Use of Computers in Biology

In 1992, we were fortunate to receive an NSF grant (NSF 9250420) to set up a computerized classroom/laboratory.  Its primary purpose was to support the teaching of an enhanced ecology course, Biology 318.  The lab also supports students in a variety of other classes, as well as student research.  Peripherals purchased in conjunction with this grant also made our biology department web pages possible.

These pages represent one of several avenues we are taking to disseminate what we have learned from this grant.  

Summary of Completed Project

A Biological Computing Laboratory consisting of eleven computers, printers, a scanner, slidemaker, digitizing board, and video adapter was created for use by undergraduates. The lab supports classes in ecology, aquatic biology, zoology, introductory biology, and environmental leadership, plus workshops for gifted high school students and Marietta College's Women in the Sciences program. Computers were particularly well-received in the workshops and the aquatic biology, zoology, leadership and introductory courses; more work is needed to integrate computers into the ecology class. Lack of funding has prevented implementation of a physiology lab. The computers have been used by students in research projects, two of which will be presented at professional scientific meetings in April, 1995. Thirteen software programs have been developed for use in classes and senior research. These programs range from data analysis and presentation packages to a GIS database for a statewide survey of Odonata. Future plans call for linking the lab to a campus network and the Internet (summer 1995), and dissemination of software developed through a WWW home page. Discussions are ongoing to link classes at Marietta to counterparts in Wisconsin and Korea via Internet to allow collaborative, comparative analysis of environmental data from sites near the respective campuses.

Technical Information

Equipment purchased:

The table below lists which items were purchased as well as their cost:

Item Price Balance
Grant $ 40,952.00
Printer network $ 891.03 $ 40,060.97
Printers (color and laser) $ 3,527.00 $ 36,533.97
Fed X $ 15.50 $ 36,518.47
Modem $ 195.00 $ 36,323.47
Slide maker $ 4,390.00 $ 31,933.47
2 computers: Gateway (desktop & laptop) $ 5,350.00 $ 26,583.47
Tape drive $ 415.00 $ 26,168.47
Targa+ video system $ 3,108.25 $ 23,060.22
Averkey video converter $ 271.00 $ 22,789.22
8 computers: Ace-Tech $14,784.50 $ 8,004.72
HP 4p printer $ 1,025.45 $ 6,979.27
Unisys color scanner $ 1,259.00 $ 5,720.27
Multimedia equipment (CD-ROM, sound, etc.) $ 656.10 $ 5,064.17
Pentium computer $ 2,475.00 $ 2,589.17
16 Mb RAM upgrade $ 360.00 $ 2,229.17
17" monitor upgrade $ 260.00 $ 1,969.17
HP 4P Laserjet Printer $ 999.00 $ 970.17
computer shipping $ 95.00 $ 875.17
printer shipping $ 45.00 $ 830.17
$ 830.17
These items were used to "remodel" the lab: $ 830.17
plywood $ 23.11 $ 807.06
surge suppressers $ 93.80 $ 713.26
equipment cart/locks $ 600.55 $ 112.71
mouse pads $ 38.04 $ 74.67
Final balance: $ 74.67
Total expenditures $40,877.33
Not spent: $ 74.67
Grant: $40,952.00

  We were able to purchase far more equipment than was originally budgeted for due to falling prices in the electronics industry. Lower prices enabled us to buy 486DX computers instead of 386SX computers and we were able to buy a Pentium computer with 16 Mb of RAM and a 17" monitor in place of one of the 486DX computers originally targeted. We were able to purchase a scanner, sound card, and some additional software and hardware with money saved by not purchasing the SigmaScan measurement system. We decided not to purchase the SigmaScan when we realized that the JAVA video analysis system and a scanner would allow us to digitize our data more effectively. The basic lab was set up in the fall of 1992; the last equipment (the Pentium computer) was purchased in December, 1994.

We had planned to integrate the computers with physiological data gathering equipment to support a physiology laboratory. The college was not able to launch a planned capitol campaign to provide, among other things, money for science equipment including the proposed physiology lab. Therefore, we were not able to match the $13,880 already on hand for the physiology lab and to complete that portion of the project, although we are hopeful of doing so in the future.

In addition to the custom-written software described later, the computers were equipped initially with Windows software and WordPerfect. The 486DX computer mounted on a cart for classroom use also was equipped with JAVA image processing software and a number of other packages, including Quatro Pro. Recently, the college has obtained site licenses for all Microsoft software and the computers have been equipped with Word and Excel; the mobile 486DX and the Pentium computer also have Microsoft Office and several graphics packages including Adobe Photoshop and Hijack Pro. Independent student use of the computers is beginning to increase as they become aware of the availability of these programs on the computers.

