Signaling pathways In D1R containing striatal spiny projection neurons (Blackwell et al 2018)

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Accession:239744
We implemented a mechanistic model of signaling pathways activated by dopamine D1 receptors, acetylcholine receptors, and glutamate. We use our novel, computationally efficient simulator, NeuroRD, to simulate stochastic interactions both within and between dendritic spines. Results show that the combined activity of several key plasticity molecules correctly predicts the occurrence of either LTP, LTD or no plasticity for numerous experimental protocols.
Reference:
1 . Blackwell KT, Salinas AG, Tewatia P, English B, Hellgren Kotaleski J, Lovinger DM (2019) Molecular mechanisms underlying striatal synaptic plasticity: relevance to chronic alcohol consumption and seeking. Eur J Neurosci 49:768-783 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Molecular Network; Synapse;
Brain Region(s)/Organism: Basal ganglia; Striatum;
Cell Type(s): Neostriatum medium spiny direct pathway neuron;
Channel(s):
Gap Junctions:
Receptor(s): D1; mGluR5; M1; M4;
Gene(s):
Transmitter(s): Acetylcholine; Dopamine; Endocannabinoid; Glutamate;
Simulation Environment: NeuroRD;
Model Concept(s): G-protein coupled; Long-term Synaptic Plasticity; Signaling pathways; Alcohol Use Disorder;
Implementer(s): Blackwell, Avrama [avrama at gmu.edu];
Search NeuronDB for information about:  Neostriatum medium spiny direct pathway neuron; M1; M4; mGluR5; D1; Acetylcholine; Dopamine; Glutamate; Endocannabinoid;
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README.html
20160830_EPACsh150_100nMISO_RawRatios.xlsx *
IC_SPNspine_alcohol.xml
IC_SPNspineAChm4R_AC1_coupleGqhigh.xml
Model_SPN_STDP-protFino-isiback.xml
Model_SPN_STDP-protFino-isifor.xml
Model_SPN_STDP-protPK-isiback.xml
Model_SPN_STDP-protPK-isifor.xml
Model_SPNspine_GapD_alcohol-stim20hz-alcCtrl.xml
Model_SPNspine_GapD_alcohol-stim20hz-alcIC.xml
Model_SPNspine_GapD_alcohol-stim20hz-alcNMDA.xml
Model_SPNspine_GapD_alcohol-stim20hz-alcNMDA_Da.xml
Model_SPNspine_GapD_alcohol-stim20hz-alcNMDA_Da_IC.xml
Model_SPNspine_GapD_alcohol-stim20hz-alcNMDA_IC.xml
Model_SPNspine_GapD_alcohol-stimtheta-alcCtrl.xml
Model_SPNspine_GapD_alcohol-stimtheta-alcIC.xml
Model_SPNspine_GapD_alcohol-stimtheta-alcNMDA.xml
Model_SPNspine_GapD_alcohol-stimtheta-alcNMDA_Da.xml
Model_SPNspine_GapD_alcohol-stimtheta-alcNMDA_Da_IC.xml
Model_SPNspine_GapD_alcohol-stimtheta-alcNMDA_IC.xml
Model_SPNspineAChm4R_Gshydr5_GapD_plc-stimtheta-blockM1.xml
Model_SPNspineAChm4R_Gshydr5_GapD_plc-stimtheta-blockM4.xml
