Understanding Networking in Bioinformatics Information

This chapter is from the book

Bioinformatics Computing

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This chapter is from the book

This chapter is from the book 

Bioinformatics Computing

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Hardware

The major network hardware components are the media and network electronics, as described here.

Media

At the lowest level of the hardware infrastructure is the media used to connect the workstations, sequencing machines, and microarray readers in a network. The most common media are coaxial cable, twisted pair wiring, fiber optics, and, for wireless networks, the ether (see Figure 3-10).

Figure 3-10 Media Characteristics. Bandwidth, cost, security, flexibility, and range reflect the innate physical characteristics of the media as well as the current state of the art in the associated electronics. In this example, ether refers to wireless LAN signals; satellite and point-to-point microwave communications links provide the bandwidth comparable to that of fiber and coaxial cable.

Coaxial Cable. Coaxial cable is popular as a medium for LANs because it's inexpensive and provides the greatest flexibility in installation; it can be folded and kinked with minimal signal loss. The coaxial design, where the center conductor is shielded by a copper or aluminum mesh or foil, provides a relatively secure connection and a high bandwidth. However, from a security perspective, it's virtually impossible to determine if an eavesdropper has tapped a run of coaxial cable. In addition, unlike fiber, it's possible for someone with a sensitive receiver and antenna to remotely pick up signals traveling through coaxial cable, amplify them, and decode the digital stream. This is especially true in coaxial cable designs in which the outer shield is formed by a copper or aluminum wire mesh, which provides incomplete shielding of the inner wire compared to cable made with a solid foil outer shield.

Fiber. As summarized in Figure 3-10, of the most popular media used in networks, glass fiber provides the greatest bandwidth, highest level of security, greatest range, and resistance to electrical noise. Although fiber provides a working range of up to several kilometers with standard electronics, it's less flexible to install compared to copper cable. For example, unlike twisted pair or coaxial cable, fiber can't be snaked through very tight turns because the glass fiber is more fragile than the copper or aluminum wire used in the coaxial cable, twisted pair, or power line cable.

From a security perspective, fiber is the superior medium because, unlike the other copper cables or wireless, there is no radio frequency signal that can be intercepted by a nearby receiver. A wire run in parallel with a twisted pair or coaxial cable acts as an antenna to pick up the signals traversing through the cable that can be amplified and interpreted. In contrast, the light in a fiber cable is confined to the optical fiber, which is additionally shielded by a tough sheath. Furthermore, whereas coaxial cable or twisted pair can be tapped without detection, tapping into a fiber strand results in a marked, detectable drop in signal level because of the loss associated with a physical tap.

Twisted Pair. Twisted pair cable, the wiring used in virtually every office and residence for telephone communications, is a comprise between cost, bandwidth, security, and availability. It's more affordable than coaxial cable or fiber, but the bandwidth isn't as great, and security is a much greater concern. When used with radio frequency network signals, twisted pair cables don't perfectly cancel out the signals traversing the two wires, but act as antennas. As a result, not only are signals in the cable more readily intercepted, but the twisted pair cable is more susceptible to electrical noise in the environment. For this reason, twisted pair may not be able to be used in laboratory settings in which electronic equipment may interfere with the network signals, or in which the radiated network signals may interfere with sensitive laboratory equipment. One option is to use shielded twisted pair cable, but this usually involves running the special cable in walls because standard telephone twisted pair cable is unshielded.

Power Line Cable. Power line cable is a low-cost, low-bandwidth solution to networking. Although it may be suitable for exchanging text-only e-mails and other small files, the limitations of the medium prevent it from being a serious network medium for bioinformatics applications. It may be a viable as part of a redundant backup network system, however.

Ether. As a conduit for light or radio frequency signals, the ether provides the greatest flexibility of the options listed here, but also presents the greatest security risk. Typical internal installations for wireless LANs are limited to the same floor in a building. However, within that space, users may have complete mobility with laptops or desktop workstations that are frequently moved. Optical LANs, based on infrared (IR) links are line-of-sight only, and are limited to a single work area.

Radio frequency communications are also commonly used between buildings, in the form of microwave links. These links tend to be line-of-sight and limited to perhaps 30 miles, depending on terrain and buildings that may interfere with line-of-sight communications. Unlike the radio frequency technology used with LANs, the bandwidth of these links is on the same order as coaxial cable. Similarly, radio frequency satellite links that extend thousands of miles support high-bandwidth transmission rates comparable to that provided by coaxial cable and fiber media.