Availability and use of the lab:

The primary purpose of the lab was to support classes in the biology department by providing an "electronic classroom" in which students would be able to follow the overall presentation at their own terminal. This has been done on numerous occasions. The ecology class, taught in Fall, 1993, in particular made extensive use of the classroom, meeting over 15 times (out of 45 class meetings) in the computer lab. Likewise, the course "Leaders in Environmental Activism" met 5 times in the computer lab. These courses will also make similar use of the laboratory next year. Other classes, including invertebrate and vertebrate zoology, aquatic biology, and environmental biology (160 students in 5 sections) have also made extensive use of the lab as a classroom.

The college has furnished work-study students to allow us to make the lab available to students about 20 hours per week in the evenings and on weekends; the lab is also open from 7-6 each weekday when school is in session. During the past ten days (March 1-10, 1995) the 8 computers in the lab averaged 10.75 log-ons by 5.125 students. Most students log on for over 1 hour at a time. This is in addition to the heavy use being made of the two additional computers (486DX and Pentium) by the students as they prepare senior research project presentations.

Successes and Failures of the Project:

Our biggest disappointment was the failure of the college to secure funding for the physiology lab, which left us unable to use the computers in one of the major and potentially most exciting areas of the grant. Also somewhat disappointing was the response of students to the increased use of computers in modeling in the ecology class in 1993. The students were somewhat negative in their opinions of the use of computers in the class when it was hoped that the computers would make them more interested in the material. Careful study of student evaluations for the course suggest that the source of student discontent was more in the nature of the assignments than in any problems with the computers per se. The course will be taught again in the Fall of 1995 and is being revised to address student concerns. It was interesting to note that students in an environmental leadership course taught in 1994 used the same programs as the ecology class and valued the presence of the computers and the software much more.

It should be noted that the grant as finally awarded reduced the number of computers in the laboratory from the 15 we had requested to 8. It has been the project director's experience that sharing a computer terminal is better when the students are in elementary school than when they are in college; I have noticed that some of the college students, when paired up at a computer, have a tendency to "zone out" if they are not the ones actively controlling the computer.

On the positive side the use of computers was greeted enthusiastically in several classes. Most notably the vertebrate zoology class was excited by the use of a custom-written dinosaur database program in an exercise on computerized data retrieval. The dinosaur program was also a hit with students in the Women in the Sciences (WITS) program; these 4th through 8th graders really enjoyed researching "their" dinosaurs on the computers. The vertebrate zoology students also made extensive use of two custom-written hypertext-like programs which together outlined the evolutionary history of the vertebrates.

The computers also made positive, though less dramatic impact in several other classes. Students in aquatic biology used the computers to produce water-quality reports from benthic macroinvertebrate data they collected in a stream. They also used various utilities in the laboratory to calculate parameters such as water volume, velocity, flow, weight, etc. Students in a cell biology class have used Kinemage (Garland Publishing) to look at 3-dimensional molecular models. Students in invertebrate zoology made extensive use of the computers and custom software to label their insect collections. Finally, and perhaps most heartening, was the enthusiasm of students in environmental biology for the use of the computer lab in an indoor/outdoor exercise on the species-area curve. Students in at least one section were profuse in their praise for this lab; in general, students in all sections thought the computers were a useful portion of the lab. Students are also becoming more accustomed to the use of computers in biology as the mobile computer is brought into classrooms and linked to a large-screen television for classroom demonstrations.

We have noted an increase in the quality of student papers as they are able to devote less time to typing and retyping and more time to actually writing and revising their papers. We are also noting a small but growing trend towards increased numeric and graphical fluency in our students as they find it easier to graph their data and analyze it. These trends are due in part to the availability of computers in the lab. We are hoping that early introduction to the computers in the environmental biology course (second semester of the freshman year) will increase this trend in the future. Further, we are noticing a similar increase in the quality of presentations of students doing senior research projects. The quality of both the graphical analysis of data and the visual aids used in the presentations has improved through use of the computers.

Two students are currently preparing presentations for the April, 1995 meeting of the Ohio Academy of Science; they also will prepare manuscripts for publication. Both of the projects involve extensive use of a database of over 14,000 records of Odonata (dragonflies) in Ohio. Their research depends heavily on computer analysis that would not have been possible without this grant.

From the project director's view, an unanticipated but welcome change due in large part to the project has been the increased computer literacy of two of the faculty members in the department. Along with the computer lab, the department independently purchased better computers for the faculty. As the faculty become more computer literate, they will be more able to utilize the computer lab with their students.

