NCSA NEWS

Using Biology Workbench, high school students learn to do bioinformatics like the professionals

Thanks to new computational tools, scientists can complete in hours research that once took days, weeks, or even months. Sometimes a new tools can even make possible what was once impossible.

A few years ago, for example, it would've been impractical, if not impossible, for high school students to do bioinformatics research in the classroom. The time involved in tracking down biological sequencing data for protein analyses was simply prohibitive; graduation day would've come before any project could've been completed. Today bioinformatics is part of the curricula for the students in Paul Lock's advanced biology class at Urbana High School in Urbana, IL. And a computational tool called Biology Workbench makes it all possible.

Biology Workbench, a Web-based tool that allows biologists and biology students to search many protein and nucleic acid sequence databases through a simple Web interface, was developed at NCSA by Shankar Subramaniam. Maintenance and further development of the workbench is now based at the San Diego Supercomputer Center, where Subramaniam is now a staff member. Development of educational applications for the workbench is based at NCSA under the direction of Senior Research Scientist Eric Jakobsson, who is also a professor of molecular and integrative physiology at the University of Illinois at Urbana-Champaign and head of the bioengineering program at the U of I.

Using Biology Workbench, Lock's students compared amino acid sequences in various organisms and learned to understand the differences and similarities among these organisms. The students then created evolutionary trees that showed how various groups of organisms are related.

"Biology Workbench gives them a hands-on way to look at and compare organisms at the chemical level," said Lock. "They have the freedom to explore and learn about things they have an interest in."

Although Biology Workbench was created to meet the needs of professional biologists who need to access massive amounts of data from a variety of sources, its potential as a teaching tool was seen early on. Lock has been using the workbench since 1998, and with support from NCSA he created his own evolutionary biology curricula that makes students use Biology Workbench in their research. So far, he has created two projects: one in which students compare different organisms by comparing their amino acid sequences, the other in which students compare the protein sequences in various primates in order to understand the different evolutionary trends in primates. Both projects required the use of various sequence databases—the same databases used everyday by biologists involved in a wide range of research projects. As a result, the Urbana High students had a taste of what it's like to be a real biologist searching for answers to perplexing scientific questions.

"Paul takes a tool that scientists use and creates applications that can be used in K-12 education," said Jo Williamson, a graduate student in the U of I College of Education and a graduate research assistant at NCSA who has been researching the use of Biology Workbench in the classroom as part of her dissertation project. "Kids get to use a real scientific tool, which he has put into the context of their biology unit. They learn a lot more than they would just reading about it."

Lock's student agree that the workbench is an interesting, creative tool to help them understand the process of evolution.

"I personally enjoyed using the Biology Workbench because you get to do stuff on your own and you discover things by working on your own," said student Ankita Patel. "It's really easy to use if you follow the instructions. We had an outline to follow, but you can get creative within the outline."

Jakobsson estimated hundreds of high school and college teachers across the country are using the workbench in classroom situations—many who have been taught to use it by another teacher. He compared learning to use the Biology Workbench environment to learning the Windows or Macintosh operating systems. For those with a good background in biology, it doesn't take long to catch on and to realize its potential as a teaching tool.

"Teachers give presentations to other teachers, and the word spreads," said Jakobsson. "That's the way to deploy it in the schools and really have an impact. Once they (teachers) get some basic training and support, they spread the word to others and they often get their own support for their projects. We at NCSA play a vital role in getting people started and contributing some stimulating ideas about scientific issues to explore with the workbench, but the most effective broad dissemination is peer-to-peer, instructor-to-instructor."

Lock is one of several Champaign-Urbana high school teachers who uses Biology Workbench in the classroom. He meets regularly with David Stone of University High School and Sue Herricks of Central Academy to share Web-based learning projects and develop strategies for using them in the classroom. Lock's protein sequencing modules for Biology Workbench are available online at http://bioweb.ncsa.uiuc.edu/educwb/tutorials_current/Anthropology/. For more information on Biology Workbench, see http://workbench.sdsc.edu/.

      --Biology Workbench for use in undergraduate and high school education is funded by the National Science Foundation (see http://bioweb.ncsa.uiuc.edu/educwb/project.html), and the
U. S. Department of Education (see http://www.eot.org/edgrid/ct_btw.shtml).

Access Online | Posted 4-10-2001