Model_SPNspineAChm4R_Gshydr5_GapD_plc-stimtheta-blockMGlu.xml
Model_SPNspineAChm4R_Gshydr5_GapD-bath_block-summary.txt
Model_SPNspineAChm4R_Gshydr5_GapD-bathCa.xml
Model_SPNspineAChm4R_Gshydr5_GapD-bathDa.xml
Model_SPNspineAChm4R_Gshydr5_GapD-bathDaCa.xml
Model_SPNspineAChm4R_Gshydr5_GapD-blockCyA.xml
Model_SPNspineAChm4R_Gshydr5_GapD-BlockCyA-bathCa.xml
Model_SPNspineAChm4R_Gshydr5_GapD-blockOA.xml
Model_SPNspineAChm4R_Gshydr5_GapD-BlockOA-bathCa.xml
Model_SPNspineAChm4R_Gshydr5_GapD-blockPap.xml
Model_SPNspineAChm4R_Gshydr5_GapD-blockRoli.xml
Model_SPNspineAChm4R_Gshydr5_GapD-Da0.1.xml
Model_SPNspineAChm4R_Gshydr5_GapD-Da0.3.xml
Model_SPNspineAChm4R_Gshydr5_GapD-Da1.xml
Model_SPNspineAChm4R_Gshydr5_GapD-Da10.xml
Model_SPNspineAChm4R_Gshydr5_GapD-noACh.xml
Model_SPNspineAChm4R_Gshydr5_GapD-nostim.xml
Model_SPNspineAChm4R_Gshydr5_GapD-sp1-stim20hz.xml
Model_SPNspineAChm4R_Gshydr5_GapD-sp1-stimtheta.xml
Model_SPNspineAChm4R_Gshydr5_GapD-sp2adj-stim20hz.xml
Model_SPNspineAChm4R_Gshydr5_GapD-sp2adj-stimtheta.xml
Model_SPNspineAChm4R_Gshydr5_GapD-sp2other-stim20hz.xml
Model_SPNspineAChm4R_Gshydr5_GapD-sp2other-stimtheta.xml
Model_SPNspineAChm4R_Gshydr5_GapD-sp2sep-stim20hz.xml
Model_SPNspineAChm4R_Gshydr5_GapD-sp2sep-stimtheta.xml
Model_SPNspineAChm4R_Gshydr5_GapD-sp3sep-stim20hz.xml
Model_SPNspineAChm4R_Gshydr5_GapD-sp3sep-stimtheta.xml
Model_SPNspineAChm4R_Gshydr5_GapD-stim20hz-AChflat.xml
Model_SPNspineAChm4R_Gshydr5_GapD-stim20hz-AChnoB.xml
Model_SPNspineAChm4R_Gshydr5_GapD-stim20hz-AChnoDip.xml
Model_SPNspineAChm4R_Gshydr5_GapD-stim20hz-blockM1.xml
Model_SPNspineAChm4R_Gshydr5_GapD-stim20hz-blockM4.xml
Model_SPNspineAChm4R_Gshydr5_GapD-stim20hz-blockMGlu.xml
Model_SPNspineAChm4R_Gshydr5_GapD-stim20hz-blockPKA.xml
Model_SPNspineAChm4R_Gshydr5_GapD-stim20hz-blockPKA2.xml
Model_SPNspineAChm4R_Gshydr5_GapD-stim20hz-noCKp.xml
Model_SPNspineAChm4R_Gshydr5_GapD-stim20hz-noDa.xml
Model_SPNspineAChm4R_Gshydr5_GapD-stim20hz-noReb_DaDelay.xml
Model_SPNspineAChm4R_Gshydr5_GapD-stim20hz-noReb_lowACh.xml
Model_SPNspineAChm4R_Gshydr5_GapD-stim20hz-noReb_lowDaDec2.xml
Model_SPNspineAChm4R_Gshydr5_GapD-stim20hz-noReb_lowDaDec3.xml
Model_SPNspineAChm4R_Gshydr5_GapD-stimtheta-AChflat.xml
Model_SPNspineAChm4R_Gshydr5_GapD-stimtheta-AChnoB.xml
Model_SPNspineAChm4R_Gshydr5_GapD-stimtheta-AChnoDip.xml
Model_SPNspineAChm4R_Gshydr5_GapD-stimtheta-blockM1.xml
Model_SPNspineAChm4R_Gshydr5_GapD-stimtheta-blockM4.xml
Model_SPNspineAChm4R_Gshydr5_GapD-stimtheta-blockMGlu.xml
Model_SPNspineAChm4R_Gshydr5_GapD-stimtheta-blockPKA.xml
Model_SPNspineAChm4R_Gshydr5_GapD-stimtheta-blockPKA2.xml
Model_SPNspineAChm4R_Gshydr5_GapD-stimtheta-noCKp.xml
