Fairlamb,Michael A. J. Ferguson,Michael L. Ginger,Christiane Hertz-Fowler,Eduard J. Kerkhoven,Pascal Mäser,Paul A.M. Michels,Archana Nayak,David W. Nes,Derek P. Nolan,Christian A. Olsen,Fatima Silva-Franco,Terry K. Smith,Martin C. Taylor,Aloysius G.M. Tielens,Michael D. Urbaniak,Jaap J. van Hellemond,Isabel M. Vincent,Shane R. Wilkinson,Susan Wyllie,Fred R. Opperdoes,Michael P. Barrett,Fabien Jourdan +40 more
TL;DR: This work presents a dynamic database, TrypanoCyc, which describes the generic and condition-specific metabolic network of Trypanosoma brucei, a parasitic protozoan responsible for human and animal African trypanosomiasis, and implements a network-based representation of the information through MetExplore, yielding a novel environment in which to visualise the metabolism of this important parasite.
Journal ArticleDOI
In silico Analysis and Experimental Improvement of Taxadiene Heterologous Biosynthesis in Escherichia coli
TL;DR: Results indicate that genetic manipulation of the DXP pathway has great potential to be used for production of terpenoids, and that chromosomal engineering is a powerful tool for heterologous biosynthesis of natural products.
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