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RuleWorld · Apr 18, 2012 · 22feed8 · 22feed8
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diff --git a/.settings/.jsdtscope b/.settings/.jsdtscope
diff --git a/.settings/org.eclipse.jdt.core.prefs b/.settings/org.eclipse.jdt.core.prefs
diff --git a/.settings/org.eclipse.pde.prefs b/.settings/org.eclipse.pde.prefs
diff --git a/.settings/org.eclipse.wst.jsdt.ui.superType.container b/.settings/org.eclipse.wst.jsdt.ui.superType.container
diff --git a/.settings/org.eclipse.wst.jsdt.ui.superType.name b/.settings/org.eclipse.wst.jsdt.ui.superType.name
diff --git a/AnotherRuleBenderProduct.product b/AnotherRuleBenderProduct.product
diff --git a/BNGEditor-lin-0.2.210.jar b/BNGEditor-lin-0.2.210.jar
diff --git a/BNGEditor-win-0.2.210.exe b/BNGEditor-win-0.2.210.exe
diff --git a/META-INF/MANIFEST.MF b/META-INF/MANIFEST.MF
diff --git a/Notes.txt b/Notes.txt
diff --git a/TODO.txt b/TODO.txt
diff --git a/build.properties b/build.properties
diff --git a/data/MWC.bngl b/data/MWC.bngl
@@ -0,0 +1,43 @@
+begin parameters
+k_RT_transition 1e-1
+k_TR_transition 1e-1
+k_f_R 1
+k_r_R 100000
+k_f_T 10
+k_r_T 100000
+R0 1000
+L0 10000
+end parameters
+
+begin molecule types
+1 Protein(b,b,Conf~R~T)
+2 Ligand(c)
+end molecule types
+
+begin seed species
+R_0: Protein(b,b,Conf~R) R0
+Free_Ligand: Ligand(c) L0
+end seed species
+
+begin reaction rules
+Rule_Transition: Protein(b,b,Conf~R)<->Protein(b,b,Conf~T) k_RT_transition,k_TR_transition 
+Rule_Ligand_Binding_for_R: Protein(b,Conf~R)+Ligand(c)<->Protein(b!0,Conf~R).Ligand(c!0) k_f_R,k_r_R 
+Rule_Ligand_Binding_for_T: Protein(b,Conf~T)+Ligand(c)<->Protein(b!0,Conf~T).Ligand(c!0) k_f_T,k_r_T 
+end reaction rules
+
+begin observables
+Molecules BoundLigand Ligand(c!+) 
+Species FreeProtein Protein(b,b) 
+Species SingleBound Protein(b!0,b).Ligand(c!0) 
+Species DoubleBound Protein(b!0,b!1).Ligand(c!0).Ligand(c!1) 
+end observables
+
+generate_network({overwrite=>1,check_iso=>1,max_iter=>25,max_stoich=>{Protein=>unlimited,Ligand=>unlimited}});
+
+setConcentration("Ligand(c)",0);
+simulate_ode({suffix=>"equil",t_end=>10000,n_steps=>100,atol=>1e-12,rtol=>1e-12,sparse=>1,steady_state=>1});
+
+setConcentration("Ligand(c)","L0");
+
+simulate_ode({t_end=>100,n_steps=>10000,atol=>1e-12,rtol=>1e-12,sparse=>0});
+
diff --git a/...97 withspace/Models2/SHP2_base_model.bngl → data/SHP2_base_model.bngl b/...97 withspace/Models2/SHP2_base_model.bngl → data/SHP2_base_model.bngl
diff --git a/...Gen-2.1.8r597 withspace/Models2/blbr.bngl → data/blbr.bngl b/...Gen-2.1.8r597 withspace/Models2/blbr.bngl → data/blbr.bngl