We've reached the end of Google Summer of Code (it was weeks ago now, but I'm writing this blog post anyway).
Although I've written a lot of code and made a lot of plans, I can't really back off of the project until I see it being used in a way that people (outside and inside of OpenWorm) are actually seeing it. When I came into the project, my long-term goal was an "annotated simulation". This is a system for adding annotations to data, carrying them through to model files, and finally exposing the annotations to end-users upon inspection into simulation results. This is to answer our long standing criticism that, in some way or another, our simulations don't line up with the actual science. (Similar concerns are addressed from a computational perspective in this thread) Over this passed summer, I've gotten the first step to a place where I almost like it, but the second step has stalled significantly, and the third was never started.