Note that the media characteristics summarized in Figure 3-10 reflect the physical properties of the media as well as the current state of the art in network electronics. For example, although wireless LANs are limited to a range of about 200 meters because of legal restrictions on the power of the electronics, the ether is capable of supporting communications across virtually infinite distances, and satellite-based wireless Internet connectivity is a viable alternative to wire, fiber, and cable in remote areas. Similarly, although glass fiber is less expensive than coaxial cable, the associated electronics and connectors are more expensive and more difficult to use.

The type of media used for Internet access depends primarily on the types of service available, and secondarily on the bandwidth, security, and cost constraints. For example, the TV cable companies that offer Internet service use coaxial cable to feed cable modems. Conversely, DSL companies provide access to the Internet through the same type of twisted pair used by the telephone companies. Because of the losses associated with ordinary twisted pair cable, DSL service is limited by the distance from a telephone switching station, and the maximum bandwidth diminishes with distance from the station. Many academic institutions and some well-funded biotech firms have access to the Internet through high-bandwidth, secure fiber.

In contrast to the media used for Internet access, the choice of media that can be used to support an internal LAN is more a function of cost, bandwidth requirements, security, ease of installation, and type of existing wiring, if any. For example, many older buildings have spare twisted pair cables running throughout their structure from the telephone service. In some of these buildings, running cables through asbestos or concrete structures many be prohibitively expensive or time-consuming, making wireless the only viable media. Another option is to use the power wiring as a data network medium. However, because the wire isn't twisted but is run parallel, it's more susceptible to noise than the other common types of media, resulting in a significantly lower maximum bandwidth.

Network Electronics

The media running from office to office and across the country become a useful communications channel with the addition of electronics capable of sending and receiving signals through the media. These electronics serve a variety of functions, including:

• Generating signals destined for a recipient somewhere in the network

• Coordinating signals through media in order to minimize interference

• Amplifying and conditioning signals so that they can continue error-free to their destination

• Blocking signals from certain paths to minimize interference in those paths

• Routing signals down the quickest or least-expensive route from source to destination

• Translating signals originally designed to work with one protocol so that they are compatible with networks designed to support other protocols

• Connecting different networks

• Monitoring the status of the network, including the functioning of network electronics and the amount of data on segments of the network

Although there are hundreds of devices on the market that transmit, receive, manage, convert, block, redirect, and monitor signals on the network, most fit into the categories listed in Table 3-3.

Table 3-3 Network Electronics. In addition to these major classifications, many devices combine features common to multiple categories.

Several of the network devices listed in Table 3-3 are illustrated in context in Figure 3-11 on page 130. However, it's important to note that the physical layout of the network depicted in this figure may have little relation to the logical functioning of the network electronics. For example, even though the workstations or clients are connected directly to the printer, all printing requests or jobs may be directed to the print server, which manages the printing queue and buffers printing requests, freeing the processors in the workstation clients to handle other computations instead of devoting machine cycles to managing individual print jobs.

Figure 3-11 Network Hardware. The physical architecture shown here may support a markedly different logical architecture.

Servers

The centerpiece of most bioinformatics networks is a server (or more than one) that supplies files and applications to workstations, printers, and other clients. Servers are typically high-speed dedicated computers with several GB of RAM, multi-GB fast hard drives, and over-engineered power supplies that can withstand power surges and other challenges. Servers vary in size and shape, degree of redundancy, performance, expansion options, amount of noise generated in normal operation, the type of operating system supported, management software, security features, power supply design, amount of cache memory, and price.

Servers are no longer relegated to footlocker-sized cases, but are available in units as small as a pizza box that can be easily stacked in racks to provide high server densities. Related to form factor is the operating environment, in that the compact size often necessitates the use of high-volume fans that not only move large quantities of air over the densely populated motherboards, but that generate considerable noise as well. As such, servers may need to be mounted in a separate room or closet, away from researchers whose work the noise may disrupt. Also related to form factor is the provision for redundancy in the two most common server failure points—the mechanical disks and the power supplies. Many server designs provide internal redundant disks and power supplies that take over as soon as the main units fail.

