Afer 8 years, I have updated this this post for 2021-era Linux (and also to fix bitrotted links). I am extremely joyful to report that the (hard) problem from 2013 appears to have been solved! There is a small addendum at the end to reflect this happy news.
Back in 2013, I started writing code to do a simulation of biological system, and I got stuck after 20 lines.