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README
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Files used to run simulations from
Oliveira R.F., Kim M., Blackwell K.T. (2012) Subcellular Location of
PKA Controls Striatal Plasticity: Stochastic Simulations in Spiny
Dendrites. PLoS Comput Biol 8:e1002383
These xml files are used as input to NeuroRD - java software for
computationally efficient stochastic simulation of reaction-diffusion
systems. NeuroRD (and information on how to use it) is available for
free download from http://krasnow1.gmu.edu/CENlab/software.html. The
version used for simulations in the publication,
stochdiff-2.0.3.3-mol.jar, is included in this tar file
Several random seeds were used for these figures, only one of the
random seeds is provided in this tar file.
A. Files to generate figures 3 - 5.
1. Top level model files:
MSPNmodel_A_5DaStim_4spine_newa.xml MSPNmodel_D_5DaStim_4spine_newa.xml
MSPNmodel_B_5DaStim_4spine_newa.xml MSPNmodel_E_5DaStim_4spine_newa.xml
MSPNmodel_C_5DaStim_4spine_newa.xml MSPNmodel_F_5DaStim_4spine_newa.xml
Letters A-F above indicate the following:
A: PKA and AC colocalized in the spine (Fig 3, 4)
B: PKA in the dendrite, AC in the spine (Fig 4)
C: AC in the spine, PKA diffusely distributed (Fig 5)
D: PKA in the spine, AC in the dendrite (Fig 3, 4)
E: PKA and AC colocalized in the dendrite (Fig 4)
F: AC in the dendrite, PKA diffusely distributed (Fig 5)
Here is an example run command (for D above) for a unix system shell
prompt:
java -jar ./stochdiff-2.0.3.3-mol.jar MSPNmodel_E_5DaStim_4spine_newa.xml \
MSPNmodel_E_5DaStim_4spine_newa.out >> MSPNmodel_E_5DaStim_4spine_newa.log
2. MSPNreactions_4spine_new.xml
File containing the reactions. This file is also used for the Da
+ Ca simulations (of figure 7), and the bath application (see
below)
3. MSPNmorph_4spinea.xml
file specifying the morphology. This file is also used for the Da
+ Ca simulations, the bath application, robustness simulations
(fig 6), and also fig 8
4. MSPNstim_5DaStim_4spine2.xml
dopamine stimulation.
5. Initial conditions files. One each for cases A through F
MSPNic_A_4spine_new.xml (Fig 3, 4)
MSPNic_B_4spine_new.xml (Fig 4)
MSPNic_C_4spine_new.xml (Fig 5)
MSPNic_D_4spine_new.xml (Fig 3, 4)
MSPNic_E_4spine_new.xml (Fig 4)
MSPNic_F_4spine_new.xml (Fig 5)
6. MSPNio_4spine_newmorph.xml
This specifies the molecules to output to the -conc.txt files
B. Files used to run bath application simulations (figure 2):
1. Top level model files:
MSPNmodel_AE_CaDaBath_4spine_newa.xml - calcium + dopamine
MSPNmodel_AE_CaBath_4spine_newa2.xml - dopamine alone
2. Same reaction files, morphology files, and io files as above
3. Initial conditions place have of PKA and AC in the spine and half
in the dendrite: MSPNic_AE_4spine_new.xml
4. stimulation files:
MSPNstim_Ca_Bath2.xml for calcium alone
MSPNstim_CaDaBath.xml for calcium plus dopamine
C. Files used for control long dendrite + 12 spine simulations (Fig 9:
panels A,B,C,E)
1. top level model file:
MSPNmodel_A_5DaStim_12spine_newa50_long.xml
2. initial conditions - multiple dendritic segments necessitates
multiple surfaceDensity specifications.
MSPNic_A_12spine_new_long.xml
3. morphology (obviously must be longer)
MSPNmorph_12spine_long.xml
4. reactions - this has slower diffusion constant that the 4 spine
reaction file to ensure a dopamine gradient
MSPNreactions_12spine_new50.xml
5. stimulation - slighly more dopamine to compensate for larger
volume to diffuse in, also need to specify the injection site that
corresponds to the differently numbered spines.
MSPNstim_5DaStim_12spine_50_long.xml
6. MSPNio_12spine_newmorph_long.xml
fewer molecules just to save disk space
Examples of how to run simulations using NeuroRD is the NeuroRD.bat.
Examples of how to use the post-processor to extract single molecule
spatial information is in NRDpost.bat
Note the NRDpost program referred to in NRDpost.bat is built with the
command
c++ nrdpost.cpp -o NRDpost
(the most recent version of NRDpost is available at
http://krasnow1.gmu.edu/CENlab/software.html under the Postprocessing
link http://krasnow1.gmu.edu/CENlab/software/PostProcess.tar.gz)