GitHub - ModelDBRepository/139655: Hippocampus CA1: Simulations of LTP signaling pathways (Kim M et al. 2011)

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Hippocampus CA1: Simulations of LTP signaling pathways (Kim M et al. 2011)

modeldb.science/139655

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Name		Name	Last commit message	Last commit date
Latest commit History 1 Commit
Fig3-CaAC.png		Fig3-CaAC.png
Fig4-PKAAUC.png		Fig4-PKAAUC.png
KimBlackwellPLoSCompBiol_NeuroRDxml.tar		KimBlackwellPLoSCompBiol_NeuroRDxml.tar
NeuroRD-README.txt		NeuroRD-README.txt
StocBatch_ABDE		StocBatch_ABDE
StocMeshMorphMol.jar		StocMeshMorphMol.jar
readme.html		readme.html
stochdiff-2.0.3-mol.jar		stochdiff-2.0.3-mol.jar

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<html><pre>
Here are files associated with a modeling paper in Press in PLoS Comp
Biol.

This computer code was contributed by Avrama Blackwell <kblackw1 at
gmu.edu>

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.

<img src="./Fig3-CaAC.png" alt="Figure 3" height="972" width="418">

Above Figure 3 shows the output from two simulations.

<img src="./Fig4-PKAAUC.png" alt="Figure 4" height="1420" width="528">

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
</pre></html>