Customize Intellij to work as a standalone application

Hi,

I would like to utilize the Intellij IDE platform to make a full blown application for my own project. I find the Intellij Project organization pretty awesome along with the language support (syntax highlighting, auto completion etc.). I would like to use all the available functionalities and add on top GUI functionalities that users can use to perform scientific work. I would like to ask where can I start with such a project? I would like to start with a freely available version of course. My project is a 3D visualization based core scientific software where users can create a project and simulation files within the scope of a chosen option (something like creating a python project or a java project and so on). The user can then utilize all the added GUI functionalities of the project and perform simulations and monitor and visualize outputs (graphs or general results). The user should be able to write python based code to add modules (if default modules are not working). I work a lot with python and I have worked with java as well. I would assume that for performing GUI tasks, I should look at c or c++ for heavy Gui tasks. However, I do not know if this is a right approach to building a software and if such a thing is allowed. Any suggestion or guidance is welcome. 

Thanks