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Good practices in web applications


I know there are many articles about good practices in web design but no one talk about web applications like for example web e-mail clients or something like that.
My point is that - soon I must rebuild applications for hospitals becouse it's horrible coded and doctors don't like this design becouse they dont know what this app do, too many inputs, buttons etc.

I need good advice in that.

ps I cannot remove those inputs :)
I'm looking for advice, maybe some pages about it, what is important, what is not, becouse there are many many pages and it's connected :)