Model_SPNspineAChm4R_Gshydr5_GapD-stimtheta-noDa.xml
Model_SPNspineAChm4R_Gshydr5_GapD-stimtheta-noReb_DaDec1.xml
Model_SPNspineAChm4R_Gshydr5_GapD-stimtheta-noReb_DaDelay.xml
Morph_1sp2umDend.xml
Morph0.9um.xml
Morph1.5um.xml *
Morph20um.xml
MSPN-mergeRateConstTable.xls
NeuroRD.bat
Neurord_stdp.bat
NeuroRDsims.bat
NeuroRDuchi.bat
Out_SPNspineCaMKII_DagL_AChm1R_AC1.xml
Out_SPNspineCaMKII_DagL_AChm1R_AC1subset.xml
Rxn_SPNspineAChm4R_Gshydr5_AC1_GiGsfast-GapD.xml
Rxn_SPNspineAChm4R_Gshydr5_AC1_GiGsfast-GapD_Glublock.xml
Rxn_SPNspineAChm4R_Gshydr5_AC1_GiGsfast-GapD_PKAblock.xml
Rxn_SPNspineAChm4R_Gshydr5_AC1_GiGsfast-GapD_PKAblock2.xml
Rxn_SPNspineAChm4R_Gshydr5_AC1_GiGsfast-GapD-CyA.xml
Stim_AChCyA.xml
Stim_AChOA.xml
Stim_AChpapaverine.xml
Stim_AChrolipram.xml
Stim_CaBathCyA.xml
Stim_CaBathOA.xml
Stim_DaBathCyA.xml
Stim20hzACh-sp1.xml
Stim20hzACh-sp2adj.xml
Stim20hzACh-sp2other.xml
Stim20hzACh-sp2sep.xml
Stim20hzACh-sp3sep.xml
StimCouple20hz_alcohol_LowDaDec3-1tr.xml
StimCouple20hz_alcoholDa_LowDaDec3-1tr.xml
StimCouple20hz_CKpblock-10sITI.xml
StimCouple20hz_DaDelay-10sITI.xml
StimCouple20hz_m1block-10sITI.xml
StimCouple20hz_m4block-10sITI.xml
StimCouple20hzAChlow_LowDaDec3-10sITI.xml
StimCouple20hzAChNoDa-10sITI.xml
StimCouple20hzAChNoDip-10sITI.xml
StimCouple20hzAChNoGlu-10sITI.xml
StimCouple20hzAChNoRebound_LowDaDec2-10sITI.xml
StimCouple20hzAChNoRebound_LowDaDec3-10sITI.xml
StimCouple20hzAChNoRebound_LowDaDec3-10sITI_onset50.xml
StimCouple20hzAChNoRebound_LowDaDec3-1tr.xml
StimCouple20hz-flatACh-10sITI.xml
StimCouple20hz-noAChburst-10sITI.xml
StimCoupleDa0.1.xml
StimCoupleDa0.3.xml
StimCoupleDa1.xml
StimCoupleDa10.xml
StimCoupleSTDP_Fino_backward.xml
StimCoupleSTDP_Fino_forward.xml
StimCoupleSTDP_PK_backward.xml
StimCoupleSTDP_PK_forward.xml
StimCoupleTheta10hz_alcohol_DaDec1-1tr.xml
StimCoupleTheta10hz_alcoholDa_DaDec1-1tr.xml
StimCoupleTheta10hz_CKpblock-15sITI.xml
StimCoupleTheta10hz_DaDelay-15sITI.xml
StimCoupleTheta10hz_m1block-15sITI.xml
StimCoupleTheta10hz_m4block-15sITI.xml
StimCoupleTheta10hzACh-15sITI.xml
StimCoupleTheta10hzAChNoDa-15sITI.xml
StimCoupleTheta10hzAChNoDip-15sITI.xml
StimCoupleTheta10hzAChNoGlu-15sITI.xml
StimCoupleTheta10hzAChNoRebound_DaDec1-15sITI.xml
StimCoupleTheta10hzAChNoRebound_DaDec1-15sITI_onset50.xml
StimCoupleTheta10hzAChNoRebound_DaDec1-1tr.xml
StimCoupleTheta10hz-flatACh-15sITI.xml
StimCoupleTheta10hz-noAChburst-15sITI.xml
StimDend_CaBath.xml
StimDend_DaBath.xml
StimDend_DaCaBath.xml
StimTheta10hzACh-sp1.xml
StimTheta10hzACh-sp2adj.xml
StimTheta10hzACh-sp2other.xml
StimTheta10hzACh-sp2sep.xml
StimTheta10hzACh-sp3sep.xml
                            
