msmbuilder/msmbuilder — pull request #380 by rmcgibbo (2014-12-07 00:12:53+00:00)
Title: Uncertainty in ContinuousTimeMSM stationary distribution

This PR fixes #379. I wasn't computing the jacobian correctly, because I blanked on the normalization.
These are the two figures produced by the notebook, which show a comparison of this model with the BayesianMarkovStateModel.

![download_1](https://cloud.githubusercontent.com/assets/641278/5329450/9303d190-7d62-11e4-871d-29279c673034.png)

![download_2](https://cloud.githubusercontent.com/assets/641278/5329449/9229ab5a-7d62-11e4-8f87-942f6f952724.png)