CELLULAR BIOPHYSICS SOFTWARE BASED ON MATLAB Thomas Fischer Weiss and Tanmaya Shubham Bhatnagar Department of Electrical Engineering and Computer Science Massachusetts Institute of Technology Fall 1997 Date of last modification: October 25, 1997iiiii Preface Historical perspective During the 1980’s the use of computers and information technologies began to have an impact on higher education (Kulik and Kulik, 1986; Balestri, 1988; Wil-son and Redish, 1989; Athena, 1990a; Athena, 1990b). As an integral part of this trend, in 1983 MIT in partnership with the Digital Equipment Corporation and the IBM Corporation launched Project Athena which was designed to make computa-tion available to undergraduate students through a network of computers located in public clusters on the MIT campus (Athena, 1990a; Athena, 1990b). A major objective of Project Athena was to improve undergraduate education through the use of computation and information technologies. Faculty were encouraged to participate, and support for faculty software developers was provided on a competitive basis. One of us (TFW) has been involved in teaching cellular biophysics at MIT since the 1960’s. The possibility of using software as a pedagogical aid was intriguing. With support from Project Athena, a software package on the Hodgkin-Huxley model for nerve excitation was developed as part of an undergraduate thesis (by David Huang), and was first used to teach cellular biophysics in the Fall 1984 semester. The software was designed to be easy to use so that a student’s atten-tion would be focussed on the Hodgkin-Huxley model and not on the computer. Informal discussions with students and a survey of student views showed that the software was an enormous success. During the first semester, the software was used primarily in lecture demonstrations and as the basis for student projects. Both pedagogic methods were found to be effective. The use of the software in lecture was very effective in motivating and engaging students. The student projects were effective in allowing students to pursue a research project of their choice with staff assistance. For many students this was their first experience with a research project. The use of these projects, developed in the first year, was so successful that it has been used ever since. The initial results with the Hodgkin-Huxley software were so successful ed-ucationally, that several other software development projects involving student programmers were launched. In all, 5 software packages were developed and have been used every year to teach the subject. All of these packages were re-vised extensively in response to suggestions from students and staff. The original software runs on UNIX workstations under MIT’s Project Athena and is available to the MIT community on a network of about 1000 UNIX workstations located in public clusters on the MIT campus as well as in some living groups. All this soft-ware was written in C and XWindows and was based on a library of graphic user interface subroutines written by one of the students (Giancarlo Trevisan). The software has been used in lectures, in recitations held in an electronic classroom in which each student uses a workstation, in homework assignments, and in stu-iv dent projects. Various modes of use of the software in teaching were developed and are described briefly elsewhere (Weiss et al., 1992) and more extensively in the last chapter of this manual. The software has become an integral part of the subject, and it is difficult to imagine teaching the subject without the software. Several problems became apparent in the development and utilization of the software. First, it was very expensive, in time and in money, to develop the soft-ware with the software tools available in the late 1980’s. Much of the time was expended in the development of graphic user interfaces that make the software easy for the user but which are tedious for the programmers to specify. These graphic user interfaces had to be written in a low-level language (XWindows). When Project Athena ended in 1991 and the funds from corporate sponsors were no longer available to support the development of new software, this develop-ment slowed considerably. Second, maintenance of the software became a major headache. It became difficult for a single faculty member with research, teaching, and other academic commitments to maintain a library of software in the face of changes in the operating systems. Third, as word spread about the existence of the software, educators and students outside of MIT requested the software. These requests accelerated dramatically after one of the software packages en-titled Hodgkin-Huxley Model won the 1990 EDUCOM/NCRIPTAL Higher Educa-tion Software award for Best Engineering Software. However, almost all of the requests came from students and faculty with access to Macintosh or PC com-puters and not to UNIX workstations. Thus, when these people were informed that the software ran only on UNIX workstations, they invariably lost interest. At the time the software was written, the computational power of workstations so exceeded that of personal computers (PCs) that it was simply not possible to provide the type of performance on PCs that was achieved on the worksta-tions. Furthermore, MIT’s Project Athena was committed to a network of UNIX workstations. Thus, for both software and hardware considerations, it did not make sense to port the existing software to PCs. Furthermore, the high cost of software development and maintenance did not justify further development of educational software on UNIX workstations alone. Thus, the development of new software was terminated in 1991. By 1995, a number of developments made it feasible to address the problems described above and to develop software for teaching cellular biophysics in a manner that would make it easier to maintain, easier to modify, and widely avail-able. Thus, all the software was rewritten to operate under MATLAB, which is a software package produced by The MathWorks, Inc., for the following reasons: MATLAB is a powerful interpretive computational and visualization soft-• ware package with a large number of higher-level built-in functions. Thus, it is suitable for the development of educational software packages. MATLAB is available for Macintosh computers running on MacOS, PCs run-• ning