This book is an introduction to the language of systems biology, which is spoken among many disciplines, from biology to engineering. Authors Thomas Sauter and Marco Albrecht draw on a multidisciplinary background and evidence-based learning to facilitate the understanding of biochemical networks, metabolic modeling and system dynamics. Their pedagogic approach briefly highlights core ideas of concepts in a broader interdisciplinary framework to guide a more effective deep dive thereafter. The learning journey starts with the purity of mathematical concepts, reveals its power to connect biological entities in structure and time, and finally introduces physics concepts to tightly align abstraction with reality. This workbook is all about self-paced learning, supports the flipped-classroom concept, and kick-starts with scientific evidence on studying. Each chapter comes with links to external YouTube videos, learning checklists, and Integrated real-world examples to gain confidence in thinking across scientific perspectives. The result is an integrated approach that opens a line of communication between theory and application, enabling readers to actively learn as they read. This overview of capturing and analyzing the behavior of biological systems will interest adherers of systems biology and network analysis, as well as related fields such as bioinformatics, biology, cybernetics, and data science.
Author(s): Thomas Sauter, Marco Albrecht
Publisher: Open Book Publishers
Year: 2023
Language: English
Pages: 170
Authors
Overview
Planning
Learning
Learning checklist
Further reading
References
Lecture summary
color2 Biological networks and graph theory
color2 Modeling of metabolic networks
Basics of Mathematics
color2 Linear algebra
References
Exercises
Solutions color2Do not betray yourself!
Lecture summary
color2 Stoichiometric Network Analysis
color2 Integration of experimental data
color2 Constraint-Based Modeling
color2 Problems & discussion
color2 Metabolic Flux Analysis
References
Exercises
Solutions color2Do not betray yourself!
Lecture summary
color2 Examples of non-linear dynamics
color2 The impact of network motifs
color2 What is a system?
color2 How to describe change mathematically
color2 What is a steady state?
color2 Stability theory: Idle state or explosion
color2 Phase portrait: How elements relate to each other
color2 Feedback revisited
color2 Bifurcation: Split it baby!
color2 Simulation-based analysis of motifs
color2 Additional reading: Cybernetics—The art of creating equilibrium in a world of constraints and possibilities
Basics of mathematics
References
Exercises
Solutions color2Do not betray yourself!
Lecture summary
color2 What is a model?
color2 Modeling procedure
color2 Mathematical analysis of models
color2 Model classification
color2 Akaike Information Criterion
color2 Extensive properties & SI units
color2 Balancing
color2 Enzyme kinetics
Basics of Mathematics
References
Exercises
Solutions color2Do not betray yourself!
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