This is a brief note for anybody using BioPhysCode to perform simulation analysis.
The omnicalc documentation is currently out of date. Many apologies! The header to this documentation instructs the users to set up paths in a file called paths.yaml. This has been deprecated in favor of a simpler, python script called config.py.
We encourage any users who wish to perform simulation analysis to use the entire factory code. To get started, clone it and run make help. Documentation for the factory and associated testsets is forthcoming and will be linked here when it’s ready.
Running a standalone instance of omnicalc
The factory prepares an omnicalc instance for a set of projects. It sets up the analysis according to a “connection file”. Users who wish to use omnicalc as a standalone product should have a python distribution with all of the necessary analysis libraries loaded. They should also set up a config.py in their omnicalc folder which looks like the following (pretty printed example).
This config file was automatically generated from the following, more readable factory connection file.
Stay tuned for instructions for using the above connection file in a factory.