Fundamentals of Bioinformatics - Ogurtsov A.N. 2013

Foundations of Bioinformatics
Bioinformatics Infrastructure
Internet Components of Bioinformatics

The Internet is a global network of computers and local computer networks connecting numerous governmental, educational, and commercial institutions. It enables computers to communicate in their own electronic languages. Biological information is stored on numerous computers scattered across the globe, and the easiest way to access this data is by linking all these computers into a single network.

Computers can be interconnected in various ways, most commonly via fiber-optic or coaxial cables and wireless communication links, enabling data exchange between remote users.

To ensure the efficient operation of this interconnected network system, a unified communication protocol was developed: TCP/IP (Transmission Control Protocol / Internet Protocol). TCP defines the rules for breaking data down into packets and subsequently reassembling the packets transmitted across the communication channel.

IP manages the addressing and routing of information packets across the network.

Computers connected to the network are treated as nodes and maintain mutual communication through the transmission of data packets.

To execute transmission, data is first divided into small packets (units of information) sent independently of one another, which are then reassembled upon reaching their destination. However, packets are not necessarily routed directly from one machine to another; they may pass through several computers along the path to the final recipient. Should any intermediate node on the chosen route fail, network protocols provide an alternative path-finding function, made possible by the overlapping intersection of various routes.

The Internet provides tools for software distribution and allows researchers to perform complex analyses on remote servers.

Until the late 1980s, there were three primary Methods for accessing Databases via the Internet:

1) email servers;

2) FTP;

3) TELNET servers.

An email server is a medium for transferring text messages from one computer to another.

FTP (File Transfer Protocol) is a protocol for transferring computer files between remote machines.

TELNET is a network protocol that allows an operator to connect to remote computers and work on them as if they had physical access to those machines.

Email servers allowed scientists to exchange information by sending a request via an email message to the mail server's address. Sooner or later, the request was processed by the server, and the result was sent back to the sender's mailbox. However, this system had its drawbacks: requests were handled poorly, prone to errors, and users had to wait indefinitely for a response.

FTP allowed a researcher to download an entire database and perform searches on their own computer. This method of database access also has its flaw: the researcher must periodically download all the databases they use every time they are updated.

TELNET gives users The ability to connect to a remote computer and access its software and hardware resources. This method is useful for sporadic queries. Its disadvantages include complex user authentication management and the overload of the remote computer's Processing capabilities.

Once computers were linked together via a network, the need arose to find an unambiguous way to designate individual computers so that messages and files could be sent strictly to their intended recipient. To facilitate communication between nodes, every computer on the Internet is assigned a unique identifying number (its IP address, or Internet Protocol address). An IP address is unique and designates only one computer. It is written as Arabic numerals separated by periods.

For example, the computer of the National Center for Biotechnology Information (NCBI) at the National Library of Medicine (NLM), part of the National Institutes of Health (NIH) under the US government, has the following IP address: 130.14.29.110.

These numbers designate the specific computer, the node where this computer is located, and the domain (and subdomain) to which this node belongs. These numbers help computers determine data transmission routes.

In addition, an alternative hierarchical domain name system was created, establishing correspondence between numerical IP addresses and text-based names, allowing Internet addresses to be written in a more comprehensible format. For example, the entry "ncbi.nlm.nih.gov" is equivalent to the numbers presented above and stands for: the node of the "National Center for Biotechnology Information" (ncbi) at the "National Library of Medicine" (nlm), part of the "National Institutes of Health" (nih) under the US government (gov).

You can determine the correspondence between numerical IP addresses and text names, as well as the geographical Location of an IP address or Internet node, at: http://smart-ip.net/tools/geoip.

The World Wide Web significantly enhanced cross-referencing capabilities by ensuring the effective integration of databases scattered across the Internet, thereby eliminating the need to download and maintain numerous local copies of databases on individual computers. As a result, researchers can easily browse database records using active hypertext cross-References with the ability to return to the last viewed record.

ExPASy (Expert Protein Analysis System, http://www.expasy.org/), the first molecular biology web server, was established in 1993 through a joint initiative of the Geneva University Hospital and the University of Geneva itself.

