Files used to perform simulations and process output for Kim et al. PLoSCompBiol 2013, 9(3):e1002953. doi: 10.1371/journal.pcbi.1002953
1. KimPLoSCompBiol2013default.tar.gz
xml files to run NeuroRD for both DSI simulations and long term synaptic plasticity simulations.  UchiModel*.xml is the top level file for the DSI simulations with one random seed (used for single trace figures, i.e., Fig 2A1, 2B1 and Fig 5C).  mglurMaster*.xml is the top level file for the long term synaptic plasticity simulations for one randome seed (used for single trace figures, i.e. Fig 5A1, B1, C, D).

2.  KimPLoSCompBiol2013Robust.tar.gz
xml files used to run robustness simulations (Fig 7).  Most robust*.xml files  are alternative reaction files (replace mglu_2ag_reac12mar20desens025.xml in the top level model file). Robust*Init*.xml are alternative initial condition file (replace mglur_2ag_init12mar1lowrGabg.xml in the top level model file).

3. KimPLoSCompBiol2013MorphLong.tar.gz
xml files used to run simulations using the longer morphology (Fig 9, 10).  Because of the larger volume, the calcium input has been increased, thus the stimulation file is different than the default.  For a similar reason, the diffusion of dhpg has been slowed down to make the dhpg at the stimulated spine similar to that in the default. The output scheme file specifies fewer molecules in order to decrease file size.

4. Version of NeuroRD used to run simulations above: stochdiff_BHK-2.1.1-newtable_NP30.jar
Also called: NeuroRD2.1.1newtableNP30.jar

PostProcess.tar.gz, which can be downloaded from the software page, has items 5 and 6
5. Version of NRDpost (c++) used to process the conc.txt files to obtain single molecules region averages:
nrdpostAB.cpp
nrdpostAB.h
compile the code using the following line:
c++ nrdpostAB.cpp -o NRDPostAB
NRDPostAB - h will list all the different options for use.
The following was used to process the data:
NRDPostAB -i[UchiModel12mar20desen025lowrG_5s0dhpg20sCa12-3-slow-conc.txt] -m[Pkct] -r[UchiModel12mar20desen025lowrG_5s0dhpg20sCa12-3-mesh.txt] -n -o[12mar205s0]  This generates the region averages for active PKC.
Note that any spines called "FAKE" that were created solely to provide dendritic injection will be ignored and not included in the output file.

6. python code
MoleculesAUC.py
This reads in the dataprocessed by NRDPostAB (file name with _avg.txt as suffix). It assumes there are 3 different stimulus durations and 4 dhpg concentrations.  It  calculates the area under the curve for PKC and 2AG for each of these 12 files, and then calculates the ratio with respect to the 0dhpg condition.  Additional molecules can be processed by specifying them in the mollist variable.  Presently, it only operates on the second to last column in the NRDPostAB output file, but additional columns can be processed by adding their column numbers to the meancol variable.

LTPratioMultiSpine.py was used to extract area under the curve and ratios from the long morphology simulations.
This reads in the data processed by NRDPostAB (file name with _avg.txt as suffix).  The number of spines in the morphology must be specified (it will vary with the spine seed), the time that stimulation is applied (stimtime), the time to end calculation of molecule activation (this should be determined by qualitiative evaluation of the results.  Do not include too much time after activation returns to basal, but this time has to be the same for all stimulation conditions.

LTPratio.py was used to extract area under the curve and ratios from the default morphology - both default and robustness reaction and initial conditions.  It is very similar to LTPratioMultiSpine.py This reads in the data processed by NRDPostAB (file name with _avg.txt as suffix).  The list of columns to process from the avg.txt file must be specified.

ReadHeaderAvg.py
This python program can process input that has not first been processed by NRDPostAB and provide output similar to that of NRDPostAB.  The limitation is that each molecule must be in a separate file (this can be achieved using a different output scheme file for NeuroRD).  
It can process multiple molecules and multiple files at once by specifying them in mollist and fnamelist variables. Headername specifies a file which contains the first header line output from NeuroRD - it can either be one of the files in the list above, or a separate file which contains ony the first line of one of the output files in the list.  The name of only one mesh file should be specified.  So, if you are processing multiple files they all must have used the same morphology. fake is the label given to the tiny injection spines that were created solely to provide input to the dendrite.  By default, the average over each spine, and other regions is caculated.  Optionally it will provide a spatial average over the dendrite.  This means it will take the entire dendrite, and subdivide it into 10 (or more or less) areas along a single dimension.  This spatial average is useful for calculating space constant for decay/spread of a molecule along the dendrite. The output of this file can be used as input to LTPratioMultiSpine.py.