###linear vs non linear pathway activation in all single pathway, Ca, cAMP and Gbg #### Amplitude and Duration ############ ####Ca #200 java -jar /home/nadia/neurord-3.2.4-all-deps.jar -t 1200000 -Dneurord.trials=5 Single_pulse/Ca/Ca/Model_ERK-stimd-C200-d1.xml Single_h5/Model_ERKCa-C200-d1& #300 java -jar /home/nadia/neurord-3.2.4-all-deps.jar -t 1200000 -Dneurord.trials=5 Single_pulse/Ca/Ca/Model_ERK-stimd-C300-d1.xml Single_h5/Model_ERKCa-C300-d1 #500 #java -jar /home/nadia/neurord-3.2.4-all-deps.jar -t 1200000 -Dneurord.trials=5 Single_pulse/Ca/Ca/Model_ERK-stimd-C500-d1.xml Single_h5/Model_ERKCa-C500-d1 #java -jar /home/nadia/neurord-3.2.4-all-deps.jar -t 1200000 -Dneurord.trials=5 Single_pulse/Ca/Ca/Model_ERK-stimd-C500-d2.xml Single_h5/Model_ERKCa-C500-d2 #java -jar /home/nadia/neurord-3.2.4-all-deps.jar -t 1200000 -Dneurord.trials=5 Single_pulse/Ca/Ca/Model_ERK-stimd-C500-d4.xml Single_h5/Model_ERKCa-C500-d4 #java -jar /home/nadia/neurord-3.2.4-all-deps.jar -t 1200000 -Dneurord.trials=5 Single_pulse/Ca/Ca/Model_ERK-stimd-C500-d5.xml Single_h5/Model_ERKCa-C500-d5 #java -jar /home/nadia/neurord-3.2.4-all-deps.jar -t 1200000 -Dneurord.trials=5 Single_pulse/Ca/Ca/Model_ERK-stimd-C500-d6.xml Single_h5/Model_ERKCa-C500-d6 #java -jar /home/nadia/neurord-3.2.4-all-deps.jar -t 1200000 -Dneurord.trials=5 Single_pulse/Ca/Ca/Model_ERK-stimd-C500-d8.xml Single_h5/Model_ERKCa-C500-d8 #java -jar /home/nadia/neurord-3.2.4-all-deps.jar -t 1200000 -Dneurord.trials=5 Single_pulse/Ca/Ca/Model_ERK-stimd-C500-d10.xml Single_h5/Model_ERKCa-C500-d10 java -jar /home/nadia/neurord-3.2.4-all-deps.jar -t 1200000 -Dneurord.trials=5 Single_pulse/Ca/Ca/Model_ERK-stimd-C500-d30.xml Single_h5/Model_ERKCa-C500-d30& java -jar /home/nadia/neurord-3.2.4-all-deps.jar -t 1200000 -Dneurord.trials=5 Single_pulse/Ca/Ca/Model_ERK-stimd-C500-d60.xml Single_h5/Model_ERKCa-C500-d60 #java -jar /home/nadia/neurord-3.2.4-all-deps.jar -t 1200000 -Dneurord.trials=5 Single_pulse/Ca/Ca/Model_ERK-stimd-C500-d100.xml Single_h5/Model_ERKCa-C500-d100 #1000 #java -jar /home/nadia/neurord-3.2.4-all-deps.jar -t 1200000 -Dneurord.trials=5 Single_pulse/Ca/Ca/Model_ERK-stimd-C1000-d1.xml Single_h5/Model_ERKCa-C1000-d1 ##java -jar /home/nadia/neurord-3.2.4-all-deps.jar -t 1200000 -Dneurord.trials=5 Single_pulse/Ca/Ca/Model_ERK-stimd-C1000-d4.xml Single_h5/Model_ERKCa-C1000-d4 ##java -jar /home/nadia/neurord-3.2.4-all-deps.jar -t 1200000 -Dneurord.trials=5 Single_pulse/Ca/Ca/Model_ERK-stimd-C1000-d100.xml Single_h5/Model_ERKCa-C1000-d100 #1500 #java -jar /home/nadia/neurord-3.2.4-all-deps.jar -t 1200000 -Dneurord.trials=5 Single_pulse/Ca/Ca/Model_ERK-stimd-C1500-d1.xml Single_h5/Model_ERKCa-C1500-d1 #2000 #java -jar /home/nadia/neurord-3.2.4-all-deps.jar -t 1200000 -Dneurord.trials=5 Single_pulse/Ca/Ca/Model_ERK-stimd-C2000-d1.xml Single_h5/Model_ERKCa-C2000-d1 ##java -jar /home/nadia/neurord-3.2.4-all-deps.jar -t 1200000 -Dneurord.trials=5 Single_pulse/Ca/Ca/Model_ERK-stimd-C2000-d4.xml Single_h5/Model_ERKCa-C2000-d4 ##java -jar /home/nadia/neurord-3.2.4-all-deps.jar -t 1200000 -Dneurord.trials=5 