Here are files associated with a modeling paper in Press in PLoS Comp
Biol.

This computer code was contributed by Avrama Blackwell 

This is a multi-compartmental, stochastic version of the Kim et
al. 2010 paper.  Here there are a few additional reactions, and some
of the rate constants have been updated.  It addresses the role of
molecule anchoring in PKA dependent hippocampal LTP.

1. KimBlackwellPLoSCompBiol_NeuroRDxml.tar contains the xml for
default parameters and for the spine neck length variations.

2. StocMeshMorphMol.jar - java program for extracting concentration of
particular molecules averaged over different spatial regions

3. StocBatch_ABDE - batch file to run the java program to extract the
molecules graphed in the figures describing default simulations
(effect of location).

4. stochdiff-2.0.3-mol.jar - version of NeuroRD, which outputs
molecule quantity, used for the simulations.  The output of this file
is processed by StocMeshMorphMol.

A single simulation takes several days to run.



Above Figure 3 shows the output from two simulations.



Figure 5 shows different molecules output from these and two
additional simulations (ModelA = spine/spine, ModelE = dend/dend,
Model B = spine/dend, Model D = dend/spine).  Most other figures show
traces averaged over multiple random seeds.  I hope that these model
use the random seed in these figures, but I don't guarantee it.

The README file for NeuroRD is also supplied under NeuroRD-README.txt