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University of Washington
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Conservation Analysis for some small models

Information Provided by Ravi Rao

Please note in the following, the blue colored nodes are boundaries while the orange colored nodes are floating species.

Small Models

The following models (in SBML) were used to test the conservation module.

Reactions

S1 → S2

S2 → S1



Conserved Cycles

1: S1 + S2

Independent & [Dep] Species

S1 & [S2]
Reactions

X1 → B + C

B + C → X2



Conserved Cycles

1: -B + C

Independent & [Dep] Species

B & [C]
Reactions

S1 → S2

S2 → S3

S3 → S2

S2 → S1
Conserved Cycles

1: S1 + S2 + S2

Independent & [Dep] Species

S1, S2 & [S3]


Reactions

S1 → S2

S2 → S3
Conserved Cycles

1: S1 + S2 + S2

Independent & [Dep] Species

S1, S2 & [S3]
Reactions

ES → E + S1

S1 → S2

S2 → E + ES
Conserved Cycles

1: E + ES

2: ES + S1 + S2

Independent & [Dep] Species

ES, S1 & [E, S2]
Reactions

X0 + A → S1 + B

S1 → S2

S2 + B → A + S3

S3 → X1
Conserved Cycles

1: S1 + S2 + A

2: - S1 - S2 + B

Independent & [Dep] Species

S1, S2, S3 & [A, B]
Reactions

X0 → S1

S1 + A → S2 + B

S1 + B → A + S3

S2 → X1

S3 → X2
Conserved Cycles

1: A + B

Independent & [Dep] Species

S1, S2, S3, A & [B]
Reactions

X0 → S1

S1 → S2

S2 → S1

S2 → X1
Conserved Cycles

NONE

Independent & [Dep] Species

S1, S2 & [NONE]
Reactions

S1 + A → S2 + B

S2 → S3

S3 + B → S1 + A
Conserved Cycles

1: S1 + S2 + S3

2: -S1 + A

3: S1 + B

Independent & [Dep] Species

S1, S2 & [S3, A, B]
Reactions

S1 + A + X → S2

S2 → X + C

C + X → S3

S3 + X → S1 + B

A → B
Conserved Cycles

1: -S1 + A + B

2: S1 + C + S2 + S3

Independent & [Dep] Species

S1, A, C, S2 & [B, S3]
Reactions

S1 + A → S2 + D

S2 + C → D + S3

S3 + B → D + S1

X → A

X → B

X → C
Conserved Cycles

1: S1 + S2 + S3

Independent & [Dep] Species

D, S2, B, A, C, S3 & [S1]
Reactions

S1 → S2

S2 → S1

S2 → S3

S3 → S2

S3 → S4

S4 → S3

S4 → S1

S1 → S4
Conserved Cycles

1: S1 + S2 + S3 + S4

Independent & [Dep] Species

S1, S2, S3 & [S4]
Reactions

S1 → S2 + A

S2 → S3

S3 → S2

S4 → S3 + B

A → S4

B → S1
Conserved Cycles

1: A + B + S1 + S4

Independent & [Dep] Species

S2, B, A, S1, S3 & [S4]
Reactions

X0 + X1 → S1 + S2

S1 + S2 → S3 + S4

S3 + S4 → S5 + S6

S5 + S6 → Y0 + Y1

X0 → S5

S1 → Y0

X1 → S6

S2 → Y1
Conserved Cycles

1: -S3 + S4

Independent & [Dep] Species

S2, S5, S1, S6, S3 & [S4]
Reactions

A → S1

S1 → S2

S2 → S3

S2 → S4

S3 + S4 → B

S3 → S1

S4 → S1
Conserved Cycles

1: 0.5 (S1 + S2 + S3 + S4 + A) + B

Independent & [Dep] Species

S1, S2, S3, S4, A & [B]
Reactions

A → S1

S1 → S2

S2 → S4

S2 + S4 → B

S2 → S3

S4 → S5

S3 + S5 + B → C
Conserved Cycles

1: 0.25 (S1 + S2 + S4 + S3 + S5 + A) + 0.5 B + C

Independent & [Dep] Species

S2, S1, S4, S3, B, S5, A & [C]
Reactions

A → S1

S1 → S2 + S4 + C

S2 → A

S4 → A

C + S6 → S3 + S5

B → S6

S3 → B

S5 → B
Conserved Cycles

1: -0.5(S4 + A + S2 + S1) + S6 + B + C + S3 + S5

Independent & [Dep] Species

S4, B, A, S3, S5, S2, S1, S6 & [C]
 
sysbio/conservationanalysis/moredetails/smallmodels.txt · Last modified: 2009/07/31 14:13 by fbergman
 

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