This is the readme for the models associated with the paper:
Luczak V, Blackwell KT, Abel T, Girault JA, Gervasi N (2017)
Dendritic diameter influences the rate and magnitude of hippocampal
cAMP and PKA transients during beta-adrenergic receptor
activation. Neurobiol Learn Mem 138:10-20
These models were contributed by KT Blackwell.
Modelxxx.xml are the top level model files. See neurord.bat for example of how to simulate these models using neurord, which is available on https://github.com/neurord/stochdiff/releases. The model files specify the reaction file - containing a list of molecule species, diffusion constants and reaction rates, morphology file - which specifies size and shape of model, initial conditions file - specifying the quantity of each molecule, and whether it is membrane localized or not. The model file also specifies the size of the voxels and thickness (third spatial dimension) of the voxels. neurord_analysis.py is used to analyze the output.Experimental data The file 20160830_EPACsh150_100nMISO_RawRatios.xls tabulates the FRET ratio versus time in response to 100 nM isoproteronol using the Epac cAMP sensor. The second time column is the time relative to drug application. The measurements were made at four different locations: soma, proximal dendrites (prox), intermediate dendrites (inter) and distal dendrites (dist). Sheet2 and sheet3 shows the calculation of % increase in FRET for two distal and two proximal dendrites to highlight the greater FRET signal increase in the thinner distal dendrites. 20181120 Note: The excel file of experimental data 20160830_EPACsh150_100nMISO_RawRatios.xls (see above description) was added to this archive.