Updates

asset-manifest.json

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 {
   "files": {
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-    "main.js": "/SimBioUI/static/js/main.3058bd7e.js",
+    "main.css": "/SimBioUI/static/css/main.d58c0048.css",
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-    "main.3058bd7e.js.map": "/SimBioUI/static/js/main.3058bd7e.js.map",
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     "498.5621b405.chunk.js.map": "/SimBioUI/static/js/498.5621b405.chunk.js.map",
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   },
   "entrypoints": [
-    "static/css/main.b43e400a.css",
-    "static/js/main.3058bd7e.js"
+    "static/css/main.d58c0048.css",
+    "static/js/main.e3f0734d.js"
   ]
 }

examples-models/enzyme-catalyzed-three-step-pathway.txt

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+// A simple three step pathway using
+// Michaelis-Menten kinetics.
+
+// Reactions:
+J0: $Node0 -> Node1; (J0_Vmax/J0_Km1)*(Node0 - Node1/J0_Keq)/(1 + Node0/J0_Km1 + Node1/J0_Km2);
+J1: Node1 -> Node2; (J1_Vmax/J1_Km1)*(Node1 - Node2/J1_Keq)/(1 + Node1/J1_Km1 + Node2/J1_Km2);
+J2: Node2 -> $Node3; (J2_Vmax/J2_Km1)*(Node2 - Node3/J2_Keq)/(1 + Node2/J2_Km1 + Node3/J2_Km2);
+
+// Species initializations:
+Node1 = 0;
+Node2 = 0;
+Node0 = 10;
+Node3 = 0;
+
+// Variable initializations:
+J0_Vmax = 1;
+J0_Km1 = 0.4;
+J0_Keq = 1;
+J0_Km2 = 1;
+J1_Vmax = 1;
+J1_Km1 = 0.8;
+J1_Keq = 1.5;
+J1_Km2 = 1;
+J2_Vmax = 1;
+J2_Km1 = 0.232;
+J2_Keq = 1.6;
+J2_Km2 = 1;

examples-models/example-large-model.txt

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+Châu Quỳnh Phan
+// This is a randomly generated model that
+// uses simple mass-action kinetics
+
+// Reactions
+J0: S15 -> $S17; E0*(k0*S15 - k0r*S17)
+J1: S3 -> S0 + S12; E1*(k1*S3 - k1r*S0*S12)
+J2: $S10 -> S8; E2*(k2*S10 - k2r*S8)
+J3: S9 -> S8 + S13; E3*(k3*S9 - k3r*S8*S13)
+J4: $S10 + S2 -> $S17; E4*(k4*S10*S2 - k4r*S17)
+J5: $S1 + S0 -> $S4; E5*(k5*S1*S0 - k5r*S4)
+J6: S5 -> $S14 + S9; E6*(k6*S5 - k6r*S14*S9)
+J7: S18 + S12 -> S5; E7*(k7*S18*S12 - k7r*S5)
+J8: $S7 + S16 -> S2; E8*(k8*S7*S16 - k8r*S2)
+J9: S6 -> S5 + S0; E9*(k9*S6 - k9r*S5*S0)
+J10: $S10 + S19 -> S5; E10*(k10*S10*S19 - k10r*S5)
+J11: S8 -> S18; E11*(k11*S8 - k11r*S18)
+J12: S6 -> S13 + S16; E12*(k12*S6 - k12r*S13*S16)
+J13: S2 + S15 -> S6 + S9; E13*(k13*S2*S15 - k13r*S6*S9)
+J14: S3 -> S13; E14*(k14*S3 - k14r*S13)
+J15: S13 -> S5; E15*(k15*S13 - k15r*S5)
+J16: S3 -> S19; E16*(k16*S3 - k16r*S19)
+J17: S0 -> S3 + S15; E17*(k17*S0 - k17r*S3*S15)
+J18: S3 -> $S14 + $S17; E18*(k18*S3 - k18r*S14*S17)
+J19: $S7 + $S1 -> $S11; E19*(k19*S7*S1 - k19r*S11)
+
+// Species initializations
+S0 = 5
+S2 = 2
+S3 = 3
+S5 = 1
+S6 = 3
+S8 = 2
+S9 = 5
+S12 = 1
+S13 = 4
+S15 = 6
+S16 = 6
+S18 = 3
+S19 = 4
+S1 = 4
+S4 = 4
+S7 = 3
+S10 = 6
+S11 = 2
+S14 = 1
+S17 = 1
+// Variable initializations
+E0 = 1;
+k0 = 0.828420614
+k0r = 0.69125685
+E1 = 1;
+k1 = 0.708821521
+k1r = 0.63838456
+E2 = 1;
+k2 = 0.118288544
+k2r = 0.21911200
+E3 = 1;
+k3 = 0.249635736
+k3r = 0.64338269
+E4 = 1;
+k4 = 0.148271098
+k4r = 0.88154458
+E5 = 1;
+k5 = 0.9772751915
+k5r = 0.344055979
+E6 = 1;
+k6 = 0.754618665
+k6r = 0.68985893
+E7 = 1;
+k7 = 0.92086958
+k7r = 0.9789804
+E8 = 1;
+k8 = 0.4925311695
+k8r = 0.032997413
+E9 = 1;
+k9 = 0.80320391
+k9r = 0.0041010
+E10 = 1;
+k10 = 0.05353786
+k10r = 0.1268534
+E11 = 1;
+k11 = 0.1727146
+k11r = 0.367270
+E12 = 1;
+k12 = 0.4561613
+k12r = 0.247974
+E13 = 1;
+k13 = 0.20598231
+k13r = 0.709211
+E14 = 1;
+k14 = 0.57478598
+k14r = 0.2114866
+E15 = 1;
+k15 = 0.70746493
+k15r = 0.7310762
+E16 = 1;
+k16 = 0.783348675
+k16r = 0.78463660
+E17 = 1;
+k17 = 0.973314149
+k17r = 0.58769631
+E18 = 1;
+k18 = 0.98747636
+k18r = 0.9768005
+E19 = 1;
+k19 = 0.767613157
+k19r = 0.85874833