Future Plans:

We have not been able to disseminate our experiences very well to date for a number of reasons. First, the ambivalent response of the students in the ecology class, our main effort in regards to the computer lab, clearly requires more investigation, and the class is taught every other year. It will not be taught again until next year, and we hope to be able to present our findings to a consortium science faculty meeting after that. Second, in our proposal we had indicated that our preferred way of disseminating the information would be over the Internet. The latest information we have is that our computers will be linked up in June, 1995 (the fiber optics have been run to the lab; we are waiting for the server and the campus Internet connection). At that time we will set up a WWW home page and FTP site and make available the software listed below. The availability of the software will be publicized in newsgroups such as sci.bio.ecology.

We are currently having discussions about linking our students to students on other campuses to collaboratively study local ecosystems. The basic concept is that students at each of the sites will make collections form a local habitat - such as a first-order stream - and then exchange and compare data over the Internet. Currently, we are pursuing such arrangements with colleagues in Wisconsin and Korea, and hope to add a site in Europe (Finland) if possible.

We are also looking at placing computers in the laboratories and classrooms as well to facilitate data gathering and analysis. Once the campus network is in place this summer, our next step (if we can find funding) will be to upgrade the computers we now have with more memory, and add computers in the introductory labs, the cell biology lab, and the two lecture halls. This will enable students to send data via the network to the present computer lab, where enough terminals and printers will be available so that the students can individually analyze and graph the data for inclusion in their reports. With faculty computers linked to the network, faculty will easily be able to monitor and assist students (and teams of students) as they work on organizing, analyzing, and drawing conclusions from their data.

Results of the Project:

To date, the computers supplied in this project have made the following presentations possible:

Drouhard, Jody A.  and S.R. Spilatro.  1996.  Aureolaria pedicularia: What specific plant(s) does this plant parasitize and how does this relate to its restricted habitat?  Annual Meeting - Ohio Academy of Science (May 3, 1996).

McShaffrey, D.  1996 - Senior Research Projects in Biology and Environmental Science: A Capstone Approach". 44th Annual Meeting of the North American Benthological Society, Kalispell, Montana. June 4, 1996

McShaffrey, D.  1996 - The Ohio Odonata Survey: A Simple and Economical Approach to a Computerized Geographical Database." 44th Annual Meeting of the North American Benthological Society, Kalispell, Montana. June 6, 1996

McShaffrey, D.  1996 - "A Computerized Geographical Database for the Ohio Odonata Survey." Annual Meeting - Ohio Academy of Science (May 3, 1996).

McShaffrey, D.  1996 - Is Environmental Preservation Possible in an Industrialized Democracy? Questions for Leadership". Leadership and the Liberal Arts Conference, Marietta College (April 14, 1996).

Westfall, D. and McShaffrey, D. 1995. Odonata of Washington County, Ohio. Annual Meeting, Ohio Academy of Science. (April, 1995)

Wooddell, A. and McShaffrey, D. 1995. Correlation of length and frequency of capture in adult Anisoptera (Odonata). Annual Meeting, Ohio Academy of Science. (April, 1995)McShaffrey, D.  1994 - A simple artificial stream and particle tracking analysis (PTA) system for research or classroom use. Annual Meeting, North American Benthological Society.

This paper was completed in part with equipment purchased for the computer lab:

McShaffrey, D. 1992. Comparative functional morphology of larval Stenacron interpunctatum and Rhithrogena pellucida (Ephemeroptera: Heptageniidae) and Ephemerella needhami (Ephemeroptera: Ephemerellidae) with applications in mayfly taxonomy and ecology. Proceedings of the VII International Conference on Ephemeroptera.

Programs developed by Dave McShaffrey for use in the Biological Computing Laboratory (all programs are written in Visual Basic and are Windows-based with graphical interfaces):

Aquatic Ecology WinMac - Benthic macroinvertebrate data analysis (water quality assessment).
Aquavol - Utility for estimating aquarium parameters.
Ecology Ecocyb - Modeling of population growth (exponential, log, age classes), Daisyworld simulation, natural selection, Reynolds number, chaos, predator-prey, competition.
DinoWin - graphics-based comprehensive dinosaur database.
Invertebrate Zoology Zoobase - Phylogenetic database of all animal phyla.
Entlab - labeling program for insect collections.
Vertebrate Zoology Vev - evolution of tetrapods (hypertext).
Fish - evolution of fish groups (hypertext).
Vflash - drill on scientific names.
Dinovol - program for estimating dinosaur weights based on models.
Environmental Biology Specarm - calculation and graphic display of species-area curve data from data collected outdoors.
Senior Research

(Ohio Odonata Survey)

Ohiosurv - GIS system for Odonata Collections in Ohio - over 14,000 records.
Odonate - GIS system for Odonata Collections in Washington County, Ohio - over 300 records.

Project Summary

Philosophical Ramblings

Software

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