Optimization Methods in Metabolic Networks. (Record no. 103995)
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| 001 - CONTROL NUMBER | |
| control field | EBC4306437 |
| 003 - CONTROL NUMBER IDENTIFIER | |
| control field | MiAaPQ |
| 005 - DATE AND TIME OF LATEST TRANSACTION | |
| control field | 20240729130201.0 |
| 006 - FIXED-LENGTH DATA ELEMENTS--ADDITIONAL MATERIAL CHARACTERISTICS | |
| fixed length control field | m o d | |
| 007 - PHYSICAL DESCRIPTION FIXED FIELD--GENERAL INFORMATION | |
| fixed length control field | cr cnu|||||||| |
| 008 - FIXED-LENGTH DATA ELEMENTS--GENERAL INFORMATION | |
| fixed length control field | 240724s2016 xx o ||||0 eng d |
| 020 ## - INTERNATIONAL STANDARD BOOK NUMBER | |
| International Standard Book Number | 9781119188919 |
| Qualifying information | (electronic bk.) |
| 035 ## - SYSTEM CONTROL NUMBER | |
| System control number | (MiAaPQ)EBC4306437 |
| 035 ## - SYSTEM CONTROL NUMBER | |
| System control number | (Au-PeEL)EBL4306437 |
| 035 ## - SYSTEM CONTROL NUMBER | |
| System control number | (CaPaEBR)ebr11152533 |
| 035 ## - SYSTEM CONTROL NUMBER | |
| System control number | (CaONFJC)MIL884680 |
| 035 ## - SYSTEM CONTROL NUMBER | |
| System control number | (OCoLC)935255323 |
| 040 ## - CATALOGING SOURCE | |
| Original cataloging agency | MiAaPQ |
| Language of cataloging | eng |
| Description conventions | rda |
| -- | pn |
| Transcribing agency | MiAaPQ |
| Modifying agency | MiAaPQ |
| 050 #4 - LIBRARY OF CONGRESS CALL NUMBER | |
| Classification number | QP171 -- .M373 2016eb |
| 082 0# - DEWEY DECIMAL CLASSIFICATION NUMBER | |
| Classification number | 612.3/9 |
| 100 1# - MAIN ENTRY--PERSONAL NAME | |
| Personal name | Maranas, Costas D. |
| 245 10 - TITLE STATEMENT | |
| Title | Optimization Methods in Metabolic Networks. |
| 250 ## - EDITION STATEMENT | |
| Edition statement | 1st ed. |
| 264 #1 - PRODUCTION, PUBLICATION, DISTRIBUTION, MANUFACTURE, AND COPYRIGHT NOTICE | |
| Place of production, publication, distribution, manufacture | Newark : |
| Name of producer, publisher, distributor, manufacturer | John Wiley & Sons, Incorporated, |
| Date of production, publication, distribution, manufacture, or copyright notice | 2016. |
| 264 #4 - PRODUCTION, PUBLICATION, DISTRIBUTION, MANUFACTURE, AND COPYRIGHT NOTICE | |
| Date of production, publication, distribution, manufacture, or copyright notice | ©2016. |
| 300 ## - PHYSICAL DESCRIPTION | |
| Extent | 1 online resource (281 pages) |
| 336 ## - CONTENT TYPE | |
| Content type term | text |
| Content type code | txt |
| Source | rdacontent |
| 337 ## - MEDIA TYPE | |
| Media type term | computer |
| Media type code | c |
| Source | rdamedia |
| 338 ## - CARRIER TYPE | |
| Carrier type term | online resource |
| Carrier type code | cr |
| Source | rdacarrier |
| 505 0# - FORMATTED CONTENTS NOTE | |
