As my PhD thesis, I wrote a software called GENtle.
Sadly, despite wide usage (including NASA!), and open-source, I found myself unable to maintain the code, time-wise. There is an independently maintained Debian package, though, which I believe lives on.
However, thanks to support from the good folks at Synbiota,
I could re-start GENtle as a pure web application.
The code is on GitHub, so come aplenty and join in the synthetic biology revolution!
If you cannot figure out how to contact me from all the links on this page, chances are you have nothing to say that would interest me. Darwinian spam filter!