Home > Articles

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.

InformIT Promotional Mailings & Special Offers

I would like to receive exclusive offers and hear about products from InformIT and its family of brands. I can unsubscribe at any time.


Pearson Education, Inc., 221 River Street, Hoboken, New Jersey 07030, (Pearson) presents this site to provide information about products and services that can be purchased through this site.

This privacy notice provides an overview of our commitment to privacy and describes how we collect, protect, use and share personal information collected through this site. Please note that other Pearson websites and online products and services have their own separate privacy policies.

Collection and Use of Information

To conduct business and deliver products and services, Pearson collects and uses personal information in several ways in connection with this site, including:

Questions and Inquiries

For inquiries and questions, we collect the inquiry or question, together with name, contact details (email address, phone number and mailing address) and any other additional information voluntarily submitted to us through a Contact Us form or an email. We use this information to address the inquiry and respond to the question.

Online Store

For orders and purchases placed through our online store on this site, we collect order details, name, institution name and address (if applicable), email address, phone number, shipping and billing addresses, credit/debit card information, shipping options and any instructions. We use this information to complete transactions, fulfill orders, communicate with individuals placing orders or visiting the online store, and for related purposes.


Pearson may offer opportunities to provide feedback or participate in surveys, including surveys evaluating Pearson products, services or sites. Participation is voluntary. Pearson collects information requested in the survey questions and uses the information to evaluate, support, maintain and improve products, services or sites, develop new products and services, conduct educational research and for other purposes specified in the survey.

Contests and Drawings

Occasionally, we may sponsor a contest or drawing. Participation is optional. Pearson collects name, contact information and other information specified on the entry form for the contest or drawing to conduct the contest or drawing. Pearson may collect additional personal information from the winners of a contest or drawing in order to award the prize and for tax reporting purposes, as required by law.


If you have elected to receive email newsletters or promotional mailings and special offers but want to unsubscribe, simply email information@informit.com.

Service Announcements

On rare occasions it is necessary to send out a strictly service related announcement. For instance, if our service is temporarily suspended for maintenance we might send users an email. Generally, users may not opt-out of these communications, though they can deactivate their account information. However, these communications are not promotional in nature.

Customer Service

We communicate with users on a regular basis to provide requested services and in regard to issues relating to their account we reply via email or phone in accordance with the users' wishes when a user submits their information through our Contact Us form.

Other Collection and Use of Information

Application and System Logs

Pearson automatically collects log data to help ensure the delivery, availability and security of this site. Log data may include technical information about how a user or visitor connected to this site, such as browser type, type of computer/device, operating system, internet service provider and IP address. We use this information for support purposes and to monitor the health of the site, identify problems, improve service, detect unauthorized access and fraudulent activity, prevent and respond to security incidents and appropriately scale computing resources.

Web Analytics

Pearson may use third party web trend analytical services, including Google Analytics, to collect visitor information, such as IP addresses, browser types, referring pages, pages visited and time spent on a particular site. While these analytical services collect and report information on an anonymous basis, they may use cookies to gather web trend information. The information gathered may enable Pearson (but not the third party web trend services) to link information with application and system log data. Pearson uses this information for system administration and to identify problems, improve service, detect unauthorized access and fraudulent activity, prevent and respond to security incidents, appropriately scale computing resources and otherwise support and deliver this site and its services.

Cookies and Related Technologies

This site uses cookies and similar technologies to personalize content, measure traffic patterns, control security, track use and access of information on this site, and provide interest-based messages and advertising. Users can manage and block the use of cookies through their browser. Disabling or blocking certain cookies may limit the functionality of this site.

Do Not Track

This site currently does not respond to Do Not Track signals.


Pearson uses appropriate physical, administrative and technical security measures to protect personal information from unauthorized access, use and disclosure.


This site is not directed to children under the age of 13.


Pearson may send or direct marketing communications to users, provided that

  • Pearson will not use personal information collected or processed as a K-12 school service provider for the purpose of directed or targeted advertising.
  • Such marketing is consistent with applicable law and Pearson's legal obligations.
  • Pearson will not knowingly direct or send marketing communications to an individual who has expressed a preference not to receive marketing.
  • Where required by applicable law, express or implied consent to marketing exists and has not been withdrawn.

Pearson may provide personal information to a third party service provider on a restricted basis to provide marketing solely on behalf of Pearson or an affiliate or customer for whom Pearson is a service provider. Marketing preferences may be changed at any time.

Correcting/Updating Personal Information

If a user's personally identifiable information changes (such as your postal address or email address), we provide a way to correct or update that user's personal data provided to us. This can be done on the Account page. If a user no longer desires our service and desires to delete his or her account, please contact us at customer-service@informit.com and we will process the deletion of a user's account.


Users can always make an informed choice as to whether they should proceed with certain services offered by InformIT. If you choose to remove yourself from our mailing list(s) simply visit the following page and uncheck any communication you no longer want to receive: www.informit.com/u.aspx.

Sale of Personal Information

Pearson does not rent or sell personal information in exchange for any payment of money.

While Pearson does not sell personal information, as defined in Nevada law, Nevada residents may email a request for no sale of their personal information to NevadaDesignatedRequest@pearson.com.

Supplemental Privacy Statement for California Residents

California residents should read our Supplemental privacy statement for California residents in conjunction with this Privacy Notice. The Supplemental privacy statement for California residents explains Pearson's commitment to comply with California law and applies to personal information of California residents collected in connection with this site and the Services.

Sharing and Disclosure

Pearson may disclose personal information, as follows:

  • As required by law.
  • With the consent of the individual (or their parent, if the individual is a minor)
  • In response to a subpoena, court order or legal process, to the extent permitted or required by law
  • To protect the security and safety of individuals, data, assets and systems, consistent with applicable law
  • In connection the sale, joint venture or other transfer of some or all of its company or assets, subject to the provisions of this Privacy Notice
  • To investigate or address actual or suspected fraud or other illegal activities
  • To exercise its legal rights, including enforcement of the Terms of Use for this site or another contract
  • To affiliated Pearson companies and other companies and organizations who perform work for Pearson and are obligated to protect the privacy of personal information consistent with this Privacy Notice
  • To a school, organization, company or government agency, where Pearson collects or processes the personal information in a school setting or on behalf of such organization, company or government agency.


This web site contains links to other sites. Please be aware that we are not responsible for the privacy practices of such other sites. We encourage our users to be aware when they leave our site and to read the privacy statements of each and every web site that collects Personal Information. This privacy statement applies solely to information collected by this web site.

Requests and Contact

Please contact us about this Privacy Notice or if you have any requests or questions relating to the privacy of your personal information.

Changes to this Privacy Notice

We may revise this Privacy Notice through an updated posting. We will identify the effective date of the revision in the posting. Often, updates are made to provide greater clarity or to comply with changes in regulatory requirements. If the updates involve material changes to the collection, protection, use or disclosure of Personal Information, Pearson will provide notice of the change through a conspicuous notice on this site or other appropriate way. Continued use of the site after the effective date of a posted revision evidences acceptance. Please contact us if you have questions or concerns about the Privacy Notice or any objection to any revisions.

Last Update: November 17, 2020