Example Models

The models found in the package directory, …/test/ , are shown below with their respective Antimony string representation. The J’s indicate reaction id and species with “$” sign in front represent boundary species which are not shown in the figures. The “v” represents reaction rate.

Test Model 1:
J1: $Xo -> S1; v;
J2: S1 => $X1; v;
J3: S1 => $X2; v;
v = 0
_images/testModel1.png
Test Model 2:
J1: $Xo -> S1; v;
J2: S1 -> $X1; v;
J3: S1 -> $X2; v;
v = 0
_images/testModel2.png
Test Model 3:
J1: $Xo -> S1; v;
J2: S1 -> S2; v;
J3: S2 => $X1; v;
J4: S2 => $X2; v;
J5: S1 => $X3; v;
v = 0
_images/testModel3.png
Test Model 4:
J1: $Xo -> S1; v;
J2: S1 -> S2; v;
J3: S2 -> S3; v;
J4: S1 -> S3; v;
J5: S3 -> $X1; v;
v = 0
_images/testModel4.png
Test Model 5:
J1: $Xo => S1; v;
J2: S1 => S2; v;
J3: S2 => S3; v;
J4: S1 => S3; v;
J5: S2 => S4; v;
J6: S3 => S4; v;
J7: S4 => $X1; v;
v = 0
_images/testModel5.png
Test Model 6:
J1: $Xo -> S1; v;
J2: S1 -> S2; v;
J3: S2 -> S3; v;
J4: S1 -> S3; v;
J5: S3 -> $X1; v;
J6: S2 -> S4; v;
J7: S2 -> S5; v;
J8: S4 -> S5; v;
J9: S5 ->; v;
v = 0
_images/testModel6.png
Test Model 7:
J1: $Xo -> S1; v;
J2: S1 -> S2; v;
J3: S2 -> S3; v;
J4: S1 -> S3; v;
J5: S3 -> $X1; v;
J6: S3 -> $X2; v;
v = 0
_images/testModel7.png
Test Model 8:
J1: S1 -> S2; v;
J2: S2 -> S1; v;
J3: S2 -> S3; v;
J4: S3 -> S2; v;
v = 0
_images/testModel8.png
Test Model 9:
J1: $Xo -> S1; v;
J2: S1 -> $X2; v;
J3: S1 -> S2; v;
J4: S2 -> $X3; v;
J5: S2 -> $X4; v;
J6: $X1 -> S3; v;
J7: S3 -> S2; v;
J8: S3 -> $X5; v;
v = 0
_images/testModel9.png
Test Model 10:
J1: $Xo -> S1; v;
J2: S1 -> S3; v;
J3: S1 -> S2; v;
J4: S2 -> S4; v;
J5: S4 -> S3; v;
J6: S3 -> S5; v;
J7: S4 -> S6; v;
J8: S6 -> $X1; v;
J9: S6 -> S5; v;
v = 0
_images/testModel10.png
Test Model 11:
J1: $Xo -> S1; v;
J2: $X1 -> S1; v;
J3: S1 -> $X2; v;
v = 0
_images/testModel11.png
Test Model 12:
J1: $Xo -> S1; v;
J2: S1 -> S2 + S4; v;
J3: S2 -> S3 + S4 ; v;
J4: S3 -> S4; v;
J5: S4 -> $X1; v;
v = 0
_images/testModel12.png
Test Model 13:
J1: $Xo -> S1; v;
J2: S1 -> S2; v;
J3: S2 -> S3; v;
J4: S1 -> S3; v;
J5: S3 -> S4; v;
J6: S3 -> S5; v;
J7: S4 -> S5; v;
J8: S5 -> $X1; v;
v = 0
_images/testModel13.png
Test Model 14:
J1: $Xo -> S1; v;
J2: S1 -> S2; v;
J3: S2 -> S3; v;
J4: S1 -> S3; v;
J5: S3 -> S4; v;
J6: S3 -> S5; v;
J7: S4 -> S5; v;
J8: S5 -> S6; v;
J9: S5 -> S7; v;
J10: S6 -> S7; v;
J11: S7 -> $X1; v;
v = 0
_images/testModel14.png
Test Model 15:
J1: $Xo -> S1 + S2; v;