examples-models/feedback-oscillator-model.txt

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+// A negative-feeback oscillator
+// I think this orginally came from a
+// model by Athel Cornish-Bowden
+
+// Reactions:
+J0: $X0 => S1; VM1*(X0 - S1/Keq1)/(1 + X0 + S1 + S4^h)
+J1: S1 => S2; (10*S1 - 2*S2)/(1 + S1 + S2)
+J2: S2 => S3; (10*S2 - 2*S3)/(1 + S2 + S3)
+J3: S3 => S4; (10*S3 - 2*S4)/(1 + S3 + S4)
+J4: S4 => $X1; V4*S4/(KS4 + S4)
+
+// Species initializations:
+S1 = 0
+S2 = 0
+S3 = 0
+S4 = 0
+X0 = 10
+X1 = 0
+
+// Variable initializations:
+VM1 = 10
+Keq1 = 10
+h = 10
+V4 = 2.5
+KS4 = 0.5

examples-models/files.json

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+[
+  {
+    "original": "enzyme-catalyzed-three-step-pathway.txt",
+    "formatted": "Enzyme Catalyzed Three Step Pathway"
+  },
+  {
+    "original": "example-large-model.txt",
+    "formatted": "Example Large Model"
+  },
+  {
+    "original": "feedback-oscillator-model.txt",
+    "formatted": "Feedback Oscillator Model"
+  },
+  {
+    "original": "files.json",
+    "formatted": "Files"
+  },
+  {
+    "original": "jana-wolf-glycolytic-model.txt",
+    "formatted": "Jana Wolf Glycolytic Model"
+  },
+  {
+    "original": "lorenz-attractor.txt",
+    "formatted": "Lorenz Attractor"
+  },
+  {
+    "original": "relaxation-oscillator:-from-heinrich-1997-review.txt",
+    "formatted": "Relaxation Oscillator: From Heinrich 1997 Review"
+  },
+  {
+    "original": "simple-bistable-model.txt",
+    "formatted": "Simple Bistable Model"
+  },
+  {
+    "original": "simple-three-step-pathway.txt",
+    "formatted": "Simple Three Step Pathway"
+  },
+  {
+    "original": "smallest-bistable-model:-thomas-wilhelm.txt",
+    "formatted": "Smallest Bistable Model: Thomas Wilhelm"
+  },
+  {
+    "original": "smallest-hopf-model:-wilhelm-and-heinrich.txt",
+    "formatted": "Smallest Hopf Model: Wilhelm And Heinrich"
+  },
+  {
+    "original": "tau-doyle-integral-controller.txt",
+    "formatted": "Tau Doyle Integral Controller"
+  },
+  {
+    "original": "twenty-step-mass-action-pathway.txt",
+    "formatted": "Twenty Step Mass Action Pathway"
+  },
+  {
+    "original": "two-moiety-converved-cycle-model.txt",
+    "formatted": "Two Moiety Converved Cycle Model"
+  }
+]