Single_pulse/Ca/Ca/Model_ERK-stimd-C2000-d100.xml Single_h5/Model_ERKCa-C2000-d100 #5000 #java -jar /home/nadia/neurord-3.2.4-all-deps.jar -t 1200000 -Dneurord.trials=5 Single_pulse/Ca/Ca/Model_ERK-stimd-C5000-d1.xml Single_h5/Model_ERKCa-C5000-d1 ###Knockout experiment: what is the role of each subpathway? what is the contribution of different molecules or step in calcium pathway? ########## STIM ######## #Ca= 2 uM for 1 sec; calcium has 2 pathways, either CamKII or RasGRF, what is the contribition of each? #java -jar /home/nadia/neurord-3.2.4-all-deps.jar -t 1200000 -Dneurord.trials=5 Single_pulse/Ca/Knockout/Model_ERK-blockCK-C2000-d1-stim.xml Knockout_h5/Model_ERK-BCK-stimC2000d1 #java -jar /home/nadia/neurord-3.2.4-all-deps.jar -t 1200000 -Dneurord.trials=5 Single_pulse/Ca/Knockout/Model_ERK-blockCK-auto-C2000-d1-stim.xml Knockout_h5/Model_ERK-BCKauto-stimC2000d1 #java -jar /home/nadia/neurord-3.2.4-all-deps.jar -t 1200000 -Dneurord.trials=5 Single_pulse/Ca/Knockout/Model_ERK-blockpSynGap-C2000-d1-stim.xml Knockout_h5/Model_ERK-BpSynGap-stimC2000d1 #java -jar /home/nadia/neurord-3.2.4-all-deps.jar -t 1200000 -Dneurord.trials=5 Single_pulse/Ca/Knockout/Model_ERK-blockpSynGapKcat-C2000-d1-stim.xml Knockout_h5/Model_ERK-BpSynGapKcat-stimC2000d1 #java -jar /home/nadia/neurord-3.2.4-all-deps.jar -t 1200000 -Dneurord.trials=5 Single_pulse/Ca/Knockout/Model_ERK-blockSynden-C2000-d1-stim.xml Knockout_h5/Model_ERK-BSynden-stimC2000d1 #java -jar /home/nadia/neurord-3.2.4-all-deps.jar -t 1200000 -Dneurord.trials=5 Single_pulse/Ca/Knockout/Model_ERK-blockCK-auto-C500-d1.xml Knockout_h5/Model_ERK-BCKauto-stimC500d1 #java -jar /home/nadia/neurord-3.2.4-all-deps.jar -t 1200000 -Dneurord.trials=5 Single_pulse/Ca/Knockout/Model_ERK-blockCK-auto-C500-d4.xml Knockout_h5/Model_ERK-BCKauto-stimC500d4 #java -jar /home/nadia/neurord-3.2.4-all-deps.jar -t 1200000 -Dneurord.trials=5 Single_pulse/Ca/Knockout/Model_ERK-blockCK-auto-C500-d10.xml Knockout_h5/Model_ERK-BCKauto-stimC500d10 java -jar /home/nadia/neurord-3.2.4-all-deps.jar -t 1200000 -Dneurord.trials=5 Single_pulse/Ca/Knockout/Model_ERK-blockCK-auto-C500-d30.xml Knockout_h5/Model_ERK-BCKauto-stimC500d30 #java -jar /home/nadia/neurord-3.2.4-all-deps.jar -t 1200000 -Dneurord.trials=5 Single_pulse/Ca/Knockout/Model_ERK-blockCK-auto-C500-d100.xml Knockout_h5/Model_ERK-BCKauto-stimC500d100 #java -jar /home/nadia/neurord-3.2.4-all-deps.jar -t 1200000 -Dneurord.trials=5 Single_pulse/Ca/Knockout/Model_ERK-blockCK-auto-C1000-d1.xml Knockout_h5/Model_ERK-BCKauto-stimC1000d1 #java -jar /home/nadia/neurord-3.2.4-all-deps.jar -t 1200000 -Dneurord.trials=5 Single_pulse/Ca/Knockout/Model_ERK-blockCK-auto-C1500-d1.xml Knockout_h5/Model_ERK-BCKauto-stimC1500d1 #java -jar /home/nadia/neurord-3.2.4-all-deps.jar -t 1200000 -Dneurord.trials=5 Single_pulse/Ca/Knockout/Model_ERK-blockCK-auto-C2000-d1.xml Knockout_h5/Model_ERK-BCKauto-stimC2000d1 #java -jar /home/nadia/neurord-3.2.4-all-deps.jar -t 1200000 -Dneurord.trials=5 Single_pulse/Ca/Knockout/Model_ERK-blockCK-auto-C5000-d1.xml Knockout_h5/Model_ERK-BCKauto-stimC5000d1