StarBiogene in the Classroom: A Shakedown Cruise from OEIT

By Charles Shubert, Senior Programmer Analyst, Office of Educational Innovation and Technology

Justin Riley, a DUE Office of Educational Innovation and Technology (OEIT) developer, in collaboration with Dr. Megan Rokop, head of the Outreach Program for the Broad Institute of MIT and Harvard took StarBiogene for a shakedown cruise with OEIT Director and Senior Associate Dean Vijay Kumar, the OEIT staff, and guests from DUE, the Department of Biology, and the Broad Institute on July 24, 2007.

StarBiogene, a software product from OEIT, will be used in the MIT Introduction to Biology courses (MIT Course numbers 7.012/3/4). StarBiogene integrates GenePattern developed by the BioInfomatics group at the Broad Institute with other genomics research software also developed at the Broad Institute for use in the classroom.
This shakedown cruise conducted by Dr. Megan Rokop was in the spirit of her Outreach sessions for high school students. The hour long session included:

  • A short lecture on the genomics of identifying tumor types based on genetic markers.

  • A classroom exercise that models the genomics research methodology called Activation Analysis.

  • Use of StarBiogene software to perform Activation Analysis on real tumor data.

The underlying assumption was that the “students” in this session would have no more understanding of the genomics material than the general public. As the result of this cruise most of the “students” left the session with a fairly rich view of how genomics software research tools are used to identify tumor type and the implication on treatment of a tumor. The consensus view is that the session was not only informative, but a lot of fun.

Toward the end of the session Dr. Eric Lander, Director of the Broad Institute, who teaches Course 7.012 dropped by to take a look at StarBiogene and see how well the software will integrate into his course this fall. His reaction was very encouraging. He identified an additional software research tool being developed at the Broad Institute that would be a very useful addition to the StarBiogene research tool set. Justin Riley is investigating.