The typical server used in a bioinformatics laboratory has between 1 and 8 GB of RAM, several hundred GB of disk storage distributed between 2 and 8 drives, 2 power supplies, BIOS password protection, and virus protection. Performance, as measured by throughput in Mbps average response time in milliseconds, and thousands of requests handled per second, is a function of the processor, operating system, amount of RAM available, cache memory, and overall design.

The most common server operating systems are Microsoft Windows 2000, Linux, Solaris, UNIX, and Microsoft .NET. Windows 2000 commands about a third of the server market, in part because of the familiar graphical user interface (GUI) and compatibility with relatively inexpensive server hardware. The relatively new Microsoft .NET Server is Windows 2000–based with added Web development tools. Linux, an increasingly popular operating system for servers and bioinformatics workstations, accounts for only about 5 percent of the overall server operating system market. An advantage of using Linux as a server operating system is cost savings and an abundance of license-free (albeit Spartan) utilities. Linux is considered more stable and reliable than Windows 2000, but more difficult to use. In comparison, Solaris commands a little over 15 percent of the server market, followed by IBM AIX and HP's UX. These various flavors of UNIX account for over a third of the server market, especially in high-end applications, such as massive sequence databases.

In addition to generic servers that serve content to clients on the network, there are specialized server designs, such as cache, file, print, mail, proxy, and terminal servers. A cache server dynamically pulls frequently accessed content from the main servers and maintains the content in cache for later use. The purpose of a cache server is to speed content to clients and to reduce network traffic at the server site. One of the challenges with cache servers is ensuring that the cached files are current and synchronized with the files on the source server. Cache servers usually double as proxy servers, which are designed to intercept and manage client requests in a way that provides increased security by matching incoming messages with outgoing requests. A proxy server acts as a filter that passes valid requests on to a file or Web server or, if it's configured as a cache server, serves the content from its cache. Because the functionality of proxy, firewall, and caching servers is so tightly integrated, they are commonly combined in a single device.

A file server is a server configured to allow workstation clients on the network to use the disk storage on the server for collaborative work, to facilitate archiving, and to provide additional disk storage. File servers typically contain large, high-speed hard drives and comprehensive data management software. Print servers provide buffering and queuing for networked printers.

Web servers provide HTML pages or files to a Web client. A mail server hosts the e-mail system for users on the network, providing processing and storage for e-mail messages. Terminal servers connect several terminals, including dial-up modems, to a single LAN connection. A terminal server has a single network interface and several ports for terminal connections, allowing several terminals to be connected to the network by a single LAN cable.

Remote access servers, also known as communications servers, provide access to users seeking to use a network remotely, especially while traveling away from the main office. A remote access server is typically configured with a firewall and a router to provide security and to limit the remote access to a specific subset of the network. For example, a remote access server may allow access to e-mail and non-confidential files. In this way, if a hacker manages to somehow gain access to the network through the remote access server, he won't be able to destroy or steal confidential data. A remote access server is typically configured with one or more telephone modems so that remote users can call in to the network and read their e-mail and access files from any location with telephone access.

Bridges

A bridge connects two or more network segments and forwards packets between them, amplifying the signal to compensate for the loss associated with splitting a signal across multiple segments. So-called dumb bridges are protocol-specific and are designed to connect networks running the same protocol. These devices simply accept data packets from one segment of a network and forward them on to the other segments. They have no built-in intelligence.

In addition to these bridges, several varieties of bridge design provide processing, enabling data sharing between otherwise incompatible networks. For example, encapsulating bridges encapsulate network data with header information so they are compatible with devices in the destination network. A translating bridge goes one step further and actually translates the data from the source network so that the protocol is compatible with that of the destination network. A filtering bridge, also called a multi-port bridge, directs data from the source network to a specific segment of the destination network, thereby reducing unnecessary traffic on some segments of the network. In addition, there are numerous bridge designs that combine filtering, routing, and security functions.

Routers

A router directs data to the portion of a network meant to receive it rather than broadcasting data to every node of a network. Instead of merely passing information like a dumb bridge, routers monitor network activity and change traffic patterns if necessary to maintain efficiency or throughput. Intelligent routers dynamically reconfigure the communications path to improve availability and reliability.

Routers are rarely used alone but are combined with other devices. For example, routers are located at every gateway and are often included as part of a network switch. Routers are also commonly combined with a network bridge in the form of a brouter. In contrast to switches, routers are typically used at the edges of a network, where intelligence is needed to determine the best path for data.