examples-models/jana-wolf-glycolytic-model.txt

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+// Jana_WolfGlycolysis
+// Effect of cellular interaction on glycolytic oscillations
+// in yeast: a theoretical investigation.
+// Wolf J, Heinrich R.
+// Biochem. J. 2000 Jan; 345 Pt 2: 321-334
+
+// Species
+species Glucose, fructose_1_6_bisphosphate;
+species glyceraldehyde_3_phosphate, glycerate_3_phosphate;
+species pyruvate, Acetyladehyde, External_acetaldehyde;
+species ATP, ADP, NAD, NADH;
+species External_glucose, ethanol, Glycerol;
+species Sink;
+
+// Reactions
+J0: $External_glucose => Glucose; J0_inputFlux;
+J1: Glucose + 2 ATP => fructose_1_6_bisphosphate + 2 ADP; J1_k1*Glucose*ATP*(1/(1 + (ATP/J1_Ki)^J1_n));
+J2: fructose_1_6_bisphosphate => glyceraldehyde_3_phosphate + glyceraldehyde_3_phosphate; J2_J2_k*fructose_1_6_bisphosphate;
+J3: glyceraldehyde_3_phosphate + NADH => NAD + $Glycerol; J3_J3_k*glyceraldehyde_3_phosphate*NADH;
+J4: glyceraldehyde_3_phosphate + ADP + NAD => ATP + glycerate_3_phosphate + NADH; (J4_kg*J4_kp*glyceraldehyde_3_phosphate*NAD*ADP - J4_ka*J4_kk*glycerate_3_phosphate*ATP*NADH)/(J4_ka*NADH + J4_kp*ADP);
+J5: glycerate_3_phosphate + ADP => ATP + pyruvate; J5_J5_k*glycerate_3_phosphate*ADP;
+J6: pyruvate => Acetyladehyde; J6_J6_k*pyruvate;
+J7: Acetyladehyde + NADH => NAD + $ethanol; J7_J7_k*Acetyladehyde*NADH;
+J8: Acetyladehyde => External_acetaldehyde; J8_J8_k1*Acetyladehyde - J8_J8_k2*External_acetaldehyde;
+J9: ATP => ADP; J9_J9_k*ATP;
+J10: External_acetaldehyde => $Sink; J10_J10_k*External_acetaldehyde;
+
+// Species initializations
+Glucose = 0;
+fructose_1_6_bisphosphate = 0;
+glyceraldehyde_3_phosphate = 0;
+glycerate_3_phosphate = 0;
+pyruvate = 0;
+Acetyladehyde = 0;
+External_acetaldehyde = 0;
+ATP = 3;
+ADP = 1;
+NAD = 0.5;
+NADH = 0.5;
+External_glucose = 0;
+ethanol = 0;
+Glycerol = 0;
+Sink = 0;
+
+// Variable initializations
+J0_inputFlux = 50;
+J1_k1 = 550;
+J1_Ki = 1;
+J1_n = 4;
+J2_J2_k = 9.8;
+J3_J3_k = 85.7;
+J4_kg = 323.8;
+J4_kp = 76411.1;
+J4_ka = 57823.1;
+J4_kk = 23.7;
+J5_J5_k = 80;
+J6_J6_k = 9.7;
+J7_J7_k = 2000;
+J8_J8_k1 = 375;
+J8_J8_k2 = 375;
+J9_J9_k = 28;
+J10_J10_k = 80;
+J2_k = 9.8;
+J3_k = 85.7;
+J5_k = 80;
+J6_k = 9.7;
+J7_k = 2000;
+J8_k1 = 375;
+J8_k2 = 375;
+J9_k = 28;
+J10_k = 80;

examples-models/lorenz-attractor.txt

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+// Example of solving ODEs using
+// using the Lorenz attractor
+// See https://en.wikipedia.org/wiki/Lorenz_system
+
+-> u; -sigma*(u - v);
+-> v; rho*u - v - u*w;
+-> w; -beta*w + u*v;
+
+// Variable initializations
+u = 0
+v = 1
+w = 1.05
+
+// Parameter initializations
+sigma = 10
+rho = 28
+beta = 2.667

examples-models/relaxation-oscillator:-from-heinrich-1997-review.txt

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+// Oscillator (Heinrich model)
+// From the review:
+// Metabolic Regulation and Mathematical Models
+// R.HEINRICH, S.M.RAPOPORT, T.A.RAPOPORT
+// In Progress in Biophysics and Molecular Biology
+// 1977, Vol 32, p1-82
+
+// Reactions:
+J0: $X0 -> S1; v0
+J1: S1 -> ; k3*S1
+J2: S1 -> S2; (k1*S1 - k_1*S2)*(1 + c*S2^q)
+J3: S2 ->; k2*S2
+
+// Species initializations
+S1 = 0; S2 = 1; X0 = 1
+
+// Variable initializations
+v0 = 8; k3 = 0
+k1 = 1; k_1 = 0
+c = 1;  q = 3
+k2 = 5;

examples-models/simple-bistable-model.txt

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+// Simple bistable model (non-mass-action)
+
+// Set S1 to 0 or S1 to 10 to observe the two stable states
+// To find the unstable state, set S1 = 3.4863321029603696
+// To examine the stabilty, change to the steady-state tab
+// and observe the eigenvalues (+ve = unstable)
+
+// Reactions
+J0: $X0 -> S1; X0*(32 + (S1/0.75)^3.2)/(1 + (S1/4.3)^3.2)
+J1: S1 ->; k1*S1;
+
+// Species initializations
+S1 = 0
+X0 = 0.1
+
+// Parameter initialization
+k1 = 3.2