Publication-ready version without data

Initial publication-ready version with all submodules' code directly included in the repository, but no data.

Trying to attach the data files to the release and see how Zenodo deals with it:

antigen_encoding_cytokine_lods.zip
antigen_encoding_cytokine_timeseries.zip
antigen_encoding_data_misc.zip
antigen_encoding_trained_networks.zip