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This chapter is from the book

This chapter is from the book


Bioinformatics R&D involves the generation, capture, management, and repurposing of vast amounts of data. Furthermore, robotic sequencers, nucleotide pattern matchers, and other sources of data can communicate with workstations and other devices on the network only to the extent that the network supports the appropriate protocols or sets of standards that enable unencumbered communications. One of the primary benefits of a computer network is interoperability—the ability of different computers running different operating systems to share data and resources over a network. Furthermore, the more devices that can communicate with each other over a network, the more valuable the network becomes. This interoperability can occur by accident, by a single powerful vendor defining standards, or, more commonly, by a proposal put forth by a recognized standards organization.

The key standards organizations that define or suggest network protocols include the Open Systems Interconnection (OSI) group, the Institute of Electrical and Electronics Engineers (IEEE), the Consultative Committee on International Telegraphy and Telephony/International Telecommunications Union-Telecommunications Sector (CCITT/ITU-T), the American National Standards Institute (ANSI), and the Exchange Carriers Standards Association (ECSA), also known as the Alliance for Telecommunications Industry Solutions (ATIS).

These organizations define protocols by consensus. Unlike laws enacted by the Federal Communications Commission (FCC) or other government agencies, there is no legal penalty for ignoring a standard—other than potential economic peril. As such, most companies abide by these and other protocols.

OSI, begun by the International Organization for Standardization in the late 1970s, defines high-level communications architectures, including the OSI Reference Model (see Table 3-1). The model, which defines everything from the physical medium to the semantics of the messages on the network, corresponds to the original ARPANET model. TCP/IP, the model upon which the current Internet is based, omits layers 5 and 6, the session and presentation levels. As such, TCP/IP illustrates the status of standards in the bioinformatics industry. Because the field is expanding so rapidly, there are multiple "standards," each of which solves a particular problem.

Table 3-1 The OSI Reference Model. OSI defines the communications process into seven different categories that deal with communications and network access.












Dialog coordination



Reliable data transfer



Routing and relaying


Data Link

Technology-specific transfer



Physical connections

The IEEE develops standards for the entire computing industry, including wired and wireless networks. Unlike the OSI protocols, these standards define specific low-level functionality, such as operating frequency, bandwidth, message format, signal voltage, and connector style for computer networks. For example, the IEEE-802.3 10BaseT standard defines Ethernet over ordinary twisted pair cable. The standard defines the cable, the connector type, pin connections, voltage levels, and noise immunity requirements. The most important IEEE standards in bioinformatics are listed in Table 3-2.

Table 3-2 Key Network Protocols.



IEEE 488

Computer to electronic instrument communications; also known as GPIB and HPIB


LAN and MAN standards


Ethernet; the most common LAN specification

IEEE-802.3 10Base-T

Ethernet over twisted pair cable


Wireless LANs


5 GHz, 54 Mbps wireless LAN; shorter range than 2.4 GHz systems, higher bandwidth, and more channels than WiFi


2.4 GHz, 11 Mbps wireless LAN; the most common, most mature; limited channels, also known as WiFi


2.4 GHz, 11 Mbps wireless LAN; enhanced quality of service


2.4 GHz, 22 Mbps wireless LAN; higher-bandwidth version of 802.11b, limited channels


2.4 GHz, 11 Mbps wireless LAN; enhanced security


Digital communications over standard phone lines


Switched packet communications


High-speed (200 Mbps) fiber backbone LAN


Very high-speed (10 Gbps) optical network standard


The protocol of the Internet

The relatively short list of standards in Table 3-2 may give the false impression that there are only a few basic standards that network manufacturers abide by. In reality, there are dozens of extensions to these and other protocols. For example, the extensions shown for IEEE 802.11 illustrate how the standard for wireless LANs has several extensions, each of which provides for significant differences in the frequency, bandwidth, and feature of the communications. The relative contribution of each factor to the overall bioinformatics project depends on the nature of the project. For example, when working with 3D images, bandwidth becomes an issue.

The CCITT/ITU-T develops international network standards that generally involve the telephone network. For example, a prominent standard developed by CCITT/ITU-T is Integrated Services Digital Network (ISDN). The ISDN standard defines digital communications at a rate of up to 128 Kbps over ordinary twisted pair cable. The X.25 protocol, also known as packet switched network, forms the basis for packet communications that is similar to that used by the Internet. ANSI is a U.S. equivalent of the CCITT/ITU-T, in that it publishes voluntary protocols for use by the U.S. computer industry. The most significant ANSI standard that applies to computer networks is the Fiber Distributed Data Interface (FDDI). This networking standard defines a fiber-optic network that operates between 100 and 200 Mbps. A FDDI LAN is often called a Backbone LAN because it's used to join LANs together. The ECSA, a relatively new domestic standards organization, is involved in defining network interconnection standards. An example of a significant ECSA protocol is the Synchronous Optical Network (SONET) a very high-speed (in excess of 10 Gbps) optical communications network.

The most significant protocol used on the Internet is TCP/IP, developed by the Defense Advanced Research Project Agency (DARPA). The Transmission Control Protocol (TCP) component of the standard defines rules for exchanging information with other Internet points at the packet level. In addition, the Internet Protocol (IP) standard defines exchange of information at the Internet address level. TCP/IP, the protocol that defines communications on the Internet, is a packet system. It is the TCP component of the standard that defines how a message is broken down into packets, sized appropriately, and then transmitted over the Internet.

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