J2: S1 -> S3; v;
J3: S2 + S3 -> $X1; v;
v = 0
_images/testModel15.png
Test Model 16:
J1: $Xo -> S1; v;
J2: S1 + $X1 -> S2; v;
J3: S2 -> S1 + $X2; v;
v = 0
_images/testModel16.png
Test Model 17:
J1: $Xo => S1; v;
J2: S1 + $X1 => S2; v;
J3: S2 => S1 + $X2; v;
v = 0
_images/testModel17.png
Test Model 18:
J1: $Xo -> S1; v;
J2: S1 + S2 -> S3 + $X1; v;
J3: S1 + S3 -> S2 + $X2; v;
v = 0
_images/testModel18.png
Test Model 19:
J1: $Xo + S2 -> S1; v;
J2: S1 -> S2 + S5; v;
J3: S5 + S4 -> S3; v;
J4: S3 -> S4 + $X1; v;
v = 0
_images/testModel19.png
Test Model 20:
J1: $Xo => S1; v;
J2: S1 => $X2; v;
J3: S1 => S2; v;
J4: S2 => $X3; v;
J5: S2 => $X4; v;
J6: $X1 => S3; v;
J7: S3 => S2; v;
J8: S3 => $X5; v;
v = 0
_images/testModel20.png
Test Model 21:
J1: $Xo => S1; v;
J2: S1 => $X2; v;
J3: S1 -> S2; v;
J4: S2 => $X3; v;
J5: S2 => $X4; v;
J6: $X1 => S3; v;
J7: S3 => S2; v;
J8: S3 => $X5; v;
v = 0
_images/testModel21.png
Test Model 22:
J1: $Xo -> S1; v;
J2: S1 => $X2; v;
J3: S1 -> S2; v;
J4: S2 => $X3; v;
J5: S2 => $X4; v;
J6: $X1 => S3; v;
J7: S3 => S2; v;
J8: S3 => $X5; v;
v = 0
_images/testModel22.png
Test Model 23:
J1: $Xo -> S1; v;
J2: S1 => $X2; v;
J3: S1 -> S2; v;
J4: S2 => $X3; v;
J5: S2 => $X4; v;
J6: $X1 => S3; v;
J7: S3 -> S2; v;
J8: S3 => $X5; v;
v = 0
_images/testModel23.png
Test Model 24:
J1: $Xo -> S1; v;
J2: S1 => $X2; v;
J3: S1 -> S2; v;
J4: S2 => $X3; v;
J5: S2 => $X4; v;
J6: $X1 -> S3; v;
J7: S3 -> S2; v;
J8: S3 => $X5; v;
v = 0
_images/testModel24.png
Test Model 25:
$X -> S1; v;
v = 0
_images/testModel25.png
Test Model 26:
J1: $Xo -> S1; v;
J2: $X1 -> S2; v;
J3: S2 -> S3; v;
J4: S3 -> S1 + S4; v;
J5: S4 -> S3 + S5; v;
J6: S5 -> $X2; v;
v = 0
_images/testModel26.png
Test Model 27:
J1: $Xo -> S1 + S2; v;
J2: S1 -> S2; v;
J3: S2 -> $X1; v;
v = 0
_images/testModel27.png
Test Model 28:
J1: $Xo + S1 => S2; v;
J2: S2 => S3 + S4; v;
J3: S1 => S5 + S3; v;
J4: S4 + S5 => S6; v;
J5: S6 => $X1; v;
v = 0
_images/testModel28.png
Test Model 29:
J1: $Xo -> S1; v
J2: S1 -> $X1; v;
v = 0
_images/testModel29.png
Test Model 30:
J1: $Xo => S1; v
J2: S1 => S3; v;
J3: S1 => S2; v;
J4: S2 => S5; v;
J5: S2 => S4; v;
J6: S3 => S6; v;
J7: S3 => S7; v;
J8: S7 => S6; v;
J9: S7 => S4;v;
J10: S5 => S4; v;
J11: S6 => $X1; v;
J12: S5 => $X2; v;
v = 0
_images/testModel30.png
Test Model 31:
J1: $Xo => S1; v;
J2: S1 => S2 + S3; v;
J3: S2 + S3 => S4 + S5; v;
J4: S5 => $X1; v;
J5: S4 => S2; v;
J6: S5 => S1; v;
v = 0
_images/testModel31.png