Seems like the problem size is small and persistence is not required, so I'm curious why you use a database at all. Is it more for the querying than the storage? If you don't mind being Windows-specific, LINQ over raw C# objects would be a (nice, simple) possibility. (I'm database-ignorant; trying to learn, not criticize.)
"When I started to develop this tool, I just used SQL, because it was the only database I knew"
You may want to correct that.
IMHO, it's kudos to her for being honest; but... PhD and now an AP? ... uhm...
The researcher in question is smart and an engaging speaker. I've had the privilege of hearing her speak about spreadsheets, which was surprisingly interesting.
Every day is a chance to learn something new.
Great post!
Interesting concept, should be turned into a SaaS!