Bringing Biology Research Software into the Classroom

By Charles Shubert, Senior Strategist and Architect, Software Tools for Academics and Researchers, OEIT

The Davis Educational Foundation and the Howard Hughes Medical Institute fund the OEIT Software Tools for Academics and Researchers (STAR) team “Bringing Biology Research Software into the Classroom” project.

The STAR team approaches all of its projects with an implicit primary goal of meeting the needs of MIT faculty and students first. A key requirement for our software and supporting materials is availability through an on demand service ( In the spirit of the MIT mission statement, the STAR team makes our software and materials accessible to all users. External funding helps us not only to improve the quality of our software and materials for the MIT faculty and students, it helps raise the awareness and use of it worldwide.

The STAR team has focused on three key project goals over the last year:

  • Presenting a workshop for New England undergraduate Biology faculty.
  • Developing teaching materials for StarBiochem and StarGenetics software.
  • Improving the quality of the STAR web site and software user experiences.

We have done extensive work with MIT’s Teaching and Learning Lab (TLL) in the preparation of teaching materials and their assessment. We believe that this collaboration has had a very positive impact on our developing quality teaching materials, and, also, on the quality of the experience in learning Biology concepts for the students who have used these materials.

On December 12, 2008 we established a baseline usage for determining our success with our worldwide outreach efforts by looking at the data from the previous year.

Current usage since establishing the baseline:
    Dec 12, 2008 to August 12, 2009
    4017 visitors making 8514 visits to the STAR web site.

Baseline usage over the same period for the previous year:
    Dec 12, 2007 to August 12, 2008
    1412 visitors making 3612 visits to the STAR web site.

Our goal was to double the usage over the two-year life of the grant. Eight months after establishing a usage baseline, we have over a three-fold increase in our year-on-year usage. We believe that this surge in usage is due in large part to the development of StarGenetics by Ivica Ceraj and its supporting materials by Dr. Lourdes Alemán* of the STAR group. StarGenetics fits nicely into a number of places in existing Biology curricula and it allows faculty to teach genetics concepts in a way that was not possible before the development of StarGenetics.

Dr. Alemán created and led an important workshop on the use of StarBiochem and StarGenetics that has already led to the adoption of STAR Biology software outside MIT. A key element of the acceptance of the STAR software was Dr. Alemán’s creation of example contextual materials and problem sets that make incorporation of the software into an existing Biology curriculum compelling and straight forward and requiring minimal effort.

Dr. Alemán has also created a community of New England Biology undergraduate faculty to promote the use of STAR Biology software by working with Leanne Greeley Bond of the Davis Educational Foundation, members of the MIT Biology faculty, members of the MIT museum, and others. The core members of this community were the participants in the StarBiochem and StarGenetics workshop

We have been working with Dr. Kathy Vandiver from the MIT Museum and have developed a standalone version of the StarBiochem for museum exhibits. The standalone version is useful not only in a museum exhibit, but also for venues with poor Internet connectivity.

We will be participating in an assessment study of the effectiveness of the StarGenetics software with Dr. Stacie Bumgarner from Suffolk University this fall. We are also working with Suffolk University and Florida International University in defining a project lab course that will allow students from those schools to take advantage of research tools, software, and data available at MIT.

Mr. Rocklyn Clarke** of the STAR team provided the technical support for the StarBiochem and StarGenetics workshop as well as a number of other venues where STAR software was used. This support activity has informed how STAR software should be packaged for standalone use.

*Dr. Alemán’s Postdoctoral Associate position is funded by the Davis Educational Foundation and the Howard Hughes Medical Institute.
**Mr. Clarke’s Discovery and Outreach position is funded by the Davis Educational Foundation.