Data for DPX expt 140724
Plots for Bid Bax DPX expt 140724
Docs for 140724 DPX expt
Updated calls to builder.parameter to patch pysb.builder

With Jeremy's removal of PySB's dependency on BayesSB (in commit
7ac1d162ee6ba9cf8a3), the estimate=True/False keyword argument to
builder.parameter was removed, in favor of using the "prior" keyword
argument to indicate if a parameter is to be estimated.

In this commit I update all calls to pysb.builder.parameter to match
this change.
Model duplicating the Almeida permeabilization equations
Ignore thesis/_build, _static directories
Fixed missing comma after fix to self.parameter call
Refactored tBid activates Bax into tBid_binds_Bax + activation
Ignore the _downloads file in docs

Created a downloads directory to allow .csv and potentially other data
files to be put there by ipython directive scripts and then referenced
for download. Then added a .gitignore entry to ignore it.
Code and doc script to output .csv files of fit values

I created a new class specific to bid_bim_nbd_release, FitResult, that
stores the results of fit values or initial slope calculations. In this
format it's easy to return the results from the plot scripts and then
convert them to .csv.

Ultimately, it would be better to have the fitting not occur twice, once
for the fitting and once for the plotting. However, that would require
the iPython directive to be able to output plots more robustly.