Oscar4 development I was involved in last year used a SCRUM approach, and has been used to discover entities of biological interest for the ChEBI database (we were interested in solvents). Aspects of extreme programming were used too, with one developer writing unit tests, and another the implementation.
The Chemistry Development Kit also uses independent unit tests extensively, though not in a pure XP style; peer review of code and unit tests is used, though very often unit tests are written to confirm bug reports by others than the person fixing the actual bug.
I recommend you to read this article by Rother et al, 2011, which contains many examples and good references. Surprisingly, it seems that there is some literature on this topic. For example, Interpro is developed using Scrum.