Metabolic Network Reconstruction and Modeling Methods and Protocols [Hardcover]

This volume looks at the latest methodologies used to study cellular metabolism with in silico approaches. The chapters in this book are divided into 3 parts: part I discusses tools and methods used for metabolic reconstructions and basic constraint-based metabolic modeling (CBMM); Part II explores protocols for the generation of experimental data for metabolic reconstruction and modeling, including transcriptomics, proteomics, and mutant generations; and Part III cover advanced techniques for quantitative modeling of cellular metabolism, including dynamic Flux Balance Analysis and multi-objective optimization. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.

Cutting-edge and thorough, Metabolic Network Reconstruction and Modeling: Methods and Protocols is a valuable resource for qualified investigators studying cellular metabolism, and novice researchers who want to start working with CBMM.

Preface&

Table of Contents&

Contributing Authors&

1. Reconstructing High-Quality Large-Scale Metabolic Models with merlin

Oscar Dias, Miguel Rocha, Eug?nio Campos Ferreira, and Isabel Rocha

Paulo Vila?a, Paulo Maia, Hugo Giesteira, Isabel Rocha, and Miguel Rocha

3. The MONGOOSE Rational Arithmetic Toolbox

Christopher Le and Leonid Chindelevitch