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Thank you for the information, from what I can understand the answer is no unless I completely want to rewrite what I have done to date.

The reason I used a notebook is because it is very convenient and the path most users would have used when starting with Sage. That is where I started. I have shifted some work to .sage files for speed and use in multiple worksheets. But for visualization of results the notebook is the most convenient from what I have been able to find. I understand that many things can be done in sage, but sometimes it can be frustrating because a lot of the documentation is pointed at programers not users who are scientists trying to solve a problem without a lot of programming heavy lifting. That is why I started with sage in the first place. I hope this does not come across as a complaint I really like Sage even with the difficulties I encounter.