| Formatted contents note | Intro -- Title Page -- Copyright Page -- Contents -- Preface -- Chapter 1 MATHEMATICAL OPTIMIZATION FUNDAMENTALS -- 1.1 MATHEMATICAL OPTIMIZATION AND MODELING -- 1.2 BASIC CONCEPTS AND DEFINITIONS -- 1.2.1 Neighborhood of a Point -- 1.2.2 Interior of a Set -- 1.2.3 Open Set -- 1.2.4 Closure of a Set -- 1.2.5 Closed Set -- 1.2.6 Bounded Set -- 1.2.7 Compact Set -- 1.2.8 Continuous Functions -- 1.2.9 Global and Local Minima -- 1.2.10 Existence of an Optimal Solution -- 1.3 Convex Analysis -- 1.3.1 Convex Sets and Their Properties -- 1.3.2 Convex Functions and Their Properties -- 1.3.3 Convex Optimization Problems -- 1.3.4 Generalization of Convex Functions -- Exercises -- References -- Chapter 2 LP AND DUALITY THEORY -- 2.1 CANONICAL AND STANDARD FORMS OF AN LP PROBLEM -- 2.1.1 Canonical Form -- 2.1.2 Standard Form -- 2.2 GEOMETRIC INTERPRETATION OF AN LP PROBLEM -- 2.3 BASIC FEASIBLE SOLUTIONS -- 2.4 SIMPLEX METHOD -- 2.5 DUALITY IN LINEAR PROGRAMMING -- 2.5.1 Formulation of the Dual Problem -- 2.5.2 Primal-Dual Relations -- 2.5.3 The Karush-Kuhn-Tucker (KKT) Optimality Conditions -- 2.5.4 Economic Interpretation of the Dual Variables -- 2.6 NONLINEAR OPTIMIZATION PROBLEMS THAT CAN BE TRANSFORMED INTO LP PROBLEMS -- 2.6.1 Absolute Values in the Objective Function -- 2.6.2 Minmax Optimization Problems with Linear Constraints -- 2.6.3 Linear Fractional Programming -- Exercises -- References -- Chapter 3 FLUX BALANCE ANALYSIS AND LP PROBLEMS -- 3.1 MATHEMATICAL MODELING OF METABOLISM -- 3.1.1 Kinetic Modeling of Metabolism -- 3.1.2 Stoichiometric-Based Modeling of Metabolism -- 3.2 GENOME-SCALE STOICHIOMETRIC MODELS OF METABOLISM -- 3.2.1 Gene-Protein-Reaction Associations -- 3.2.2 The Biomass Reaction -- 3.2.3 Metabolite Compartments -- 3.2.4 Scope and Applications -- 3.3 FLUX BALANCE ANALYSIS (FBA). |
| 505 8# - FORMATTED CONTENTS NOTE | |
| Formatted contents note | 3.3.1 Cellular Inputs, Outputs and Metabolic Sinks -- 3.3.2 Component Balances -- 3.3.3 Thermodynamic and Capacity Constraints -- 3.3.4 Objective Function -- 3.3.5 FBA Optimization Formulation -- 3.4 SIMULATING GENE KNOCKOUTS -- 3.5 MAXIMUM THEORETICAL YIELD -- 3.5.1 Maximum Theoretical Yield of Product Formation -- 3.5.2 Biomass vs. Product Trade-Off -- 3.6 FLUX VARIABILITY ANALYSIS (FVA) -- 3.7 Flux Coupling Analysis -- Exercises -- References -- Chapter 4 MODELING WITH BINARY VARIABLES AND MILP FUNDAMENTALS -- 4.1 Modeling with Binary Variables -- 4.1.1 Continuous Variable On/Off Switching -- 4.1.2 Condition-Dependent Variable Switching -- 4.1.3 Condition-Dependent Constraint Switching -- 4.1.4 Modeling AND Relations -- 4.1.5 Modeling OR Relations -- 4.1.6 Exact Linearization of the Product of a Continuous and a Binary Variable -- 4.1.7 Modeling Piecewise Linear Functions -- 4.2 SOLVING MILP PROBLEMS -- 4.2.1 Branch-and-Bound Procedure for Solving MILP Problems -- 4.2.2 Finding Alternative Optimal Integer Solutions -- 4.3 EFFICIENT FORMULATION STRATEGIES FOR MILP PROBLEMS -- 4.3.1 