Executive Summary
The goal of the Biology Research Software team is to make biological research databases and a suite of software applications accessible to university and high school students and their teachers. This project builds on the success of the collaboration of Professor Graham Walker of the MIT Biology Department; Professor John Belcher of the MIT Physics Department; and Mr. Charles Shubert of the MIT Software Tools for Academics and Researchers (STAR) Program. The intent of this work is to lead the student from introduction to mastering fundamental biology research concepts, and ultimately to independent discovery.
Three additional collaborators for this project are:
History
In the summer of 2005, Mr. Shubert’s project, Bringing Research Tools into the Classroom, was funded as an MIT Information Services and Technology (IS&T) “Big Initiative.” The purpose of the project was to address the need identified by Professor Walker that undergraduate students at MIT should gain a deeper insight into the three-dimensional structure of proteins. Tight time constraints of the MIT Introduction to Biology courses required that the three-dimensional visualization software be easy to use. None of the currently available research software tools were considered sufficiently user-friendly to meet this need. After consulting with Professor Belcher, it was decided that his TEALsim software would be a good platform for developing a new protein visualization software tool. The result of this collaboration is a software application called StarBiochem.
StarBiochem is an application that displays molecules from the Protein Data Bank. It allows users to explore fundamental biological research concepts, select parts of the molecule, and control how the selected parts are displayed.
As of January 24, 2008, over 1100 undergraduate students at MIT and 200 students at Brandeis University have successfully used early versions of the StarBiochem in introductory biology courses. The high school outreach programs of the Broad Institute and the Biology Department at MIT demonstrate the broader impact of this project. Over 300 high school students have successfully used StarBiochem during field trips to MIT and the Broad Institute.
The Need
StarBiochem is an example of how MIT is addressing the need to make research software easier to use in undergraduate courses. For software to be useful in the classroom, the software needs to be instantly available and easy to use. The students do not have the time to learn new software or read a complex manual.
The Project Work
The emphasis of this project will be the dissemination of a growing suite of software applications used for MIT Biology courses. The MIT Biology Department is currently moving to incorporate new computational components into the Biology curriculum. The STAR group is working with MIT’s Biology Department to produce this suite by adapting existing research software and developing new software to access research databases for Biochemistry and Genomics.
This project will take advantage of the ongoing STAR development work in expanding and improving the offerings of the suite of software applications to be disseminated. Examples of this continuing effort to upgrade the suite are the development of a new application for Genetics and the next version of StarBiochem (with more Biochemistry functionality and an improved user interface).
For the suite of software applications to be useful in the classroom, it is necessary to develop curriculum nuggets. A curriculum nugget is composed of the software application, a user guide, a tutorial, and a sample problem set. Curriculum nuggets are designed to be used in the context of an existing core curriculum or to be used independently. This project will facilitate the development of new curriculum nuggets and the improvement of existing ones.
The Dissemination
As with the dissemination of any new technology, it is important to raise awareness of the technology’s merits. We plan to raise awareness and disseminate STAR technology by:
As part of the dissemination emphasis of this project, influential Biology faculty from other institutions, such as Dartmouth, Middlebury, UNH, UConn, Bowdoin, and the University of Maine in the New England area, will be invited to MIT to become familiar with and assist in improving the software suite and the associated pedagogical materials. This type of activity is intended to improve the quality of the software and materials while informing the participants. Both are important to early adoption of new technology and are the focus for this project. The New England Higher Education Recruitment Consortium (http://www.faculty.harvard.edu/01/013.html) lists over 30 institutions that will help identify initial target institutions for disseminating STAR technology.
We expect to participate in conferences that attract Biology and Biochemistry faculty such as American Chemical Society national and regional conferences and meetings on Chemistry and Science Education. We expect to participate in both formal presentation and informal demonstration settings. We will also participate in North East Regional Computing Program (NERCOMP) and other New England based outreach organization conferences.
We will continue to collaborate with existing outreach programs such as the Broad Institute Outreach program to publicize the STAR Biology software. The Broad Outreach program goal is to form connections between the Broad Institute and high school students and teachers in the Boston/Cambridge area that will generate excitement and interest in cutting edge biomedical research. Two features of this program are of particular interest:
The STAR Biology software is used in many of the Broad Institute Outreach program Class Visits. Beyond having the students become familiar with using the biology behind the software, the STAR team regularly uses these events to pilot the classroom use of new STAR software.
