JBioFramework

The 1D electrophoresis application was originally designed as part of a web page. It enables the user to separate and identify proteins by their molecular weights. This is useful as a pre-lab exercise for a basic biochemistry class. The ion exchange application separates proteins based on their charge behavior as a function of pH. It contains about 8 different proteins that can be separated using different stationary phases, pH and salt gradient conditions. This is also a good pre-lab for protein separations. The 2D electrophoresis is the most powerful and accomplished simulation. It has the ability to load any collection of protein sequences in genbank, fasta or pdb format. Separation conditions can be varied. Following the separation the user can explore individual protein spots further through direct links to Internet databases. It also contains some information on protein digestion and mass spectral analysis of proteins. JBioFramework is a freestanding Java application that works in Windows and Mac OS. It should also work in Linux, but has not been tested. It contains three separation simulations for biochemistry and bioinformatics: 1D gel electrophoresis, 2D gel electrophoresis and ion exchange chromatography. The application works with real data sets and each simulation has its own interface, inputs and outputs