I'd say, make sure it's backwards compatible with the old way of doing it because there's a lot of scientists who have been using it for a looong time and don't like change. You have to remember, for a scientist, a tool is just a tool, not all of them are going to invest a lot of time in learning a whole new process.
The old way doesn't have to change. It still exists. Make a wrapper GUI that makes it far more approachable. Syncing and other funtions could be handled by a library that works with either
