/LimitsExptDesign

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Latest commit 310d1a5 Oct 3, 2016 @mktranstrum Commiting all files as described in our Manuscript, 'The limitations … 
…of experimental design in sloppy systems'
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browndata Commiting all files as described in our Manuscript, 'The limitations … Oct 3, 2016
fits
modeling
Compile.sh Commiting all files as described in our Manuscript, 'The limitations … Oct 3, 2016
Exponential.py Commiting all files as described in our Manuscript, 'The limitations … Oct 3, 2016
Exponential.pyc Commiting all files as described in our Manuscript, 'The limitations … Oct 3, 2016
FitApgarDatatoMM.py
FitBrownDatatoMA.py Commiting all files as described in our Manuscript, 'The limitations … Oct 3, 2016
GenerateApgarData.py
Model_PC12_48.py
Optimize_48Model.py Commiting all files as described in our Manuscript, 'The limitations … Oct 3, 2016
README.txt Commiting all files as described in our Manuscript, 'The limitations … Oct 3, 2016
RegenerateBrownData.py
TrueParameters.txt
White2016.sbml
__PC12_48__.c
__PC12_48__.pyf Commiting all files as described in our Manuscript, 'The limitations … Oct 3, 2016
__PC12_MA__.c
__PC12_MA__.pyf Commiting all files as described in our Manuscript, 'The limitations … Oct 3, 2016
__d2PC12_48__.c
__d2PC12_48__.pyf Commiting all files as described in our Manuscript, 'The limitations … Oct 3, 2016
__d2PC12_MA__.c Commiting all files as described in our Manuscript, 'The limitations … Oct 3, 2016
__d2PC12_MA__.pyf Commiting all files as described in our Manuscript, 'The limitations … Oct 3, 2016
__dPC12_48__.c Commiting all files as described in our Manuscript, 'The limitations … Oct 3, 2016
__dPC12_48__.pyf Commiting all files as described in our Manuscript, 'The limitations … Oct 3, 2016
__dPC12_MA__.c Commiting all files as described in our Manuscript, 'The limitations … Oct 3, 2016
__dPC12_MA__.pyf

README.txt 

The scripts in this folder should be used in the following order:
1.  Compile daskr, and models
./Compile.sh
2.  Regenerate data from brown
RegenerateBrownData.py
data saved in folder browndata
3.  Fit Brown data with mass action model
FitBrownDatatoMA.py seed
where seed is the value that will seed the random number generator
Note that this script requires geodesiclm package from https://sourceforge.net/projects/geodesiclm/
Edit this file to control the strength of the regularizing "Prior(s)"
parameter values are saved in folder fits
A good fit will have a Cost (1/2 Chi-squared) of a little more than 800.
4.  Generate artificial data to Apgar expts using MA model with fit parameters
GenerateApgarData.py
Edit this file to determie which parameter values (from step 3) are loaded
data saved in folder apgardata
5.  Fit Apgar data with Michael Menten model
FitApgarDatatoMM.py seed
where seed is the value that will seed the random number generator
Edit this file to determine the strength of the regulariging "Prior" and where it is centered
Typical fits have a Cost (1/2 Chi-squared) of ~50,000.