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hofmeyr1

The SBML for this model was obtained from the BioModels database (BioModels ID: BIOMD0000000284) Biomodels notes: Comparison of the steady with results of the SBML model with results from the original publication (figure 4) . The steady state was calculated and metabolic control analysis performed using Copasi 4.6. JWS Online curation: This model was curated by reproducing the figures as described in the BioModels Notes. No additional changes were made.

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Manuscript information

METAMOD: software for steady-state modelling and control analysis of metabolic pathways on the BBC microcomputer.

  • J H S Hofmeyr
  • KJ van der Merwe
Comput. Appl. Biosci. 1986; 2 (4): 243-249
Abstract
METAMOD, a BBC microcomputer-based software package for steady-state modelling and control analysis of model metabolic pathways, is described, The package consists of two programs. METADEF allows the user to define the pathway in terms of reactions, rate equations and initial concentrations of metabolites. METACAL uses one of two algorithms to calculate the steady-state concentrations and fluxes. One algorithm uses the current ratio of production and consumption rates of variable metabolites to adjust iteratively their concentrations in such a way that they converge towards the steady state. The other algorithm solves the roots of the system equations by means of a quasi-Newtonian procedure. Control analysis allows the calculation of elasticity, control and response coefficients, by means of finite difference approximation. METAMOD is interactive and easy to use, and suitable for teaching and research purposes.

Unit definitions 2

Unit definitions have no effect on the numerical analysis of the model. It remains the responsibility of the modeler to ensure the internal numerical consistency of the model. If units are provided, however, the consistency of the model units will be checked.

Name Definition
— 1.0 dimensionless
— 1.0 dimensionless

Compartments 1

Id Name Spatial dimensions Size
cell cell 3.0 1.0

Species 9

Id Name Initial quantity Compartment Fixed
A A 0.0 cell (cell) ✘
B B 0.0 cell (cell) ✘
C C 0.0 cell (cell) ✘
D D 0.0 cell (cell) ✘
E E 0.0 cell (cell) ✘
F F 0.0 cell (cell) ✘
X X 10.0 cell (cell) ✔
Y Y 2.0 cell (cell) ✔
Z Z 1.0 cell (cell) ✔

Initial assignments 0

Initial assignments are expressions that are evaluated at time=0. It is not recommended to create initial assignments for all model entities. Restrict the use of initial assignments to cases where a value is expressed in terms of values or sizes of other model entities. Note that it is not permitted to have both an initial assignment and an assignment rule for a single model entity.

Definition
Reactions 8
Id Name Objective coefficient Reaction Equation and Kinetic Law Flux bounds
R1 R1 X = A

cell * ((10 * X - A) / (1 + X + A + pow(B, 2)))
R2 R2 A = B

cell * ((2 * A - B) / (1 + A + B))
R3 R3 B = C

cell * ((B - C) / (1 + B + C + pow(D, 2)))
R4 R4 C = D

cell * ((5 * C - D) / (1 + C + D))
R5 R5 D = Y

cell * ((10 * D - Y) / (1 + D + Y))
R6 R6 B = E

cell * ((B - E) / (1 + B + E + pow(F, 2)))
R7 R7 E = F

cell * ((5 * E - F) / (1 + E + F))
R8 R8 F = Z

cell * ((10 * F - Z) / (1 + F + Z))

Parameters 0   0

Global parameters

Id Value

Local parameters

Id Value Reaction

Rules 0   0   0

Assignment rules

Definition

Rate rules

Definition

Algebraic rules

Definition

Events 0

Trigger Assignments