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Current UI design and guidelines
Disclaimer: I am not a GUI expert, but I have some experience working with GUI for tools and am mostly self-taught in that field. I have a background of computer engineering and am currently doing a master's degree in biomedical engineering. I'm a very poor artist, and I don't have enough experience with web GUI to build a whole html5 experience that would blow everyone away. That being said, I think that my plan (for until everyone feels like going another route) goes the way explained in this page.
Also, English is not my native language so bear with me.
To build the GUI, I thought we could use JavaFX. If you use Eclipse, here's the link to the Eclipse Addon
Model-View-Controller (MVC) is a widely used design pattern in making tools to manipulate data with a user interface. There are many variations of it but the principle mostly stays the same.
I found FXML easy to use and think would provide what we need. With JavaFX Scene Builder You can easily manage the UI and use the template generation tool to rapidly generate controller skeleton for the GUI layout you just made.
FXML supports css, so you can let your imagination wild and do gorgeous styles. You can always embed html5 content in webViews, so you could probably even run javascript or other sorts of thing with that.