While trying to merge code last night, the main author and I found a major bug that prevented WebLogo from functioning as a standalone server on Windows machines. Running WebLogo from the command line hadn't been tested until, I tried and failed. WebLogo couldn't find the python environment variables needed to run on a windows machine b/c the os.path was being demarcated by colons ":" , which is the case in unix and linux, while in windows the path is being demarcated by ";". It was a puzzle to figure out what was happening. And there are probably many more windows specific errors that may need to be addressed. However, now WebLogo is more portable for use on different operating systems.