Computational workspace for the Thyme Lab for summer 2024.
Things to go this repository (non-exhaustive):
-Guides to explain workflows for gathering data
-All (commented) scripts used to handle data for any step in benchmarking and recovering placements from Enamine papers.
-All processed data (i.e. RMSDs of benchmark placements, center coordinates of DUD-E ligands)
-Graphics (and corresponding Jupyter notebooks/scripts/excel files) of data for publishing
-All ligand files used in attempting to replicate Enamine papers
Things to NEVER go in this repository (because you can go back in the repo history and get these at any point):
-Anything containing a license key - Part of the license agreements is to not share the keys beyond the scope of our lab. Make sure any uploaded scripts that could use a key are scrubbed of using it before uploading. Ideally, if a script does require a license for some reason, make the key or path to the key an argument.
-Anything containing a password - Protect your logins. If you have any files/scripts that uses a password or security key, make sure that it is scrubbed before you push it so that no one else can access your logins.
-Individual files over 50MB - We want to try to keep this repo lightweight (<1GB total would be awesome). Github won't allow you to upload individual files that are over 50MB (I think that is the current limit) anyway. Anything that big is raw data that wouldn't need to go here.