    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