Introduction and Preliminaries
The main focus of systems biology is to understand in quantitative, predictable ways the regulation of complex cellular pathways and of intercellular communication, so as to shed light on complex biological functions, such as metabolism, cell signaling, c
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Introduction and Preliminaries
Abstract The main focus of systems biology is to understand in quantitative, predictable ways the regulation of complex cellular pathways and of intercellular communication, so as to shed light on complex biological functions, such as metabolism, cell signaling, cell cycle, apoptosis, differentiation, and transformation. In this chapter, we firstly introduce the background of systems biology, and then, we introduce some preliminaries of the book, including some statistical analysis methods, complex networks theory as well as some software tools.
1.1 Systems Biology 1.1.1 Overviews Systems biology is the computational and mathematical modeling of complex biological systems, which applies computational, mathematical, statistical, and engineering approach to biomedical and biological scientific research. Particularly from the year 2000, the concept has been used widely in the biosciences in a variety of contexts. For example, the Human Genome Project is an example of applied systems thinking in biology, which has led to new, collaborative ways of working on problems in the biological field of genetics [1–3]. One of the outreaching aims of systems biology is to model and discover emergent properties, properties of cells, tissues and organisms functioning as a system whose theoretical description is only possible using techniques which fall under the remit of systems biology [4]. The definition of systems biology has been given by different people or organizations. One definition is described as: Systems biology is a biology-based interdisciplinary field that focuses on complex interactions within biological systems, using a holistic approach to biological and biomedical research, instead of the traditional reductionism [5]. Another alternative definition is described as: Systems biology is the science that discovers the principles underlying the emergence of the functional properties of living organisms from interactions among macromolecules (DNA, mRNA, proteins, etc.) [2]. © The Editor(s) (if applicable) and The Author(s), under exclusive license to Springer Nature Singapore Pte Ltd. 2020 J. Lü, P. Wang, Modeling and Analysis of Bio-molecular Networks, https://doi.org/10.1007/978-981-15-9144-0_1
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1 Introduction and Preliminaries
Systems biology can be understood from different ways. Firstly, systems biology is the study of the interactions between the components of certain biological system, and how these interactions give rise to the functions and behaviors of that system. For example, the interactions among the enzymes and metabolites in a metabolic pathway, and how the interactions give rise to the functions and behaviors of the metabolic pathway [2, 5]. Secondly, as a paradigm, systems biology is usually defined in antithesis to the so-called reductionist paradigm, although fully consistent with the scientific method. The distinction between the two paradigms is as follows: The reductionist approach has successfully identified most of the components and many of the interact
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