Web pages are documents that appear in a browser window when we navigate the World Wide Web. Every document in the network displayed by a browser is called a web page, and the collection of web pages on a given server is collectively referred to as a web site.

In terms of their content, web pages are similar to conventional text documents, except that they are far more flexible, as they can contain links to any other pages and files located within the network.

A website is a collection of interconnected web pages hosted on a single computer. Every website on the Internet is assigned a unique address. The most remarkable feature of web pages is the presence of links. A link on a web page (hyperlink) allows the user to navigate to another page located on the same website, or even to a page on a different website anywhere in the world.

A highly valuable feature of the World Wide Web is straightforward access to static pages containing highlighted clickable text, thereby allowing users to browse interconnected pages with information distributed across them.

An object network is designed to support highly functional dialogue systems. It is a multi-tier architecture comprising two objects and a communication layer.

One object may represent the user interface, while the other handles the necessary computations. To transfer data between these two objects, it is necessary to define the messages they are capable of receiving.

Message exchange between two or more objects is carried out using a special ORB (Object Request Broker) code installed on each machine, which is capable of interpreting the descriptions of transmitted messages and translating them into the native language of each object.

Using an object network, a system can be broken down into independent components written in different languages and running on different hardware platforms.

CORBA (Common Object Request Broker Architecture) provides the standards that unify this communication. CORBA includes a language for describing message structures, IDL (Interface Definition Language), as well as an architecture for intermediary software, or ORBs. ORBs ensure "transparent" communication between remote objects and form the backbone (the object network infrastructure).

Internet browsers or web browsers. The full potential of the Internet was only fully realized with the advent of browsers, which for the first time provided free access to information located across various websites.

Browsers are client Applications that send requests to servers using a set of standard protocols and conventions. A typical web browser contains the minimum set of software tools required to search for, retrieve, display, and transmit information across the Internet.

The first point of contact between a browser and a server is the home page. Once this initial page is loaded, the browser opens up an interface convenient for document retrieval, file access, database searching, and so on.

The most popular web browsers have included Internet Explorer, Google Chrome, Mozilla Firefox, Opera, Lynx, Mosaic, and Netscape Navigator.

Using a browser, users can navigate through the window content or between internet windows by clicking on special words, buttons, or images. These click-activated objects are collectively known as hyperlinks.

When hovered over with the mouse pointer, hyperlinks are usually highlighted in some way—with a contrasting color, underlining, a border, etc. Clicking on a highlighted link retrieves the required document regardless of its location: whether on the same server or on a server in another part of the world.

Every hypertext document is assigned a unique address called a URL (Uniform Resource Locator). A URL string has the following standardized format:

Class="center">http://actual_address.

Here, http is the abbreviation for the communication protocol used by network servers—the HyperText Transfer Protocol (HTTP). This protocol is used for exchanging information within the World Wide Web. The actual address indicates the LOCATION OF THE hypertext document on the Internet.

Hypertext documents are written in a standard markup language known as HTML (HyperText Markup Language). HTML code is strictly text-oriented, and any accompanying graphic or audio information in the document exists as separate files in a common format.

Markup commands allow the author of a web page to format text in bold (<B> tag), insert horizontal rules (<HR>), embed images (<IMG>), and so forth; each of these modes is terminated by the corresponding tag with a slash, such as </> (for example, </B>).

XML (Extensible Markup Language) is another technology that Supports the creation of functional Genetic information repositories. Like HTML, XML can be used to create web pages. XML tags data in a way that is understandable to any other application. This technology provides a common language for data representation in a standard format. It allows files to be described According to the type of data they contain.

XML is a text format designed for storing structured data (as an alternative to existing database files), for exchanging information between programs, and for building more specialized markup languages (such as XHTML) on its basis, sometimes referred to as vocabularies.

XML is more flexible and reliable compared to HTML. It provides a method for describing the meaning, or semantics, of document content. One of its advantages lies in the ability to control not only how data is displayed on a web page, but also how this data is processed by various applications or a DBMS (DataBase Management System).

XML is a simplified subset of SGML (Standard Generalized Markup Language), a metalanguage used to define markup languages for documents. SGML is a descendant of GML (Generalized Markup Language), developed at IBM in 1969.