Fundamentals of Bioinformatics - Ogurtsov A.N. 2013

Introduction

METABOLISM/2.html">THE CONCEPT OF "information" permeates all spheres of human activity, uniting them into a single, interconnected, and interdependent complex. Relatively recently, even the term "infosphere" emerged, denoting information structures, systems, and processes in science, society, and industry. At the same time, a unified consensus on the subject of informatics is still lacking, and the relationships between various information disciplines associated with different subject areas remain insufficiently clear.

It is intuitively clear that bioinformatics aims to apply information and information technologies in The Study of biological systems. Within bioinformatics, biology, computer science, and mathematics merge into a single discipline. In a sense, bioinformatics—which explores the application of information technology to manage biological data—is an extension of computational biology, which investigates the application of quantitative analysis Methods in modeling biological systems.

The intensity of genome research across various organisms grows every year. Annual updates bring new Databases storing information on investigated genomes, while existing databases continuously expand their capacities. Consequently, the volume of biological information available to researchers is growing at an astronomical rate. Without modern information technologies, it is no longer possible to retrieve or process the specific biological information required for a given study or biotechnological process.

In a broad sense, biotechnology refers to any production of commercial goods generated by microorganisms through their vital activity. More formally, biotechnology is defined as the application of scientific, engineering, and informational principles to the Processing of Materials by living organisms to create goods and services.

The success of any modern biotechnology—from industrial, environmental, and agricultural to pharmaceutical and molecular—is directly determined both by the efficiency of utilizing and managing the biological information contained in producer organisms and by the generation of new biological information for the genetic modification of these organisms to produce novel biotechnological products required in specific manufacturing processes.

The goal of informational biotechnology in general, and Pharmacoinformatics as a specific application of informational biotechnology for Drug Discovery and development, is to utilize existing and develop new computational and informational resources for the analysis and interpretation of various types of biological data (DNA, RNA, and protein sequences, spatial structures of RNA and Proteins, expression profiles, metabolic pathways, etc.) in order to develop novel biotechnological products.

The tasks of informational biotechnology and pharmacoinformatics are organically linked to the stages of new product development:

1) analysis of genome Organization and evolution, which is the subject of genoinformatics;

2) decoding, Structure prediction, and design of required proteins and Protein Complexes;

3) elucidation of the Mechanisms of action of BIOLOGICALLY ACTIVE SUBSTANCES within the Gene — protein — function chain, and the application of this information both to develop new biotechnologies and to create pharmaceutical drugs.

Success in solving these tasks is determined by the effective and complementary use, alongside bioinformatic approaches, of methods from sciences such as Genomics (structural, functional, comparative, medical, etc.), Proteomics (expression, cytographic, structural, functional, etc.), computational pharmacology and toxicology, combinatorial chemistry, and high-throughput screening techniques.

The threefold objective of bioinformatics includes:

1) organization and preservation of biological data;

2) development of software tools and creation of specialized information resources;

3) automation of biological Data analysis, interpretation, and utilization of the obtained results.

Thus, bioinformatics is the science of storing, retrieving, organizing, analyzing, interpreting, and utilizing biological information.

Modern bioinformatics emerged in the late 1970s, coinciding with the advent of efficient methods for sequencing DNA NUCLEOTIDES.

The establishment of bioinformatics as a distinct scientific field can be traced to 1980, marked by the launch of the journal Nucleic Acids Research, which was entirely dedicated to computational sequence analysis methods (see [1], cl. 1.2). Notably, 1980 is also widely regarded as the birth year of molecular biotechnology: on October 15, 1980, on the New York Stock Exchange, the share price of Genentech—the biotech company that first organized the Production of Human recombinant Insulin using Escherichia coli—jumped from $35 to $89. This event is conventionally considered THE START OF the biotechnological revolution (see [4], cl. 1.1), As a result of which biotechnology, alongside information technology and nanotechnology, formed the "technological triad" of human civilization's development in the 21st century (see [5], sec. 1).

An important milestone in the ESTABLISHMENT AND DEVELOPMENT of bioinformatics was the Human Genome Project. From that point on, bioinformatics ceased to be merely an auxiliary tool. The transition to processing, analyzing, and comparing complete organismal genomes was impossible without computational methods of information analysis, which ultimately shaped these studies into an independent scientific direction. Genomes contain a vast number of genes, many of which have not yet been experimentally identified.

Since genetic reading technologies rely heavily on computer hardware and computational methods, the emergence and rapid growth of bioinformatics occurred synchronously with the rise and widespread adoption of computer technologies. This serves as yet another confirmation that the depth of scientific knowledge is profoundly dependent on technical capabilities.

Another major milestone in The Development of bioinformatics was the advent of the World Wide Web and the ubiquitous spread of internet technologies. Today, there is no longer any need to develop software products within every individual research laboratory, as a vast array of diverse databases and software tools are accessible via the Internet. Bioinformatics is arguably one of those scientific fields that depends heavily on the Internet and thrives thanks to it. Indeed, the pivotal political decision—crucial for biology and medicine—to make the most complex biological text of our time, The Human Genome, entirely open access made this information genuinely available to scientists worldwide exclusively through the Internet.

Today, we stand at the initial stage of utilizing Genetic information about living matter; however, the development of increasingly efficient methods for decoding biological texts and the advancement of bioinformatics methods give hope for significant progress in understanding the structure, functioning mechanisms, and regulation of living systems. As a result, it becomes possible to study and comprehend increasingly complex biological systems, paving the way for their systematic investigation, the establishment of evolutionary relationships in nature, and the creation of new drugs, therapeutic methods, and novel biotechnologies.

The subjects of the academic disciplines "Bioinformatics and Information Biotechnology" and "Bioinformatics and Pharmacoinformatics" are computer-oriented methods for solving informational problems in industrial and pharmaceutical biotechnology. The scientific foundation of these courses comprises molecular biophysics, molecular biology, and general and Molecular Genetics.

The METHODOLOGICAL FOUNDATIONS OF the course include lectures outlining the core principles of each section, Practical Classes, and students' independent work, which serves as the primary method for mastering the material outside of classroom hours.

More than half of the total time allocated for studying this discipline is dedicated to independent work, which covers all topics included in the syllabus. Through independent work, students learn to acquire knowledge autonomously, which is subsequently applied during individual Assignments, practical classes, preparation for tests, and the final exam.

This study guide has been prepared based on revised and expanded manuals [1-3] and adapted works [4-67], which also served as a source of illustrations, and is designed to make mastering the courses "Bioinformatics and Information Biotechnology" and "Bioinformatics and Pharmacoinformatics" as easy as possible for students majoring in "Biotechnology".