 #Always run NeuroRD with the following command line, to direct output into the o utput directory.
 #To start multiple NeuroRD simulations at once, add & at end of each line.
 #run the batch file using: at -f NeuroRD.bat NOW (or you can specify a different time)
#place the following at the top of the file to get additional output
#set -ex

#First line will elminate output, 
#java -Dstochdiff.writers= -jar stochdiff
#Alternatively, can get only h5, only text, or both
#-Dstochdiff.writers=h5
#-Dstochdiff.writers=text
#-Dstochdiff.writers=text,h5

#To avoid information scrolling on screen (and not getting a huge .log file):
#> /dev/null 

#To run things in parallel (instead of batch file):
#parallel --gnu java -Dstochdiff.writers=text -Dstochdiff.log=false -jar /home/neuroware/stochdif/stochdiff-3.0.0-1.jar ::: Model_cAMPassaySoma*.xml

#result: ran very fast: 3 min for 9 voxel model (2.1.9 required 33 min)

#ptdump to look at h5 file.
#-Dneurord.writers=h5,text for text output
#-Dneurord.trials=3 specify number of trials
#-Dneurord.threads=1 to use a single processor for multiple trials.  Omit to run in parallel
# other switches have to come after the jar file specification
# -v to get more information (but not too much) in log (eventually including number of particles injected for each type), -vv to get way too much information
#-Dneurord.SDRun.runtime=1 will override the runtime in the Model file
# --ic-time -1 --ic ss_bath/Model_SPNspineCaMKII_DagL_AChm4R-nostim.h5 Specify file from which to obtain initial conditions (for re-start), specify time to take IC.
#java -jar -Dneurord.writers=h5  /home/neuroware/stochdif/neurord-3.1.2.jar -Dneurord.SDRun.runtime=1 -v Model_SPNspineCaMKII_DagL_AChm4R_Gshydr5_AC1-nostim.xml#This will be useful to avoid awkward updating of initial conditions, or to have very little initial simulation time for equilibrium
#Unknown how this command will work with multi-trial h5 files

#ls UchiNew/Model_SPNspineAChm4R_Gshydr5_AC1_GiGsfast_Uchi-Ca*.xml |xargs sed -i s/"<runtime>          100000"/"<runtime>          150000"/g

#stimulate 1 spine, evaluate dendritic signature vs spine, and spatial specificity

#6 processors available bath-block and PDE block (2 sets of 2) :
#java -jar  /home/neuroware/stochdif/neurord-3.2.3-all-deps.jar --ic-time -1 --ic Model_SPNspineAChm4R_Gshydr5_GapD-nostim.h5 -v -s injections -Dneurord.trials=3 Model_SPNspineAChm4R_Gshydr5_GapD-BlockOA-bathCa.xml ss_bath/ &
#java -jar  /home/neuroware/stochdif/neurord-3.2.3-all-deps.jar --ic-time -1 --ic Model_SPNspineAChm4R_Gshydr5_GapD-nostim.h5 -v -s injections -Dneurord.trials=3 Model_SPNspineAChm4R_Gshydr5_GapD-BlockCyA-bathCa.xml ss_bath/ 

#1 -T
java -jar  /home/neuroware/stochdif/neurord-3.2.3-all-deps.jar --ic-time -1 --ic Model_SPNspineAChm4R_Gshydr5_GapD-nostim.h5 -v -s injections -Dneurord.trials=3 UchiNew/Model_SPNspineAChm4R_Gshydr5_AC1_GiGsfast_Uchi-Ca100m-dhpg25.xml UchiNew/ &
java -jar  /home/neuroware/stochdif/neurord-3.2.3-all-deps.jar --ic-time -1 --ic Model_SPNspineAChm4R_Gshydr5_GapD-nostim.h5 -v -s injections -Dneurord.trials=3 UchiNew/Model_SPNspineAChm4R_Gshydr5_AC1_GiGsfast_Uchi-Ca100m-dhpg0.xml UchiNew/ &
java -jar  /home/neuroware/stochdif/neurord-3.2.3-all-deps.jar --ic-time -1 --ic Model_SPNspineAChm4R_Gshydr5_GapD-nostim.h5 -v -s injections -Dneurord.trials=3 UchiNew/Model_SPNspineAChm4R_Gshydr5_AC1_GiGsfast_Uchi-Ca100m-dhpg1.xml UchiNew/ &
java -jar  /home/neuroware/stochdif/neurord-3.2.3-all-deps.jar --ic-time -1 --ic Model_SPNspineAChm4R_Gshydr5_GapD-nostim.h5 -v -s injections -Dneurord.trials=3 UchiNew/Model_SPNspineAChm4R_Gshydr5_AC1_GiGsfast_Uchi-Ca100m-dhpg5.xml UchiNew/ 

