add benchmarking files

data/sosbench/00009/00009-settings.txt

@@ -0,0 +1,9 @@
+start: 0
+duration: 150
+steps: 150
+variables: E1, E2, KKK, P_KKK, KK, P_KK, PP_KK, K, P_K, PP_K, KPase, KKPase, E1_KKK, E2_P_KKK, P_KKK_KK, P_KKK_P_KK, PP_KK_K, PP_KK_P_K, KKPase_PP_KK, KKPase_P_KK, KPase_PP_K, KPase_P_K, K_PP_norm, KK_PP_norm, KKK_P_norm, rel_K_PP_max
+absolute: 1.0e-15
+relative: 1.0e-9
+amount: 
+concentration: E1, E2, KKK, P_KKK, KK, P_KK, PP_KK, K, P_K, PP_K, KPase, KKPase, E1_KKK, E2_P_KKK, P_KKK_KK, P_KKK_P_KK, PP_KK_K, PP_KK_P_K, KKPase_PP_KK, KKPase_P_KK, KPase_PP_K, KPase_P_K, K_PP_norm, KK_PP_norm, KKK_P_norm, rel_K_PP_max
+

data/sosbench/00009/bench.py

@@ -0,0 +1,27 @@
+def run():
+    from roadrunner import *
+
+    o=SimulateOptions()
+
+    #o.stiff = True
+
+    o.duration=150
+
+    o.steps = 300
+
+    o.absolute = 1e-15
+    o.relative = 1e-9
+
+    o.resetModel = True
+
+    r=RoadRunner("00001-sbml-l2v4.xml")
+
+    Logger.setLevel(Logger.LOG_INFORMATION)
+
+    r.simulate(o);
+
+    plot(r.getSimulationResult())
+
+
+if __name__ == "__main__":
+    run()

data/sosbench/00014/00014-settings.txt

@@ -0,0 +1,14 @@
+start: 0
+duration: 300
+steps: 300
+variables: MAPKP, MEKP, RAFK, RAFP, K_1_0, K_1_1, K_1_2, K_2_0, K_2_1, K_2_2, K_3_0, K_3_1, K_K_1_0_2_2, K_K_1_1_2_2, K_K_2_0_3_1, K_K_2_1_3_1, K_MAPKP_1_1, K_MAPKP_1_2, K_MEKP_2_1, K_MEKP_2_2, K_RAFK_3_0, K_RAFP_3_1, S_m1_m1_m1, S_m1_m1_0, S_m1_m1_1, S_m1_0_m1, S_m1_0_0, S_m1_0_1, S_m1_1_m1, S_m1_1_0, S_m1_1_1, S_m1_2_m1, S_m1_2_0, S_m1_2_1, S_0_m1_m1, S_0_m1_0, S_0_m1_1, S_0_0_m1, S_0_0_0, S_0_0_1, S_0_1_m1, S_0_1_0, S_0_1_1, S_0_2_m1, S_0_2_0, S_0_2_1, S_1_m1_m1, S_1_m1_0, S_1_m1_1, S_1_0_m1, S_1_0_0, S_1_0_1, S_1_1_m1, S_1_1_0, S_1_1_1, S_1_2_m1, S_1_2_0, S_1_2_1, S_2_m1_m1, S_2_m1_0, S_2_m1_1, S_2_0_m1, S_2_0_0, S_2_0_1, S_2_1_m1, S_2_1_0, S_2_1_1, S_2_2_m1, S_2_2_0, S_2_2_1, S_RAFK_m1_m1_0, S_RAFK_m1_0_0, S_RAFK_m1_1_0, S_RAFK_m1_2_0, S_RAFK_0_m1_0, S_RAFK_0_0_0, S_RAFK_0_1_0, S_RAFK_0_2_0, S_RAFK_1_m1_0, S_RAFK_1_0_0, S_RAFK_1_1_0, S_RAFK_1_2_0, S_RAFK_2_m1_0, S_RAFK_2_0_0, S_RAFK_2_1_0, S_RAFK_2_2_0
+absolute: 1.0e-4
+relative: 1.0e-9
+amount: 
+concentration: MAPKP, MEKP, RAFK, RAFP, K_1_0, K_1_1, K_1_2, K_2_0, K_2_1, K_2_2, K_3_0, K_3_1, K_K_1_0_2_2, K_K_1_1_2_2, K_K_2_0_3_1, K_K_2_1_3_1, K_MAPKP_1_1, K_MAPKP_1_2, K_MEKP_2_1, K_MEKP_2_2, K_RAFK_3_0, K_RAFP_3_1, S_m1_m1_m1, S_m1_m1_0, S_m1_m1_1, S_m1_0_m1, S_m1_0_0, S_m1_0_1, S_m1_1_m1, S_m1_1_0, S_m1_1_1, S_m1_2_m1, S_m1_2_0, S_m1_2_1, S_0_m1_m1, S_0_m1_0, S_0_m1_1, S_0_0_m1, S_0_0_0, S_0_0_1, S_0_1_m1, S_0_1_0, S_0_1_1, S_0_2_m1, S_0_2_0, S_0_2_1, S_1_m1_m1, S_1_m1_0, S_1_m1_1, S_1_0_m1, S_1_0_0, S_1_0_1, S_1_1_m1, S_1_1_0, S_1_1_1, S_1_2_m1, S_1_2_0, S_1_2_1, S_2_m1_m1, S_2_m1_0, S_2_m1_1, S_2_0_m1, S_2_0_0, S_2_0_1, S_2_1_m1, S_2_1_0, S_2_1_1, S_2_2_m1, S_2_2_0, S_2_2_1, S_RAFK_m1_m1_0, S_RAFK_m1_0_0, S_RAFK_m1_1_0, S_RAFK_m1_2_0, S_RAFK_0_m1_0, S_RAFK_0_0_0, S_RAFK_0_1_0, S_RAFK_0_2_0, S_RAFK_1_m1_0, S_RAFK_1_0_0, S_RAFK_1_1_0, S_RAFK_1_2_0, S_RAFK_2_m1_0, S_RAFK_2_0_0, S_RAFK_2_1_0, S_RAFK_2_2_0
+
+
+
+
+
+