The Broad Institute Outreach program Teacher Forums has been used to inform teachers of the STAR software, work with teachers to understand how they can use the software in their classrooms and get a sense of their interest in using the software.
Extensive use will be made of professional networks, personal contacts, and articles in biology newsletters and other publications to raise the awareness of the STAR Biology software and materials.
The STAR Biology software suite, the pedagogical materials, and the public databases of research data are freely accessible on the Internet and are the key to wide dissemination. This facilitates the incorporation of the suite into an existing curriculum with little effort or training.
The Project Leadership
The project Principle Investigator is MIT Biology Professor Graham C. Walker. Beyond his leadership in his research field, Professor Walker is well known for his interest in improving the quality of the educational experience of biology students. His interest in this work is best described by quoting from his Final Annual Report 2007 on his Howard Hughes Medical Institute (HHMI) Professorship:
My major effort during the one-year extension of my HHMI Professorship has been to continue to develop and refine StarBiochem, a freely available, platform-independent 3D protein and nucleic acid viewer designed for educational purposes. StarBiochem combines the power of professional 3D viewers with an easy to use interface designed for undergraduate teaching that incorporates features not found in other 3D viewers intended for educational purposes. We also continued our efforts to learn how to use this new tool most effectively to give undergraduate and high school students a deeper understanding of the 3D structure of proteins and nucleic acids…
Rationale. This project started with my conviction that a very efficient way to teach to structure-function relationships comes from letting students view some of the many deposited PDB (Protein Data Bank) molecules in a 3D environment. This type of hands-on interaction with the molecule provides levels of insights that are not possible by viewing static images on a page on a computer screen. For example, students can not only identify binding pockets and partners, see disease-associated mutations, and observe structural contexts, but they can gain an additional sense of the molecules by physically manipulating them in real-time. Nevertheless, implementing such an interactive yet understandable series of exercises in the average college-level introductory biology course is a daunting task for many reasons. These hurdles include class size, computer and technology availabilities both in the classroom and at home, time devoted to the topic in the syllabus, time involved in creating this type of homework, and the level of understanding of the incoming student. Although there are many freely available software packages that allow the students to explore in 3D, few present the material in a format that makes sense to the average biology student and are simple enough so that the student can use the program outside of the classroom on their own for additional practice.
Goal. I wanted to create a viewer and a series of exercises that presented structures and functions in the same way we presented them in class, was usable outside of the classroom without staff supervision, and that allowed students many of the freedoms and exploratory options of the research-level PDB viewers.
The Project Manager is Mr. Charles Shubert of MIT’s Software Tools for Academics and Researchers (STAR) Program. Mr. Shubert came to MIT in September 2000 to fill a need in the Information Systems Department for expertise in Object-Oriented Programming. Prior to coming to MIT, Mr. Shubert had a long career in commercial software including development of spreadsheet software, presentation graphics software, distributed database software, and communications software. His interest in programming methodologies led to his developing a number of techniques that have become standards for the Open Knowledge Initiative.
Mr. Shubert’s motivation for coming to MIT was the potential for working with researchers to help make their research tools accessible to a larger audience. His hard won experience turning research software into commercial products convinced him that scientific and engineering research was fertile ground for this work.
In late 2004 as Mr. Shubert’s software architecture for the Open Knowledge Initiative Project neared completion, he was urged to meet with Professor Walker to discuss teaching structural biology using visualization software. That meeting quickly led to the collaboration that produced the first version of StarBiochem and, ultimately, to the current work.
The Project Methodology
The software suite development borrows heavily from the techniques for managing the production of commercial software. Emphasis is put on usability testing and developing highly effective user interfaces, as users tend to avoid software that is difficult to use.
An approach that has proved very useful in preparing software for undergraduate courses is to use high school students in outreach programs to try out the software. These field trips provide an early test of the software, the delivery mechanisms, the problem sets, and the software’s usability is a low risk setting. High school students tend to be much closer in age and experience to the undergraduates who will use the software in class than is the case for either STAR developers or graduate teaching assistants.
STAR software and pedagogical materials will be disseminated from http://web.mit.edu/star. This approach allows for monitoring usage, handling problem reporting, and updating software and materials. It also serves as a location where interested students can browse other STAR software and pedagogical materials.
Office of Educational Innovation and Technology
Building NE48, Cambridge, MA 02139-4044
Phone: (617) 252-1981; Fax: (617) 452-4044