Switches

A switch is a device that selects a circuit for sending data through a network. A switch, which tends to be simpler, faster, and less expensive than a router, lacks information about the network that a router may use in determining the best circuit or path to use to move data from one part of a network to another. Switches, which lack the intelligence of a router, are normally used in the network backbone and at gateways, where speed is of the essence. Also called LAN switches, data switches, and packet switches, they typically contain buffer memory to hold packets briefly until network resources become available.

Gateways

A gateway links two networks running different protocols by functioning as a router and providing translation and amplification of network signals. Because gateways can connect networks using different protocols, they are slower than simple routers.

Hubs

A standard wired hub is the center of a network physically connected in a star configuration. These hubs generally have little intelligence and serve primarily as a common connection point. However, hubs can also be complex devices that provide bridging and routing between multiple LAN architectures.

Wireless hubs, also known as access points, function like wired hubs but use different protocols that provide for different levels of interoperability. With a wireless hub, a wireless LAN can be established quickly with only a server and wireless modem cards (or PCMCIA cards for laptops). Except for the wired connection to the Internet, there is no need to drill holes in walls and pull cables to individual workstations.

Content Filters

A content filter is a device that prevents workstations from accessing specific types of external Web content, such as high-bandwidth streaming video entertainment. Content filters, which can also be implemented in software, maximize available network bandwidth for work-related content.

Firewalls

A firewall is a dedicated device or suite of programs running on a server that protects a network from unauthorized external access. Firewalls are especially relevant in establishing collaborative intranets that allow, for example, researchers in China to work with information in a U.S. laboratory's intranet around the clock. A flexible firewall is one component in a system that allows external collaborators to freely access the laboratory's internal intranet. Firewalls are typically used in conjunction with routers, gateways, and proxy servers to limit access to internal network resources.

Modems

Modems (short for modulator/demodulator) provide connectivity between a workstation or network with a remote network such as the Internet. Telephone modems translate digital data into analog signals for transmission over a twisted pair telephone line and convert incoming analog data into digital form. Telephone modems have a maximum bandwidth of about 56 Kbps. Cable modems provide the same digital-to-analog and analog-to digital conversion as telephone modems, but they connect to a cable TV circuit and provide a bandwidth of about 1.5 Mbps.

A wireless modem, the equivalent of a telephone modem or NIC, allows a computer to access a wireless hub or access point through radio frequency (RF), or, less frequently, IR light. Wireless modems are protocol-specific, in that they only work with access points following the same communications standard.

Satellites

Orbiting satellites are special cases of servers connected to workstation clients through long-distance radio frequency links. The major complicating factor is the need for local uplink and downlink hardware, including a satellite dish, on the client side. The capabilities of communications satellites are defined by their orbit—GEO (geostationary earth orbit), MEO (medium earth orbit), or LEO (low earth orbit)—as well as their operating frequency and bandwidth. The orbit affects the availability and reliability of communications, the terrestrial antenna requirements, and the latency or lag time associated with transmit and receive operations.

For example, a GEO satellite provides continental coverage and can be used with a fixed terrestrial antenna, but has a significant latency because the satellite is orbiting at 36,000 kilometers. In contrast, a LEO satellite provides only a few Km ground coverage but latency is low because of the 500 to 2000 km orbit. Latency is an issue when data need to be frequently retransmitted because of errors, which is often the case when the receiver is operating at the fringe of the satellite coverage area. As a result, a LEO satellite can provide greater throughput than a GEO satellite, all else being equal.

Network Interface Cards

A Network Interface Card (NIC) is a card or, more often, the part of the workstation motherboard that provides the client-side connectivity to the network. The NIC is connected to the network through a variety of media, including coaxial cable, twisted pair, and fiber.

Network Monitors

A network monitor is a specialized device that can monitor or sniff packets and determine throughput of hardware, as well as detect sources of error, such as a defective network interface card. A network monitor can also be implemented in the form of a software utility running on a workstation attached to the network.

Uninterruptible Power Supplies

An Uninterruptible Power Supply (UPS) is a battery and power-filtering device that can provide emergency power for up to several hours, allowing the hardware to be automatically shut down without data loss. UPSs, especially those with built-in power conditioners, protect sensitive equipment and the data they contain from power surges and sudden, unplanned power outages.