#1.3
java -jar  /home/neuroware/stochdif/neurord-3.2.3-all-deps.jar --ic-time -1 --ic Model_SPNspineAChm4R_Gshydr5_GapD-nostim.h5 -v -s injections -Dneurord.trials=3 UchiNew/Model_SPNspineAChm4R_Gshydr5_AC1_GiGsfast_Uchi-Ca1s-dhpg25.xml UchiNew/ &
java -jar  /home/neuroware/stochdif/neurord-3.2.3-all-deps.jar --ic-time -1 --ic Model_SPNspineAChm4R_Gshydr5_GapD-nostim.h5 -v -s injections -Dneurord.trials=3 UchiNew/Model_SPNspineAChm4R_Gshydr5_AC1_GiGsfast_Uchi-Ca1s-dhpg5.xml UchiNew/ &
java -jar  /home/neuroware/stochdif/neurord-3.2.3-all-deps.jar --ic-time -1 --ic Model_SPNspineAChm4R_Gshydr5_GapD-nostim.h5 -v -s injections -Dneurord.trials=3 UchiNew/Model_SPNspineAChm4R_Gshydr5_AC1_GiGsfast_Uchi-Ca1s-dhpg0.xml UchiNew/ &
java -jar  /home/neuroware/stochdif/neurord-3.2.3-all-deps.jar --ic-time -1 --ic Model_SPNspineAChm4R_Gshydr5_GapD-nostim.h5 -v -s injections -Dneurord.trials=3 UchiNew/Model_SPNspineAChm4R_Gshydr5_AC1_GiGsfast_Uchi-Ca1s-dhpg1.xml UchiNew/ 

#1.6 
java -jar  /home/neuroware/stochdif/neurord-3.2.3-all-deps.jar --ic-time -1 --ic Model_SPNspineAChm4R_Gshydr5_GapD-nostim.h5 -v -s injections -Dneurord.trials=3 UchiNew/Model_SPNspineAChm4R_Gshydr5_AC1_GiGsfast_Uchi-Ca5s-dhpg0.xml UchiNew/ &
java -jar  /home/neuroware/stochdif/neurord-3.2.3-all-deps.jar --ic-time -1 --ic Model_SPNspineAChm4R_Gshydr5_GapD-nostim.h5 -v -s injections -Dneurord.trials=3 UchiNew/Model_SPNspineAChm4R_Gshydr5_AC1_GiGsfast_Uchi-Ca5s-dhpg1.xml UchiNew/ &
java -jar  /home/neuroware/stochdif/neurord-3.2.3-all-deps.jar --ic-time -1 --ic Model_SPNspineAChm4R_Gshydr5_GapD-nostim.h5 -v -s injections -Dneurord.trials=3 UchiNew/Model_SPNspineAChm4R_Gshydr5_AC1_GiGsfast_Uchi-Ca5s-dhpg25.xml UchiNew/ &
java -jar  /home/neuroware/stochdif/neurord-3.2.3-all-deps.jar --ic-time -1 --ic Model_SPNspineAChm4R_Gshydr5_GapD-nostim.h5 -v -s injections -Dneurord.trials=3 UchiNew/Model_SPNspineAChm4R_Gshydr5_AC1_GiGsfast_Uchi-Ca5s-dhpg5.xml UchiNew/  

#3 -W
java -jar  /home/neuroware/stochdif/neurord-3.2.3-all-deps.jar --ic-time -1 --ic Model_SPNspineAChm4R_Gshydr5_GapD-nostim.h5 -v -s injections -Dneurord.trials=3 Model_SPNspineAChm4R_Gshydr5_GapD-blockPap.xml ss_bath/ &
java -jar  /home/neuroware/stochdif/neurord-3.2.3-all-deps.jar --ic-time -1 --ic Model_SPNspineAChm4R_Gshydr5_GapD-nostim.h5 -v -s injections -Dneurord.trials=3 Model_SPNspineAChm4R_Gshydr5_GapD-blockRoli.xml ss_bath/ & 

