Hi Mario,
The second two issues can be solved with appmode and ipywidgets. Or possibly even Jupyter book.
Examples
https://hub.mybinder.org/user/gwastro-gwapps-37r8r8mg/apps/gw150914.ipynb
For example of features for Jupyter Book start here.
The documentation on the underlying resources
https://ipywidgets.readthedocs.io/en/stable/index.html
https://jupyter.org/jupyter-book/intro.html
I don’t yet know a good way to handle the first part because presumably you want them to be able to add their own data. Maybe you could have related example data already be there and have a link documenting how to upload and get back to appmode? Or if this is stuff that they can put into a cell and then you can trigger processing via Jupyter Book?
Wayne