choderalab / assaytools

Modeling and Bayesian analysis of fluorescence and absorbance assays.
http://assaytools.readthedocs.org
GNU Lesser General Public License v2.1
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Adding more experimental design with simulated data in ipynb. #78

Closed sonyahanson closed 7 years ago

sonyahanson commented 7 years ago

Added simulated data with varying Kd to ipynb 2b Bayesian fit for two component binding - simulated data.ipynb.

jchodera commented 7 years ago

Looks neat!

Some specific oddities I noticed:

sonyahanson commented 7 years ago

Updated legends, and added plots for other parameter samples in last commit.

Note the point of this ipython notebook is not to show the feasible range of affinities, but rather to show that indeed when the Kd is lower than the protein concentration our resolving power for delG estimates gets worse.

I realize this image gets cutoff in the github rendering of the notebook, and I'm not sure how to fix that right now, but here is the resulting figure that shows this (already posted on Slack a while ago): image [Vertical lines are real Kd, histogram is our prediction.]

sonyahanson commented 7 years ago

I'm going to merge this, as I'd like to try and implement the emcee sampling methods to see if this improves the equilibration of the trace for the delG, since now it doesn't look that great. Though the result itself is spot on:

image2 [Only blue points (after eqil) used in histogram, real delG is -20.03 k_B T.]