Biology Computing Facilities

Open-access lab. This is a student computing lab, the 'BioMicroLab,' with 27 Power Macintosh computers, two printers, and two scanners: Computers in the lab are regularly updated as funds become available. All are now PowerMac G4's, ranging in power up to models with dual-1.25GHz. PowerPC CPUs. The lab is available to all University students on an 'open-access basis, monitored by student managers, 12 hours a day, Mondays through Fridays, and at all times, via ID-card keyed access, to graduate students and undergraduates working on selected, faculty-supervised projects.

Software on all BioMicroLab computers includes a standard suite of over 30 applications, some for general productivity and scientific use (word processing, spreadsheet, graphics, graphing, math, statistics) and others of special utility in particular areas of Biology (e.g., construction and manipulation of phylogenetic trees, analysis and enhancement of captured images, molecular modeling). Additional communications software on all stations provides a full set of Internet tools and access to various Campus resources such as library catalogs and CD-ROM databases. Other software, some restricted to selected stations in the Lab, is available for special purposes, among them manipulation of scanned data (e.g., conversion of scanned to editable text), conversion of data between Macintosh and Windows/PC environments, multimedia authoring tools, and the full SAS statistics package.

Network access from computers in the BioMicroLab, including access to 'key authorization' required for use of licensed commercial software them, is restricted to those with University Network IDs (uNIDs). All registered students, faculty, and staff have such IDs; for information about passwords associated with uNIDs, see the Campus Information System Web site.

Laboratory-course classrooms ('data-acquisition' labs). There are presently four teaching labs employed for upper-division undergraduate laboratory courses, each equipped with six Power Macintosh G4 computers and a printer. Stations in various of the labs are equipped for image capture (e.g., for video microscopy, time-lapse developmental studies, or analysis of electrophoretic-gel separations) and/or for data-acquisition and experimental control (A/D, D/A, and digital in/out, used, e.g., for physiology and neurobiology lab courses).

All stations in these labs have the same standard software (general productivity, scientific, and communications) available on the BioMicroLab computers. In addition, those with hardware for data-acquisition and experimental control have special software (LabVIEW or BIOPAC AcqKnowledge) for control of that hardware and for analysis of data collected by it.

The Department also has four additional teaching labs, supported by a an Undergraduate Teaching grant from the Howard Hughes Medical Institute and used primarily for lower-division lab courses. These are equipped with a total of 72 PowerMac G4 computers (24 in one of the labs, 16 in each of the oters), all providing the same standard software found on other Biology student stations.

Special Teaching Facilities. Each of the Department's five largest classrooms has a high-quality, LCD-based data projector, a permanently installed Power Mac computer for use with the projector, and ports accepting connections of Mac or PC laptops for data projection. A sixth, similar projector is installed in the open-access BioMicroLab, others are installed in several smaller classroms, including three seminar/discussion-session rooms in the new Skaggs Biology building. Three more are available as mobile systems that can be 'checked out' for use in smaller classrooms or in other small seminar rooms.

There are also four PowerBook G3 laptop computers that can be checked out for teaching or lab-seminar use, either with the permanently installed data projectors or with the mobile ones. Two of these are specifically designated for use by Biology field courses and are equipped for wireless network exchange of data with each other. All these PowerBooks have the standard complement of software installed on student stations.

A fifth teaching-loaner laptop is available for those preferring a Windows/PC system. It is a new Dell Latitude C810, with a 1.13GHz. Pentium III CPU, running Windows 2000 and providing the Microsoft Office XP suite of application software.

Servers. The Department has three high-speed, general-purpose compute servers (Digital/Compaq Alpha systems, two running OpenVMS and one running Digital Unix), two Department-wide AppleShare file servers (PowerMac G4's running MacOS 9), two Web servers (also PowerMac G4's, but running MacOS X/Unix), and a remote-access modem server.

The compute servers are employed for general CPU-intensive applications involving e.g., math (MapleV), statistics (SAS), and phylogenetic-tree constructions (PHYLIP) or for user-specific applications (e.g., energy calculations for large families of protein-folding configurations). One of them provides the powerful 'GCG' set of software programs for comparison and manipulation of genetic-sequence data. Another hosts a special genetics database and associated software devoted to the C. elegans genome. Applications on all three of these servers are accessible to students and faculty via Telnet connections or X-windows server software running on all stations in the BioMicroLab and data-acquisition labs and on stations in Departmental research labs.

