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What is flux balance analysis?
This primer covers the theoretical basis of the approach, several practical examples and a software toolbox for performing the calculations.
A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information
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.
Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0
Over the past decade, a growing community of researchers has emerged around the use of constraint-based reconstruction and analysis (COBRA) methods to simulate, analyze and predict a variety of…
A protocol for generating a high-quality genome-scale metabolic reconstruction
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.
Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox
- S. Becker, A. Feist, Monica L. Mo, G. Hannum, B. Palsson, Markus J. Herrgård
- Biology, Computer ScienceNature Protocols
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.
Metabolic Flux Balancing: Basic Concepts, Scientific and Practical Use
The flux balance methodology allows the quantitative interpretation of metabolic physiology, gives an interpretation of experimental data, provides a guide to metabolic engineering, enables optimal medium formulation, and provides a method for bioprocess optimization.
Stoichiometric flux balance models quantitatively predict growth and metabolic by-product secretion in wild-type Escherichia coli W3110
A predictive algorithm is formulated in order to apply the flux balance model to describe unsteady-state growth and by-product secretion in aerobic batch, fed-batch, and anaerobic batch cultures.
Systems Biology: Properties of Reconstructed Networks
- B. Palsson
- 16 January 2006
Preface 1. Introduction 2. Basic concepts in systems biology Part I. Reconstruction of Biochemical Networks: 3. Metabolic networks 4. Regulatory networks 5. Signalling networks Part II. Mathematical…
Global reconstruction of the human metabolic network based on genomic and bibliomic data
- Natalie C Duarte, S. Becker, B. Palsson
- BiologyProceedings of the National Academy of Sciences
- 6 February 2007
The reconstruction process is described and it is demonstrated how the resulting genome-scale (or global) network can be used for the discovery of missing information, for the formulation of an in silico model, and as a structured context for analyzing high-throughput biological data sets.
An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR)
iJR904 will help to outline the genotype-phenotype relationship for E. coli K-12, as it can account for genomic, transcriptomic, proteomic and fluxomic data simultaneously, and has improved capabilities over iJE660a.