#Da dur 
java -jar  /home/neuroware/stochdif/neurord-3.2.3-all-deps.jar --ic-time -1 --ic Model_SPNspineAChm4R_Gshydr5_GapD-nostim.h5 -v -s injections -Dneurord.trials=3 Model_SPNspineAChm4R_Gshydr5_GapD-Da0.1.xml ss_bath/ &
java -jar  /home/neuroware/stochdif/neurord-3.2.3-all-deps.jar --ic-time -1 --ic Model_SPNspineAChm4R_Gshydr5_GapD-nostim.h5 -v -s injections -Dneurord.trials=3 Model_SPNspineAChm4R_Gshydr5_GapD-Da0.3.xml ss_bath/ &
java -jar  /home/neuroware/stochdif/neurord-3.2.3-all-deps.jar --ic-time -1 --ic Model_SPNspineAChm4R_Gshydr5_GapD-nostim.h5 -v -s injections -Dneurord.trials=3 Model_SPNspineAChm4R_Gshydr5_GapD-Da1.xml ss_bath/ 
java -jar  /home/neuroware/stochdif/neurord-3.2.3-all-deps.jar --ic-time -1 --ic Model_SPNspineAChm4R_Gshydr5_GapD-nostim.h5 -v -s injections -Dneurord.trials=3 Model_SPNspineAChm4R_Gshydr5_GapD-Da10.xml ss_bath/ & 

# 4 -W 
java -jar  /home/neuroware/stochdif/neurord-3.2.3-all-deps.jar --ic-time -1 --ic Model_SPNspineAChm4R_Gshydr5_GapD-nostim.h5 -v -s injections -Dneurord.trials=3 Model_SPNspineAChm4R_Gshydr5_GapD-noACh.xml ss_bath/ &
java -jar  /home/neuroware/stochdif/neurord-3.2.3-all-deps.jar --ic-time -1 --ic Model_SPNspineAChm4R_Gshydr5_GapD-nostim.h5 -v -s injections -Dneurord.trials=3 Model_SPNspineAChm4R_Gshydr5_GapD-stim20hz-noReb_DaDelay.xml &

java -jar  /home/neuroware/stochdif/neurord-3.2.3-all-deps.jar --ic-time -1 --ic Model_SPNspineAChm4R_Gshydr5_GapD-nostim.h5 -v -s injections -Dneurord.trials=3 Model_SPNspine_GapD_alcohol-stimtheta-alcCtrl.xml &
java -jar  /home/neuroware/stochdif/neurord-3.2.3-all-deps.jar --ic-time -1 --ic Model_SPNspineAChm4R_Gshydr5_GapD-nostim.h5 -v -s injections -Dneurord.trials=3 Model_SPNspine_GapD_alcohol-stim20hz-alcCtrl.xml 

#5 -R 
java -jar  /home/neuroware/stochdif/neurord-3.2.3-all-deps.jar --ic-time -1 --ic Model_SPNspineAChm4R_Gshydr5_GapD-nostim.h5 -v -s injections -Dneurord.trials=3 Model_SPNspine_GapD_alcohol-stim20hz-alcNMDA.xml &
java -jar  /home/neuroware/stochdif/neurord-3.2.3-all-deps.jar --ic-time -1 --ic Model_SPNspineAChm4R_Gshydr5_GapD-nostim.h5 -v -s injections -Dneurord.trials=3 Model_SPNspine_GapD_alcohol-stimtheta-alcNMDA.xml &
java -jar  /home/neuroware/stochdif/neurord-3.2.3-all-deps.jar --ic-time -1 --ic Model_SPNspineAChm4R_Gshydr5_GapD-nostim.h5 -v -s injections -Dneurord.trials=3 Model_SPNspine_GapD_alcohol-stim20hz-alcNMDA_Da.xml &
java -jar  /home/neuroware/stochdif/neurord-3.2.3-all-deps.jar --ic-time -1 --ic Model_SPNspineAChm4R_Gshydr5_GapD-nostim.h5 -v -s injections -Dneurord.trials=3 Model_SPNspine_GapD_alcohol-stimtheta-alcNMDA_Da.xml &

java -jar  /home/neuroware/stochdif/neurord-3.2.3-all-deps.jar -v -s injections -Dneurord.trials=3 Model_SPNspine_GapD_alcohol-stim20hz-alcIC.xml 
java -jar  /home/neuroware/stochdif/neurord-3.2.3-all-deps.jar -v -s injections -Dneurord.trials=3 Model_SPNspine_GapD_alcohol-stimtheta-alcIC.xml &