The AppleShare servers are used for storage and distribution of course-related materials (lab handouts, sample data sets, etc.), for storage of special purpose graphics (e.g., anatomy) databases accessible for display at student stations, for distribution of free software of special interest to Biology students and faculty or specially configured for their use, for storage of student data generated in the data-acquisition labs, for backup and restoration of software on stations in both the BioMicroLab and the data-acquisition labs, and for copy-protection and monitoring of license compliance for software used in those labs.

Students taking laboratory courses taught in the data-acquisition labs, for example, regularly collect data (e.g., physiological records or video-microscopy images) during lab sessions, store it on one of the Departmental AppleShare servers, then later analyze it and employ it in lab reports at stations in the open-access BioMicroLab or elsewhere.

The computers used for projection control in each of the five projector-equipped classrooms are also configured as AppleShare servers, permitting instructors to transfer files to them, via network, from office or home, for later class presentations.

One of the Web servers, www.biology.utah.edu,' offers general Departmental information, including faculty profiles, event calendars, and descriptions of graduate and undergraduate programs. It also serves individual sites prepared by some faculty with more extensive information about their laboratories and research. The other Web server, 'courses.biology.utah.edu,' hosts faculty sites providing teaching materials associated with specific Biology classes.

The modem server provides off-campus access, via SLIP, ARAP (Apple Remote Access Protocol), or PPP connections, to the Internet (TCP/IP protocols), as well as to Departmental or individual office or lab systems configured as AppleShare or Windows (NetBEUI) servers, and to network-connected printers, for Biology faculty and staff, and for faculty-authorized students and post-docs. (Other routes of remote Internet access are offered by the Campus to all faculty, staff, and students.)

Three of the Department's general servers (one OpenVMS system, the Digital Unix system, and one AppleShare server) also run e-mail software, providing a choice of e-mail 'flavors' and features to faculty, staff, and faculty-authorized students.

Networks. All of Biology's five buildings have full, switched 10/100Mbps. Ethernet service to all offices, labs, and student stations, with infrastructure presently involving 26 fully managed high-performance switches and over 500 connected systems. In buildings containing more than one switch, connections among switches are provided by high-speed, 1Gbps., fiber backbones.

In addition, two large classrooms in the new Skaggs Biology building have Ethernet and power wiring to every seat (combined capacity over 350 seats). An additional seven high-performance 10/100Mbps. switches serves these classroom ports plus another set of 'public' ports along an enclosed bridge joining the Department's two largest buildings, which provides an open-study area for students. Network access via these classroom and study-area ports is controlled by a password-based network identification system that is also used for student network access from dormitories.

The Campus provides fiber connections from buildings to a central fiber-based network and, from that, to both the standard Internet and the newer, high-speed vBNS net. Two of Biology's building connections to the central network were recently upgraded 1Gbps speed; the others have 100Mbps connections to the central campus.

Finally, as in other parts of the College of Science, wireless network access is now available in all of Biology's buildings and in some of the outside areas surrounding them. For further information about this resource, see Biology Department Wireless Network.

Staffing. During periods when the BioMicroLab is open for walk-in access by students, its use is monitored by student lab managers who can respond to simple computer-related questions from users of the lab, e.g., about Internet access or use of printers and scanners.

Management of student and teaching stations and provision of individual help for faculty and staff computers is handled by a full-time computer professional, Spencer Streeter help@

, with expertise in both Macintosh and Windows operating systems.

General planning of computer facilities and setting of usage policies is handled by a Departmental Computer Advisory Committee, with a broad selection of faculty members and a representative designated by the Department's graduate students. A faculty member, Larry Okun okun@

, serves as chair of this committee and, as Director of Biology Computing Facilities has responsibility for general oversight of the Department's computing environment as well as direct management of its central servers and networks.

Another faculty member, Jon Seger, created the Department's Web site and, along with a Web-content Advisory Committee, manages its content.