File name: stoic.xml
SBML Level 2 Version 1
Model name: stoichiometry_matrix_example
Model id: stoichiometry_matrix_example
|
Compartments
|
| ID |
Name |
Dimension |
Size |
Units |
Derived Units |
Outside |
Constant |
| C |
C |
3 |
... |
volume |
litre |
... |
True |
|
Species
|
| ID |
Name |
Compartment |
initialType |
Value |
Units of the Species |
Derived Units of the Species |
B.C |
Constant |
Charge |
| S1 |
S1 |
C |
initialAmount |
1 |
substance/volume |
mole/litre |
False |
False |
... |
| S2 |
S2 |
C |
initialAmount |
1 |
substance/volume |
mole/litre |
False |
False |
... |
| S3 |
S3 |
C |
initialAmount |
1 |
substance/volume |
mole/litre |
False |
False |
... |
| S4 |
S4 |
C |
initialAmount |
1 |
substance/volume |
mole/litre |
False |
False |
... |
| S5 |
S5 |
C |
initialAmount |
1 |
substance/volume |
mole/litre |
False |
False |
... |
|
Reactions, global and local contexts suppressed
|
| ID |
Name |
Fast |
Reaction |
Modifiers |
Parameters |
Formula |
Contribution to ODEs |
| reaction1 |
reaction1 |
False |
S1 → S2 |
... |
... |
... |
... |
| reaction2 |
reaction2 |
False |
S2 + 5S3 → 2S2 + 4S3 |
... |
... |
... |
... |
| reaction3 |
reaction3 |
False |
S3 → S4 |
... |
... |
... |
... |
| reaction4 |
reaction4 |
False |
S4 → S5 |
... |
... |
... |
... |
|
Stoichiometry Matrix based on Reaction Stoichiometries
|
| Species |
reaction1 |
reaction2 |
reaction3 |
reaction4 |
| S1 |
-1 |
0 |
0 |
0 |
| S2 |
1 |
1 |
0 |
0 |
| S3 |
0 |
-1 |
-1 |
0 |
| S4 |
0 |
0 |
1 |
-1 |
| S5 |
0 |
0 |
0 |
1 |
|
Mass Balance Equations based on Stoichiometry Matrix
|
| Species |
[Species']=[Stoichometries][rates] |
| S1 |
S1' = -v[1] |
| S2 |
S2' = v[1] + v[2] |
| S3 |
S3' = -v[2] - v[3] |
| S4 |
S4' = v[3] - v[4] |
| S5 |
S5' = v[4] |
|
Mass Action Equations based on Stoichiometry Matrix
|
| Species |
[Species']=[Stoichometries][mass-action-rates] |
| S1 |
S1'=-(S1*v[1]) |
| S2 |
S2'=S1*v[1] + S2*S3^5*v[2] |
| S3 |
S3'=-(S2*S3^5*v[2]) - S3*v[3] |
| S4 |
S4'=S3*v[3] - S4*v[4] |
| S5 |
S5'=S4*v[4] |
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