The SD card is part of my plan.
Right now I am using serial communication to talk to a program I wrote to log the arduino.
Ideally, what I want is for the chemist to be able to open the program, set parameters, save that to and SD card, and then the SD card fills the arduino program with the parameters.
The idea is that the chemist can set it and forget it. To put it into context, imagine a professor that has been working on a long synthesis starting from expensive chemicals. Instead of giving the instructions to the undergrad lab assistant and risk ruining weeks of work, he can put the instructions on an SD card and let the machine do the technical stuff.
If it is the first time doing a reaction, he could log everything about the reaction, add reagents mechanically, and then once he has finished, analyze the data and see where he can make improvements. By using the arduino, you can eliminate the human variables. That is the dream of this project. Right now, for my purposes, it is to make it so I do not have to babysit my hood, which would make the chemistry much more enjoyable.
Thanks for the input, if you have any specific ideas or solutions from your project that you are working on, you are more than welcome to post them here.