###linear vs non linear pathway activation in all single pathway, Ca, cAMP and Gbg #### Amplitude and Duration ############ ####cAMP #100 nm java -jar /home/nadia/neurord-3.2.4-all-deps.jar -t 1200000 -Dneurord.trials=5 Single_pulse/cAMP/cAMP/Model_ERK-stimd-C100-d1.xml Single_h5/Model_ERKcAMP-C100-d1 #200 java -jar /home/nadia/neurord-3.2.4-all-deps.jar -t 1200000 -Dneurord.trials=5 Single_pulse/cAMP/cAMP/Model_ERK-stimd-C200-d1.xml Single_h5/Model_ERKcAMP-C200-d1 #500 java -jar /home/nadia/neurord-3.2.4-all-deps.jar -t 1200000 -Dneurord.trials=5 Single_pulse/cAMP/cAMP/Model_ERK-stimd-C500-d1.xml Single_h5/Model_ERKcAMP-C500-d1 java -jar /home/nadia/neurord-3.2.4-all-deps.jar -t 1200000 -Dneurord.trials=5 Single_pulse/cAMP/cAMP/Model_ERK-stimd-C500-d4.xml Single_h5/Model_ERKcAMP-C500-d4 java -jar /home/nadia/neurord-3.2.4-all-deps.jar -t 1200000 -Dneurord.trials=5 Single_pulse/cAMP/cAMP/Model_ERK-stimd-C500-d10.xml Single_h5/Model_ERKcAMP-C500-d10 java -jar /home/nadia/neurord-3.2.4-all-deps.jar -t 1200000 -Dneurord.trials=5 Single_pulse/cAMP/cAMP/Model_ERK-stimd-C500-d30.xml Single_h5/Model_ERKcAMP-C500-d30 java -jar /home/nadia/neurord-3.2.4-all-deps.jar -t 1200000 -Dneurord.trials=5 Single_pulse/cAMP/cAMP/Model_ERK-stimd-C500-d100.xml Single_h5/Model_ERKcAMP-C500-d100 #1000 java -jar /home/nadia/neurord-3.2.4-all-deps.jar -t 1200000 -Dneurord.trials=5 Single_pulse/cAMP/cAMP/Model_ERK-stimd-C1000-d1.xml Single_h5/Model_ERKcAMP-C1000-d1 #1500 java -jar /home/nadia/neurord-3.2.4-all-deps.jar -t 1200000 -Dneurord.trials=5 Single_pulse/cAMP/cAMP/Model_ERK-stimd-C1500-d1.xml Single_h5/Model_ERKcAMP-C1500-d1 #2000 java -jar /home/nadia/neurord-3.2.4-all-deps.jar -t 1200000 -Dneurord.trials=5 Single_pulse/cAMP/cAMP/Model_ERK-stimd-C2000-d1.xml Single_h5/Model_ERKcAMP-C2000-d1 ###knockout cAMP #cAMP= 500 uM for 100 and 30 sec; cAMP has 2 pathways, either direct route epac or indirect PKA, what is the contribition of each? java -jar /home/nadia/neurord-3.2.4-all-deps.jar -t 1200000 -Dneurord.trials=5 Single_pulse/cAMP/Knockout/Model_ERK-blockEpacRap-C500-d100-stim.xml Knockout_h5/Model_ERK-BEpacRap100 java -jar /home/nadia/neurord-3.2.4-all-deps.jar -t 1200000 -Dneurord.trials=5 Single_pulse/cAMP/Knockout/Model_ERK-blockEpacRap-C500-d30-stim.xml Knockout_h5/Model_ERK-BEpacRap30 java -jar /home/nadia/neurord-3.2.4-all-deps.jar -t 1200000 -Dneurord.trials=5 Single_pulse/cAMP/Knockout/Model_ERK-blockPKARap-C500-d100-stim.xml Knockout_h5/Model_ERK-BPKARap100 java -jar /home/nadia/neurord-3.2.4-all-deps.jar -t 1200000 -Dneurord.trials=5 Single_pulse/cAMP/Knockout/Model_ERK-blockPKARap-C500-d30-stim.xml Knockout_h5/Model_ERK-BPKARap30 ####Gbg #5 #java -jar /home/nadia/neurord-3.2.4-all-deps.jar -t 1200000 -Dneurord.trials=5 Single_pulse/Gbg/Model_ERK-stimd-C5-d1.xml Single_h5/Model_ERKGbg-C5-d1 #30 java -jar /home/nadia/neurord-3.2.4-all-deps.jar -t 1200000 -Dneurord.trials=5 Single_pulse/Gbg/Model_ERK-stimd-C30-d1.xml Single_h5/Model_ERKGbg-C30-d1 #100 java -jar /home/nadia/neurord-3.2.4-all-deps.jar -t 1200000 -Dneurord.trials=5 Single_pulse/Gbg/Model_ERK-stimd-C100-d1.xml Single_h5/Model_ERKGbg-C100-d1 java -jar /home/nadia/neurord-3.2.4-all-deps.jar -t 1200000 -Dneurord.trials=5 Single_pulse/Gbg/Model_ERK-stimd-C100-d4.xml Single_h5/Model_ERKGbg-C100-d4 java -jar /home/nadia/neurord-3.2.4-all-deps.jar -t 1200000 -Dneurord.trials=5 Single_pulse/Gbg/Model_ERK-stimd-C100-d10.xml Single_h5/Model_ERKGbg-C100-d10 java -jar /home/nadia/neurord-3.2.4-all-deps.jar -t 1200000 -Dneurord.trials=5 Single_pulse/Gbg/Model_ERK-stimd-C100-d30.xml Single_h5/Model_ERKGbg-C100-d30 java -jar /home/nadia/neurord-3.2.4-all-deps.jar -t 1200000 -Dneurord.trials=5 Single_pulse/Gbg/Model_ERK-stimd-C100-d100.xml Single_h5/Model_ERKGbg-C100-d100 #500 java -jar /home/nadia/neurord-3.2.4-all-deps.jar -t 1200000 -Dneurord.trials=5 Single_pulse/Gbg/Model_ERK-stimd-C500-d1.xml Single_h5/Model_ERKGbg-C500-d1 #1000 java -jar /home/nadia/neurord-3.2.4-all-deps.jar -t 1200000 -Dneurord.trials=5 Single_pulse/Gbg/Model_ERK-stimd-C1000-d1.xml Single_h5/Model_ERKGbg-C1000-d1 #3000 java -jar /home/nadia/neurord-3.2.4-all-deps.jar -t 1200000 -Dneurord.trials=5 Single_pulse/Gbg/Model_ERK-stimd-C3000-d1.xml Single_h5/Model_ERKGbg-C3000-d1 #10000 java -jar /home/nadia/neurord-3.2.4-all-deps.jar -t 1200000 -Dneurord.trials=5 Single_pulse/Gbg/Model_ERK-stimd-C10000-d1.xml Single_h5/Model_ERKGbg-C10000-d1