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An introduction to computational systems biology : systems-level modelling of cellular networks.

By: Raman, KarthikMaterial type: TextTextSeries: Chapman and Hall/CRC Computational Biology SerPublisher: Milton : CRC Press LLC, 2021Copyright date: ©2021Description: 1 online resource (359 pages)Content type: text Media type: computer Carrier type: online resourceISBN: 9780429944529Subject(s): Molecular biology-Data processing | Biological systems-Computer simulation | Systems biology | Computational biologyAdditional physical formats: Print version:: An Introduction to Computational Systems BiologyDDC classification: 570.113 LOC classification: QH324.2 .R363 2021Online access: Open e-book
Contents:
Cover -- Half Title -- Series Page -- Title Page -- Copyright Page -- Dedication -- Contents -- Preface -- CHAPTER 1: Introduction to modelling -- 1.1. WHAT IS MODELLING? -- 1.1.1. What are models? -- 1.2. WHYBUILD MODELS? -- 1.2.1. Why model biological systems? -- 1.2.2. Why systems biology? -- 1.3. CHALLENGES IN MODELLING BIOLOGICAL SYSTEMS -- 1.4. THE PRACTICE OF MODELLING -- 1.4.1. Scope of the model -- 1.4.2. Making assumptions -- 1.4.3. Modelling paradigms -- 1.4.4. Building the model -- 1.4.5. Model analysis debugging and (in)validation -- 1.4.6. Simulating the model -- 1.5. EXAMPLES OF MODELS -- 1.5.1. Lotka-Volterra predator-prey model -- 1.5.2. SIR model: A classic example -- 1.6. TROUBLESHOOTING -- 1.6.1. Clarity of scope and objectives -- 1.6.2. The breakdown of assumptions -- 1.6.3. Is my model fit for purpose? -- 1.6.4. Handling uncertainties -- EXERCISES -- REFERENCES -- FURTHER READING -- PART I: Static Modelling -- CHAPTER 2: Introduction to graph theory -- 2.1. BASICS -- 2.1.1. History of graph theory -- 2.1.2. Examples of graphs -- 2.2. WHY GRAPHS? -- 2.3. TYPES OF GRAPHS -- 2.3.1. Simple vs. non-simple graphs -- 2.3.2. Directed vs. undirected graphs -- 2.3.3. Weighted vs. unweighted graphs -- 2.3.4. Other graph types -- 2.3.5. Hypergraphs -- 2.4. COMPUTATIONAL REPRESENTATIONS OF GRAPHS -- 2.4.1. Data structures -- 2.4.2. Adjacency matrix -- 2.4.3. The Laplacian matrix -- 2.5. GRAPH REPRESENTATIONS OF BIOLOGICAL NETWORKS -- 2.5.1. Networks of protein interactions and functionalassociations -- 2.5.2. Signalling networks -- 2.5.3. Protein structure networks -- 2.5.4. Gene regulatory networks -- 2.5.5. Metabolic networks -- 2.6. COMMON CHALLENGES &amp -- TROUBLESHOOTING -- 2.6.1. Choosing a representation -- 2.6.2. Loading and creating graphs -- 2.7. SOFTWARE TOOLS -- EXERCISES -- REFERENCES -- FURTHER READING.
13.4. SOFTWARE TOOLS.
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Cover -- Half Title -- Series Page -- Title Page -- Copyright Page -- Dedication -- Contents -- Preface -- CHAPTER 1: Introduction to modelling -- 1.1. WHAT IS MODELLING? -- 1.1.1. What are models? -- 1.2. WHYBUILD MODELS? -- 1.2.1. Why model biological systems? -- 1.2.2. Why systems biology? -- 1.3. CHALLENGES IN MODELLING BIOLOGICAL SYSTEMS -- 1.4. THE PRACTICE OF MODELLING -- 1.4.1. Scope of the model -- 1.4.2. Making assumptions -- 1.4.3. Modelling paradigms -- 1.4.4. Building the model -- 1.4.5. Model analysis debugging and (in)validation -- 1.4.6. Simulating the model -- 1.5. EXAMPLES OF MODELS -- 1.5.1. Lotka-Volterra predator-prey model -- 1.5.2. SIR model: A classic example -- 1.6. TROUBLESHOOTING -- 1.6.1. Clarity of scope and objectives -- 1.6.2. The breakdown of assumptions -- 1.6.3. Is my model fit for purpose? -- 1.6.4. Handling uncertainties -- EXERCISES -- REFERENCES -- FURTHER READING -- PART I: Static Modelling -- CHAPTER 2: Introduction to graph theory -- 2.1. BASICS -- 2.1.1. History of graph theory -- 2.1.2. Examples of graphs -- 2.2. WHY GRAPHS? -- 2.3. TYPES OF GRAPHS -- 2.3.1. Simple vs. non-simple graphs -- 2.3.2. Directed vs. undirected graphs -- 2.3.3. Weighted vs. unweighted graphs -- 2.3.4. Other graph types -- 2.3.5. Hypergraphs -- 2.4. COMPUTATIONAL REPRESENTATIONS OF GRAPHS -- 2.4.1. Data structures -- 2.4.2. Adjacency matrix -- 2.4.3. The Laplacian matrix -- 2.5. GRAPH REPRESENTATIONS OF BIOLOGICAL NETWORKS -- 2.5.1. Networks of protein interactions and functionalassociations -- 2.5.2. Signalling networks -- 2.5.3. Protein structure networks -- 2.5.4. Gene regulatory networks -- 2.5.5. Metabolic networks -- 2.6. COMMON CHALLENGES &amp -- TROUBLESHOOTING -- 2.6.1. Choosing a representation -- 2.6.2. Loading and creating graphs -- 2.7. SOFTWARE TOOLS -- EXERCISES -- REFERENCES -- FURTHER READING.

13.4. SOFTWARE TOOLS.

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Electronic reproduction. Ann Arbor, Michigan : ProQuest Ebook Central, 2021. Available via World Wide Web. Access may be limited to ProQuest Ebook Central affiliated libraries.

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