Fundamentals of Bioinformatics - Ogurtsov A.N. 2013

Foundations of Bioinformatics
Bioinformatics Infrastructure
Computer Components of Bioinformatics

Today, information and computer components are an integral part of biotechnology. Computers are essential for managing biological data, the volume and complexity of which are continuously growing. The advent of the global Internet revolutionized the communications world. The creation of the World Wide Web (WWW) facilitated the successful Structure/175.html">Implementation and expansion of the Internet. Acting as a global information superhighway, the Internet enables users to freely navigate the WWW—the largest collection of diverse information resources.

A computer is an electronic device used for storing and Processing information using binary arithmetic. The Emergence of bioinformatics would have been impossible without advancements in hardware design and software development. Information storage requires high-speed, high-capacity media, while specialized programs are needed to retrieve and analyze data.

Computer hardware consists of physical devices such as the processor, disk drives, and display monitor.

Software is a collective term referring to a set of various programs designed to run on computers. Software is divided into two main categories: system software and application software.

System software includes the computer's operating system and any other programs required to launch Applications, whereas application software is installed by the user to perform specific tasks.

Computer programs are written in A wide variety of programming languages, ranging from machine code and assembly languages to high-level languages. Programs written in assembly or high-level languages must be converted into machine code through assembling and compilation.

In the Windows operating system, files written in machine code are called executable files, whereas the corresponding files in Unix are known as executable images. These files are executed directly by the computer's processor.

Scripts are files executed by another program. They are written in scripting languages such as Microsoft Visual Basic, JavaScript, and Perl.

There are numerous programming, scripting, and markup languages that have found applications in bioinformatics.

HTML (HyperText Markup Language) is designed to define the layout and appearance of a hypertext document, including the positioning of hyperlinks. It is worth noting that HTML is not a programming language.

JavaScript is a popular scripting language that extends the functionality of hypertext documents by allowing web pages to include elements such as pop-up windows, animations, and objects that change appearance when hovered over with the mouse pointer.

Java is a versatile, platform-independent programming language designed to create applications that can run across various hardware platforms. The source code of Java is "C++". Java differs from JavaScript. Java applets can be embedded directly into hypertext documents.

XML (Extensible Markup Language) allows files to be described According to the type of data they contain.

Python is a fully object-oriented, interpreted, portable, ultra-high-level scripting language created by Guido van Rossum in 1991. Programming in Python allows for the fast and efficient development of required software modules. The Python interpreter can be ported to virtually any platform, whether Unix, Windows, Linux, RiscOS, MAC, or Sun. When writing code in Python, developers do not need to worry about the target platform, except when using system-specific modules. Thus, Python is a strong competitor to Java, offering easy portability while combining access to operating system resources. Python includes tools for rapid and easy GUI development, a library of Functions used in structural biology, and an extensive collection of numerical Methods. Python can be downloaded from its official homepage: http://python.org.

Perl (Practical Extraction and Reporting Language) is a versatile scripting language widely used in sequencing Data analysis. Perl was developed by Larry Wall, drawing elements from "Sed", "Awk", the Unix shell, and "C". Perl offers exceptional regular expression matching, a flexible syntax or grammar, and requires relatively few lines of code to implement various operations. It excels at string processing—the fundamental operation in sequence analysis and database management. The language controls and optimizes computer memory allocation and boasts excellent compatibility with Unix-based computing systems. It is freely available for copying, compilation, and distribution over the network. Perl can be downloaded from its official homepage: http://www.perl.org.

Perl and Python are the most suitable languages for developing bioinformatics applications, largely due to their efficiency and ability to meet the diverse functional requirements of this field.

BSML (Bioinformatic Sequence Markup Language) graphically describes genetic sequences, methods for storing and transmitting encoded sequence structure information, and associated graphical data.

BIOML (Biopolymer Markup Language) provides a data type definition for annotating molecular biopolymer sequence information and its structural data.

An operating system (OS) is the core software that manages all peripheral devices and controls the execution of other (application) programs.

BIOS (Basic Input-Output System) is a low-level operating system implemented partially or entirely in hardware (i.e., stored in ROM). BIOS manages fundamental computer operations, such as initializing hardware devices upon boot-up, reading and writing disks, handling input responses, and displaying system reports and diagnostic data for utility devices. Control is then handed over to the high-level operating system, and a typical graphical user interface appears on the screen. Files containing operating system commands are referred to as batch files in Windows and shell scripts in Unix.

Microsoft Windows is the most familiar operating system for home and office personal computers.

The majority of corporate workstations and servers run on various versions of the Unix operating system. The GNU and Linux operating systems comply with Unix standards.

The operating system provides access to the files and programs available on the computer.

Unix is a powerful multi-user operating system. The initial software for the World Wide Web was developed precisely on a Unix-based OS. Unix abounds in various commands and functionalities—ranging from networking tools to text editors, and from email clients to news readers. Furthermore, it provides easy access to downloadable programs written for Unix systems. Today, Unix exists in various forms and implementations.

Linux is considered a non-commercial version of Unix for personal computers, as it can be downloaded for free from the internet and installed on a computer. Powered by Linux, personal computers have proven to be exceptionally versatile and convenient workstations. Several important computational biology software packages are designed to run on Linux.

IBION is a novel machine-independent and functionally complete bioinformatics system. It is a large-scale server tailored specifically for bioinformatics needs, incorporating an Apache web server, the postgreSQL relational database, and the "R" statistical language. It runs on Intel hardware equipped with a pre-installed Linux operating system and a comprehensive suite of bioinformatics software and Databases.

Software is typically supplied on floppy disks or CDs. We say that a file is downloaded when it is copied from a remote source to a local computer, and that it is uploaded when it is copied from a computer's hard drive and transmitted to a remote source.

Downloading from the Internet can be performed in three ways:

1) directly from a hypertext document;

2) from an FTP server;

3) via email.