Software By James

Because I would rather spend my mental energy figuring out how to automate work flow rather than performing the actual work myself, I have authored much software to eliminate tedium from my life. I have made a majority of my software available under OSS compatible licenses. Most are scientific programs with a focus on x-ray crystallography. But I have written at least one program, Passerby, for general users. Here is a list of several of my favorites, in order of how much I like and use them and how impressive they might be to visitors:

• Passerby - A full featured, python powered, open source password keeper.
• Fluorit - A graphical program for managing fluorometric fibrillogenesis data.
• make-na - A web-based utility to easily create linear DNA and RNA models using Nucleic Acid Builder from David Case's lab at Scripps.
• Desktop DNA Calculator - A program for automating the typical DNA quantitation calculations that professional molecular biologists must do every day.
• extpdb - A program for extracting parts from pdb files.
• dssp2pdb - Converts dssp file to HELIX/SHEET type records for PDB files.
• rib_bone - An extension to Alwyn Jones's O model building program that allows interactive designation of hydrogen bonding and hydration of molecular models.
• stride2pdb - A program to convert stride output to HELIX/SHEET type records for PDB files.