#6 -R aft
java -jar  /home/neuroware/stochdif/neurord-3.2.3-all-deps.jar -v -s injections -Dneurord.trials=3 Model_SPNspine_GapD_alcohol-stim20hz-alcNMDA_Da_IC.xml &
java -jar  /home/neuroware/stochdif/neurord-3.2.3-all-deps.jar -v -s injections -Dneurord.trials=3 Model_SPNspine_GapD_alcohol-stimtheta-alcNMDA_Da_IC.xml &
java -jar  /home/neuroware/stochdif/neurord-3.2.3-all-deps.jar -v -s injections -Dneurord.trials=3 Model_SPNspine_GapD_alcohol-stim20hz-alcNMDA_IC.xml &
java -jar  /home/neuroware/stochdif/neurord-3.2.3-all-deps.jar -v -s injections -Dneurord.trials=3 Model_SPNspine_GapD_alcohol-stimtheta-alcNMDA_IC.xml 

#Da or PKA blocked (no Da) should worsen theta LTP and enhance 20hz LTD -F aft
java -jar  /home/neuroware/stochdif/neurord-3.2.3-all-deps.jar --ic-time -1 --ic Model_SPNspineAChm4R_Gshydr5_GapD-nostim.h5 -v -s injections -Dneurord.trials=3 Model_SPNspineAChm4R_Gshydr5_GapD-stim20hz-noDa.xml &
java -jar  /home/neuroware/stochdif/neurord-3.2.3-all-deps.jar --ic-time -1 --ic Model_SPNspineAChm4R_Gshydr5_GapD-nostim.h5 -v -s injections -Dneurord.trials=3 Model_SPNspineAChm4R_Gshydr5_GapD-stimtheta-noDa.xml &

java -jar  /home/neuroware/stochdif/neurord-3.2.3-all-deps.jar --ic-time -1 --ic Model_SPNspineAChm4R_Gshydr5_GapD-nostim.h5 -v -s injections -Dneurord.trials=3 Model_SPNspineAChm4R_Gshydr5_GapD-stim20hz-blockPKA2.xml &
java -jar  /home/neuroware/stochdif/neurord-3.2.3-all-deps.jar --ic-time -1 --ic Model_SPNspineAChm4R_Gshydr5_GapD-nostim.h5 -v -s injections -Dneurord.trials=3 Model_SPNspineAChm4R_Gshydr5_GapD-stimtheta-blockPKA2.xml

#7 begin Fri Jun 30 - takes two weeks - ready mid July
java -jar  /home/neuroware/stochdif/neurord-3.2.3-all-deps.jar -v -s injections -Dneurord.trials=3 Model_SPNspineAChm4R_Gshydr5_GapD-sp2adj-stim20hz.xml&
java -jar  /home/neuroware/stochdif/neurord-3.2.3-all-deps.jar -v -s injections -Dneurord.trials=3 Model_SPNspineAChm4R_Gshydr5_GapD-sp2other-stimtheta.xml&
java -jar  /home/neuroware/stochdif/neurord-3.2.3-all-deps.jar -v -s injections -Dneurord.trials=3 Model_SPNspineAChm4R_Gshydr5_GapD-sp2other-stim20hz.xml &

#re-run into different directory: 
############## 3 spine sims: 
java -jar  /home/neuroware/stochdif/neurord-3.2.3-all-deps.jar -v -s injections -Dneurord.trials=3 Model_SPNspineAChm4R_Gshydr5_GapD-sp3sep-stimtheta.xml&
java -jar  /home/neuroware/stochdif/neurord-3.2.3-all-deps.jar -v -s injections -Dneurord.trials=3 Model_SPNspineAChm4R_Gshydr5_GapD-sp3sep-stim20hz.xml
#re-run into different directory (start once 3 spine sims are completed): 
java -jar  /home/neuroware/stochdif/neurord-3.2.3-all-deps.jar -v -s injections -Dneurord.trials=3 Model_SPNspineAChm4R_Gshydr5_GapD-sp2sep-stimtheta.xml ss_bath/ &


############# Start the new DaDelay THurs aft - DONE
java -jar  /home/neuroware/stochdif/neurord-3.2.3-all-deps.jar --ic-time -1 --ic Model_SPNspineAChm4R_Gshydr5_GapD-nostim.h5 -v -s injections -Dneurord.trials=3 Model_SPNspineAChm4R_Gshydr5_GapD-stim20hz-noReb_DaDelay.xml &

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