Developing and Sustaining Scientific Software Applications for Biochemistry Education

The separations simulations team at RIT has been developing interactive simulations of biological separation processes for over 10 years. Simulations of 1D electrophoresis, 2D electrophoresis and ion exchange chromatography have been presented at ASBMB conferences during that time. The simulations have recently undergone a number of significant changes. Our presentation will detail the challenges overcome in dealing with expanding data resources, advances in Internet technology and the options in computing platforms and operating systems. Early simulations dealt with very limited datasets based only on the Protein Data Bank format; recent developments include Genbank and FASTA formats. First attempts were designed to work only in Windows; this has been expanded to include Mac OSX, Linux and the popular web browsers in all of those platforms. Early programming was done in C++ and Java AWT, which were both platform dependent; our current approach is to develop applications using Java Swing, which in most cases leads to applications that operate on the most common operating systems and browsers. Support for this work has been provided by the RIT Colleges of Science and Computing and Information Science and by the Merck/AAAS Undergraduate Science Research Program.