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Cell Systems Initiative Develops I2 Application

Under the leadership of Bob Franza, Cell Systems Initiative has taken the first steps in enabling biology to make the conceptual leap from describing the cell to understanding how a living system works. Franza believes that to do this, scientists will need three things: a specialized language for biological systems, a new array of tools, and the means for extensive collaboration. Future biologists will need to enter the field with experience in these areas, and so CSI has embarked upon an educational initiative that will create a virtual space to bridge the gap between the activities of the research laboratory and the science classroom.

"Understanding cell systems will require the efforts of several generations of biologists. We need to use animations and other techniques to intrigue students and promote the study of biology," Franza explains.

The first step toward the creation of a virtual classroom is the Labscape digital laboratory assistant, a model-based structure that provides scientists (and students) a clear overview of the scientific/experimental process.

Computer Scientist Larry Arnstein, the PI on the project, first began thinking about computer uses in biology in 1999, although the Labscape design and development process did not begin until earlier this year. The development team includes Chia-Yang Hung, Jing Su, Jong-Hee Kang, Gary Look, Stefan Sigurdsson, and Gaetano Borriello.

"The major challenge was to cast the project in the right light," Arnstein says. "In looking for a way for biologists to communicate better we realized that we had to come up with a language and tools to make their lives easier. We needed to produce something immediately sharable and understandable by others without any extra effort on the part of the scientist. That something turned out to be the ubiquitous lab assistant that we call Labscape."

Larry designed the Labscape user interface (a flow graph) so that it can be used in a number of ways. Using live or recorded video feed from a working biology laboratory, the Labscape assistant will allow students to participate in experiments by following a protocol in progress in the lab and watching the scientists perform the steps. Students would link to the protocol interface used by the scientist to see the recording and analysis of the real data generated by the experiment. Mentoring relationships between students and scientists would allow for a dialog to develop around the steps of the protocol.

A long-term goal for Labscape is to provide an easy way to design experiments to test their hypotheses by selecting from preprogrammed steps and protocols. Students or teams of students could design and submit experiments to be carried out in the biology laboratory, and could watch video of their experiments being performed, and receive and analyze the results.

Students could also use Labscape to learn a protocol before actually performing it in the school laboratory. Or the user interface can provide an interactive experiment simulation tutorial, where the students assemble the reagents and samples and perform the experiment online.

CSI's Lisa Jenschke feels that one of the main strengths of the Labscape assistant is that it will provide both an overview of the procedure and accurate capture of details and results without the need to record details in the traditional lab notebook and then transfer them to the computer.

Labscape's transfer of large data sets, and use of live video feed and extensive simulations make high bandwidth essential.

Over the next few months, the CSI development team and Joe Duncan, Lisa Jenschke, Neil Fanger, and Paul Loriaux will be working with selected high-school students on the further development of Labscape.

Joe Duncan explains why it is so important to include high-school students in the development process. "Our hope and expectation is that the next generation of biologists, which is in high school now, will really embrace this type of tool. By the time these students enter university, using tools like Labscape will be second nature to them."

By Fall 2002, Labscape will be operational in an area high school, with plans to expand the program to at least one other high school the following year.

 

 Bob Franza and Joe Duncan

Bob Franza and Joe Duncan

 Larry Arnstein

Larry Arnstein

Amy PhilipsonInternet2