Using the Fewest Possible Binary Variables -- 4.3.2 Fix All Binary Variables that do not Affect the Optimal Solution -- 4.3.3 Group All Coupled Binary Variables -- 4.3.4 Segregate Binary Variables in Constraints Rather than in the Objective Function -- 4.3.5 Use Tight Bounds for All Continuous Variables -- 4.3.6 Introduce LP Relaxation Tightening Constraints -- 4.4 IDENTIFYING MINIMAL REACTION SETS SUPPORTING GROWTH -- Exercises -- References -- Chapter 5 THERMODYNAMIC ANALYSIS OF METABOLIC NETWORKS -- 5.1 THERMODYNAMIC ASSESSMENT OF REACTION DIRECTIONALITY -- 5.2 ELIMINATING THERMODYNAMICALLY INFEASIBLE CYCLES (TICs) -- 5.2.1 Cycles in Cellular Metabolism -- 5.2.2 Thermodynamically Infeasible Cycles -- 5.2.3 Identifying Reactions Participating in TICs. |
| 505 8# - FORMATTED CONTENTS NOTE | |
| Formatted contents note | 5.2.4 Thermodynamics-Based Metabolic Flux Analysis -- 5.2.5 Elimination of the TICs by Applying the Loop Law -- 5.2.6 Elimination of the TICs by Modifying the Metabolic Model -- Exercises -- References -- Chapter 6 RESOLVING NETWORK GAPS AND GROWTH PREDICTION INCONSISTENCIES IN METABOLIC NETWORKS -- 6.1 FINDING AND FILLING NETWORK GAPS IN METABOLIC MODELS -- 6.1.1 Categorization of Gaps in a Metabolic Model -- 6.1.2 Gap Finding -- 6.1.3 Gap Filling -- 6.2 RESOLVING GROWTH PREDICTION INCONSISTENCIES -- 6.2.1 Quality Metrics for Quantifying the Accuracy of Metabolic Models -- 6.2.2 Automated Reconciliation of Growth Prediction Inconsistencies Using GrowMatch -- 6.2.3 Resolution of Higher-Order Gene Deletion Inconsistencies -- 6.3 VERIFICATION OF MODEL CORRECTION STRATEGIES -- Exercise -- References -- Chapter 7 IDENTIFICATION OF CONNECTED PATHS TO TARGET METABOLITES -- 7.1 USING MILP TO IDENTIFY SHORTEST PATHS IN METABOLIC GRAPHS -- 7.2 USING MILP TO IDENTIFY NON-NATIVE REACTIONS FOR THE PRODUCTION OF A TARGET METABOLITE -- 7.3 DESIGNING OVERALL STOICHIOMETRIC CONVERSIONS -- 7.3.1 Determining the Stoichiometry of Overall Conversion -- 7.3.2 Identifying Reactions Steps Conforming to the Identified Overall Stoichiometry -- Exercises -- References -- Chapter 8 COMPUTATIONAL STRAIN DESIGN -- 8.1 EARLY COMPUTATIONAL TREATMENT OF STRAIN DESIGN -- 8.2 OptKnock -- 8.2.1 Solution Procedure for OptKnock -- 8.2.2 Improving the Computational Efficiency of OptKnock -- 8.2.3 Connecting Reaction Eliminations with Gene Knockouts -- 8.2.4 Impact of Knockouts on the Biomass vs. Product Trade-Off -- 8.3 OptKnock MODIFICATIONS -- 8.3.1 RobustKnock -- 8.3.2 Tilting the Objective Function -- 8.4 OTHER STRAIN DESIGN ALGORITHMS -- Exercises -- References -- Chapter 9 NLP Fundamentals -- 9.1 UNCONSTRAINED NONLINEAR OPTIMIZATION. |
| 505 8# - FORMATTED CONTENTS NOTE | |
