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!