Systems Biology

Systems biology is a field of research that focuses on understanding whole biological systems, such as protein complexes, metabolic pathways, or gene regulatory networks, and it attempts to understand cells, tissues, and organisms and how they behave and function from a systems perspective. In other words, systems biology is a computational and mathematical analysis and modeling of complex biological systems, and a systemic view of biological issues means that the function of no organ is independent of the other so that the behavior of all components will affect the behavior of the whole system.
Also, systems biology is defined as a set of computational methods whose purpose is to integrate all molecular measurements taken from the elements of a biological system to create a model that describes and predicts the overall behavior of the system. The goal of systems biology is to understand the basics of designing living systems, and conducting extensive research on biological interactions with the aim of generalization is the main indicator in systems biology.
According to Westerhoff and Palsson (2004), systems biology has two historical roots. The first and most commonly cited etymology relates to the structure and function of genetic material and the discovery of methods of genetic manipulation. The second route relates to thermodynamic aspects of organisms introduced into biology in the 1940s.
Here we discuss the three evolutionary stages of systems biology. The first step involved transforming molecular biology into systems molecular biology. This phase was related to the discovery of gene structure and function and genetic engineering (Westerhoff and Palsson, 200).
Since 1953, molecular biologists have discovered the structure and function of genes, and finally, at the beginning of the 21st century, they also discovered the human genome. During the postgenomic era, the purpose of molecular biology has changed. The search for an explanation of how complex molecular pathways and networks support biological structure and function has become a central question in molecular biology. The transition from a single molecule to a molecular network marked the birth of systems molecular biology. The second phase is the development of systems-mathematical biology, related to general systems theory (GSS) and the nonlinear dynamics of living organisms. The third phase, followed by the convergence of molecular systems biology and mathematical systems biology, is related to systems-based medicine, biotechnology, and drug development.

Although the term systems biology was widely used at the beginning of the 21st century with the advances in experimental methods, biological data analysis has always been a dynamic field of research, and with the emergence of so-called high-throughput approaches, This made it possible to simultaneously observe the behavior of a large number of distinct molecular species.
The main purpose of such analysis is to process the measurements obtained from the biological system to describe the functions and behavior of the system. Using high-power computing technologies, biological data were obtained at the molecular level, which requires new computational methods to process the data and generate answers to new questions in biology. The use of high-power computing technologies helps to understand complex biological systems and cellular interdependence and allows researchers to discover the function of a system. Understanding the complex relationship between the paths of biological systems is the most important challenge in biology, and the use of powerful computing technology has had a significant impact on solving this challenge.

A few major topics of research in the field of systems biology include:

• Gene regulatory networks
• Modelling metabolic interactions
• Model protective mechanisms induced by antibiotics
• Studying cell signaling pathways

According to the definition of systems biology as the ability to acquire, integrate and analyze complex experimental data sets using interdisciplinary tools, some of the main technologies of this field are as follows:

• Phenomics
• Genomics
• Epigenetics
• Transcriptomics
• Interactomics

For more information, please refer to the following sources:

1. Najarian, K., Najarian, S., Gharibzadeh, S., & Eichelberger, C. N. (2009). Systems biology and bioinformatics: a computational approach. CRC Press.
   Palsson, B. (2015). Systems biology. Cambridge university press.
2. Klipp, E., Herwig, R., Kowald, A., Wierling, C., & Lehrach, H. (2005). Systems biology in practice: concepts, implementation and application. John Wiley & Sons.
3. https://medium.com/computational-biology/research-in-computational-biology-and-bioinformatics-121d92681aad