| Formatted contents note | 9.1.1 Optimality Conditions for Unconstrained Optimization Problems -- 9.1.2 An Overview of the Solution Methods for Unconstrained Optimization Problems -- 9.1.3 Steepest Descent (Cauchy or Gradient) Method -- 9.1.4 Newton's Method -- 9.1.5 Quasi-Newton Methods -- 9.1.6 Conjugate Gradients (CG) Methods -- 9.2 CONSTRAINED NONLINEAR OPTIMIZATION -- 9.2.1 Equality-Constrained Nonlinear Problems -- 9.2.2 Nonlinear Problems with Equality and Inequality Constraints -- 9.2.3 Karush-Kuhn-Tucker Optimality Conditions -- 9.2.4 Sequential (Successive) Quadratic Programming -- 9.2.5 Generalized Reduced Gradient -- 9.3 LAGRANGIAN DUALITY THEORY -- 9.3.1 Relationships between the Primal and Dual Problems -- Exercises -- References -- Chapter 10 NLP APPLICATIONS IN METABOLIC NETWORKS -- 10.1 MINIMIZATION OF THE METABOLIC ADJUSTMENT -- 10.2 INCORPORATION OF KINETIC EXPRESSIONS IN STOICHIOMETRIC MODELS -- 10.3 METABOLIC FLUX ANALYSIS (MFA) -- 10.3.1 Definition of the Relevant Parameters and Variables -- 10.3.2 Isotopomer Mass Balance -- 10.3.3 Optimization Formulation for MFA -- Exercises -- References -- Chapter 11 MINLP FUNDAMENTALS AND APPLICATIONS -- 11.1 AN OVERVIEW OF THE MINLP SOLUTION PROCEDURES -- 11.2 GENERALIZED BENDERS DECOMPOSITION -- 11.2.1 The Primal Problem -- 11.2.2 The Master Problem -- 11.2.3 Steps of GBD Algorithm -- 11.3 OUTER APPROXIMATION -- 11.3.1 The Primal Problem -- 11.3.2 The Master Problem -- 11.3.3 Steps of the OA Algorithm -- 11.4 OUTER APPROXIMATION WITH EQUALITY RELAXATION -- 11.4.1 The Master Problem -- 11.5 KINETIC OPTKNOCK -- 11.5.1 k-OptKnock Formulation -- 11.5.2 Solution Procedure for k-OptKnock -- Exercises -- References -- Appendix A CODING OPTIMIZATION MODELS IN GAMS -- Index -- EULA. |
| 588 ## - SOURCE OF DESCRIPTION NOTE | |
| Source of description note | Description based on publisher supplied metadata and other sources. |
| 590 ## - LOCAL NOTE (RLIN) | |
| Local note | Electronic reproduction. Ann Arbor, Michigan : ProQuest Ebook Central, 2024. Available via World Wide Web. Access may be limited to ProQuest Ebook Central affiliated libraries. |
| 650 #0 - SUBJECT ADDED ENTRY--TOPICAL TERM | |
| Topical term or geographic name entry element | Metabolism--Regulation. |
| 655 #4 - INDEX TERM--GENRE/FORM | |
| Genre/form data or focus term | Electronic books. |
| 700 1# - ADDED ENTRY--PERSONAL NAME | |
| Personal name | Zomorrodi, Ali R. |
| 776 08 - ADDITIONAL PHYSICAL FORM ENTRY | |
| Relationship information | Print version: |
| Main entry heading | Maranas, Costas D. |
| Title | Optimization Methods in Metabolic Networks |
| Place, publisher, and date of publication | Newark : John Wiley & Sons, Incorporated,c2016 |
| 797 2# - LOCAL ADDED ENTRY--CORPORATE NAME (RLIN) | |
| Corporate name or jurisdiction name as entry element | ProQuest (Firm) |
| 856 40 - ELECTRONIC LOCATION AND ACCESS | |
| Uniform Resource Identifier | <a href="https://ebookcentral.proquest.com/lib/orpp/detail.action?docID=4306437">https://ebookcentral.proquest.com/lib/orpp/detail.action?docID=4306437</a> |
| Public note | Click to View |
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