I save the data from python or matlab and use pgfplots to create stunning plots. Nothing I saw in any other plotting lib came ever close to pgfplots in terms of beauty and flexibility.
I think asymmetric encryption would solve all problems. The sever only ever stores the users public key and uses challenge-response to prevent replay attacks.
This is a bad idea, but if you are required that your uses have passwords, you could use their password to seed an elliptic curve private key to create the user key on the fly.