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BIOMD0000000284 - Hofmeyer1986_SeqFb_Proc_AA_Synthesis

 

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Reference Publication
Publication ID: 3450367
Hofmeyr JH, van der Merwe KJ.
METAMOD: software for steady-state modelling and control analysis of metabolic pathways on the BBC microcomputer.
Comput. Appl. Biosci. 1986 Dec; 2(4): 243-249
Department of Biochemistry, University of Stellenbosch, South Africa.  [more]
Model
Original Model: BIOMD0000000284.xml.origin
Submitter: Kieran Smallbone
Submission ID: MODEL1010190003
Submission Date: 19 Oct 2010 11:38:31 UTC
Last Modification Date: 05 Jul 2012 14:47:32 UTC
Creation Date: 10 Oct 2010 10:10:10 UTC
Encoders:  Lukas Endler
   Kieran Smallbone
set #1
bqbiol:occursIn Taxonomy Bacteria
bqbiol:isVersionOf Gene Ontology cellular amino acid biosynthetic process
Notes

This model is the reaction sequence SEQFB, a model pathway of a branched system with sequential feedback interactions found in bacterial amino acid synthesis. Its steady state is presented in Fig 4.

The model is described in:
METAMOD: software for steady-state modelling and control analysis of metabolic pathways on the BBC microcomputer.
JHS Hofmeyr and KJ van der Merwe, Comput Appl Biosci 1986 2:243-9; PubmedID: 3450367
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.


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To cite BioModels Database, please use: Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novere N, Laibe C (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol., 4:92.

Model
Publication ID: 3450367 Submission Date: 19 Oct 2010 11:38:31 UTC Last Modification Date: 05 Jul 2012 14:47:32 UTC Creation Date: 10 Oct 2010 10:10:10 UTC
Mathematical expressions
Reactions
R1 R2 R3 R4
R5 R6 R7 R8
Physical entities
Compartments Species
cell A B C
D E F
X Y Z
Reactions (8)
 
 R1 [X] ↔ [A];   {B}
 
 R2 [A] ↔ [B];  
 
 R3 [B] ↔ [C];   {D}
 
 R4 [C] ↔ [D];  
 
 R5 [D] ↔ [Y];  
 
 R6 [B] ↔ [E];   {F}
 
 R7 [E] ↔ [F];  
 
 R8 [F] ↔ [Z];  
 
 cell Spatial dimensions: 3.0  Compartment size: 1.0
 
 A
Compartment: cell
Initial concentration: 0.0
 
 B
Compartment: cell
Initial concentration: 0.0
 
 C
Compartment: cell
Initial concentration: 0.0
 
 D
Compartment: cell
Initial concentration: 0.0
 
 E
Compartment: cell
Initial concentration: 0.0
 
 F
Compartment: cell
Initial concentration: 0.0
 
 X
Compartment: cell
Initial concentration: 10.0
Constant
 
 Y
Compartment: cell
Initial concentration: 2.0
Constant
 
 Z
Compartment: cell
Initial concentration: 1.0
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000284

Curator's comment: (updated: 25 Nov 2010 01:09:43 GMT)

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.

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