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1 | (18) |
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1.1 Introduction: The Systems Biology Paradigm Shift |
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1 | (1) |
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1.2 What Is Computational Modelling? |
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1 | (2) |
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1.3 Why Nutrition Needs Modelling |
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3 | (1) |
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1.4 Computer Models and Nutrition Research |
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3 | (9) |
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4 | (1) |
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1.4.2 Models of Folate Metabolism |
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4 | (3) |
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1.4.3 Cholesterol Metabolism |
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7 | (1) |
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1.4.4 Models of Cholesterol Metabolism |
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8 | (4) |
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1.5 Can Modelling Unravel the Relationship Between Diet and Healthspan? |
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12 | (1) |
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13 | (1) |
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13 | (6) |
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19 | (12) |
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19 | (1) |
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2.2 Deterministic Kinetics and the Law of Mass Action |
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20 | (1) |
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20 | (2) |
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2.4 First Order Reactions |
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22 | (4) |
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2.5 Second Order Rate Laws |
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26 | (3) |
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29 | (1) |
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29 | (2) |
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31 | (10) |
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31 | (6) |
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3.1.1 Michaelis-Menten Kinetics |
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33 | (3) |
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3.1.2 Michaelis Menten (Reversible) |
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36 | (1) |
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37 | (1) |
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38 | (1) |
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39 | (1) |
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40 | (1) |
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4 Model Building: Part One |
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41 | (14) |
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4.1 The Steps in Building a Kinetic Model |
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41 | (1) |
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4.2 Step One: Identifying a System to Model and Defining a Hypothesis |
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42 | (1) |
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4.3 Step Two: Listing the Variables and How They Interact |
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43 | (1) |
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4.4 Step Three: Creating a Network Diagram |
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44 | (1) |
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4.5 Step Four: Identifying and Using a Software Tool |
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44 | (1) |
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4.6 Step Five: Adding Biochemical Reactions |
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45 | (8) |
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4.6.1 Adding a Rate Law Which Does Not Exist in COPASI/CellDesigner |
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49 | (4) |
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53 | (1) |
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54 | (1) |
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5 Model Building: Part Two |
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55 | (8) |
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55 | (1) |
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5.2 Step Six: Model Parameterization |
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55 | (1) |
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5.3 Step Seven: Model Simulation |
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56 | (2) |
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5.4 Step Eight: Validation and Hypothesis Exploration |
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58 | (2) |
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5.5 Step Ten: Model Archiving |
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60 | (1) |
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61 | (1) |
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62 | (1) |
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6 Model Analysis in Greater Depth |
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63 | (16) |
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6.1 Steady State Analysis |
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63 | (2) |
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65 | (1) |
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6.3 Parameter Perturbations and Bifurcations |
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66 | (2) |
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6.4 The Brusselator and Limit Cycles |
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68 | (2) |
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6.5 Identifying the Stability of Larger Models |
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70 | (2) |
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6.5.1 Identifying Model Stability Using COPASI |
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72 | (1) |
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6.6 Performing a Local Parameter Scan |
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72 | (2) |
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6.7 Metabolic Control Analysis |
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74 | (2) |
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6.8 Performing a Sensitivity Analysis |
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76 | (2) |
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78 | (1) |
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78 | (1) |
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7 Investigating Cholesterol Metabolism and Its Intersection with Ageing |
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79 | (14) |
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7.1 Cholesterol Metabolism: Some Mechanistic Detail |
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79 | (2) |
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7.2 Cholesterol Absorption and Ageing |
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81 | (5) |
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7.3 Hepatic LDLr and Ageing |
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86 | (1) |
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7.4 Cholesterol Biosynthesis |
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87 | (1) |
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88 | (2) |
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90 | (3) |
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8 Modelling Folate Metabolism and DNA Methylation |
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93 | (8) |
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93 | (1) |
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8.2 Explore Folate Metabolism and Health |
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93 | (3) |
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8.3 Computationally Modelling DNA Methylation |
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96 | (1) |
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8.4 Stochastic Modelling DNA Methylation |
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97 | (1) |
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8.5 Rationale for Modelling DNA Methylation Using a Stochastic Framework |
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98 | (1) |
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99 | (1) |
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100 | (1) |
Index |
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101 | |