Model Identifier
Short description

SBML Level 2 code generated for the JWS Online project by Jacky Snoep using PySCeS .

Run this model online at .

To cite JWS Online please refer to: Olivier, B.G. and Snoep, J.L. (2004) Web-based modelling using JWS Online , Bioinformatics, 20:2143-2144.

This model originates from BioModels Database: A Database of Annotated Published Models. It is copyright (c) 2005-2010 The BioModels Team.
For more information see the terms of use .

To cite BioModels Database, please use Le Novère N., Bornstein B., Broicher A., Courtot M., Donizelli M., Dharuri H., Li L., Sauro H., Schilstra M., Shapiro B., Snoep J.L., Hucka M. (2006) BioModels Database: A Free, Centralized Database of Curated, Published, Quantitative Kinetic Models of Biochemical and Cellular Systems Nucleic Acids Res., 34: D689-D691.

To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication for more information.

In summary, you are entitled to use this encoded model in absolutely any manner you deem suitable, verbatim, or with modification, alone or embedded it in a larger context, redistribute it, commercially or not, in a restricted way or not.

Related Publication
  • Analysis of sucrose accumulation in the sugar cane culm on the basis of in vitro kinetic data.
  • Rohwer JM, Botha FC
  • The Biochemical journal , 9/ 2001 , Volume 358 , pages: 437-445 , PubMed ID: 11513743
  • Department of Biochemistry, University of Stellenbosch, Private Bag X1, 7602 Matieland, South Africa.
  • Sucrose accumulation in developing sugar cane (Saccharum officinarum) is accompanied by a continuous synthesis and cleavage of sucrose in the storage tissues. Despite numerous studies, the factors affecting sucrose accumulation are still poorly understood, and no consistent pattern has emerged which pinpoints certain enzyme activities as important controlling steps. Here, we develop an approach based on pathway analysis and kinetic modelling to assess the biochemical control of sucrose accumulation and futile cycling in sugar cane. By using the concept of elementary flux modes, all possible routes of futile cycling of sucrose were enumerated in the metabolic system. The available kinetic data for the pathway enzymes were then collected and assembled in a kinetic model of sucrose accumulation in sugar cane culm tissue. Although no data were fitted, the model agreed well with independent experimental results: in no case was the difference between calculated and measured fluxes and concentrations greater than 2-fold. The model thus validated was then used to assess different enhancement strategies for increasing sucrose accumulation. First, the control coefficient of each enzyme in the system on futile cycling of sucrose was calculated. Secondly, the activities of those enzymes with the numerically largest control coefficients were varied over a 5-fold range to determine the effect on the degree of futile cycling, the conversion efficiency from hexoses into sucrose, and the net sucrose accumulation rate. In view of the modelling results, overexpression of the fructose or glucose transporter or the vacuolar sucrose import protein, as well as reduction of cytosolic neutral invertase levels, appear to be the most promising targets for genetic manipulation. This offers a more directed improvement strategy than cumbersome gene-by-gene manipulation. The kinetic model can be viewed and interrogated on the World Wide Web at
Submitter of the first revision: Nicolas Le Novère
Submitter of this revision: Nicolas Le Novère
Modellers: Nicolas Le Novère

Metadata information

BioModels Database MODEL6618063111
BioModels Database BIOMD0000000023
KEGG Pathway Starch and sucrose metabolism
PubMed 11513743

Curation status


Connected external resources

SBGN view in Newt Editor

Name Description Size Actions

Model files

BIOMD0000000023_url.xml SBML L2V4 representation of Rohwer2001_Sucrose 54.57 KB Preview | Download

Additional files

BIOMD0000000023-biopax2.owl Auto-generated BioPAX (Level 2) 33.79 KB Preview | Download
BIOMD0000000023-biopax3.owl Auto-generated BioPAX (Level 3) 46.41 KB Preview | Download
BIOMD0000000023.m Auto-generated Octave file 11.34 KB Preview | Download
BIOMD0000000023.pdf Auto-generated PDF file 193.97 KB Preview | Download
BIOMD0000000023.png Auto-generated Reaction graph (PNG) 98.72 KB Preview | Download
BIOMD0000000023.sci Auto-generated Scilab file 9.67 KB Preview | Download
BIOMD0000000023.svg Auto-generated Reaction graph (SVG) 25.55 KB Preview | Download
BIOMD0000000023.vcml Auto-generated VCML file 55.45 KB Preview | Download
BIOMD0000000023.xpp Auto-generated XPP file 7.87 KB Preview | Download
BIOMD0000000023_urn.xml Auto-generated SBML file with URNs 53.80 KB Preview | Download

  • Model originally submitted by : Nicolas Le Novère
  • Submitted: Sep 13, 2005 2:28:04 PM
  • Last Modified: May 20, 2012 1:43:33 PM
  • Version: 2 public model Download this version
    • Submitted on: May 20, 2012 1:43:33 PM
    • Submitted by: Nicolas Le Novère
    • With comment: Current version of Rohwer2001_Sucrose
  • Version: 1 public model Download this version
    • Submitted on: Sep 13, 2005 2:28:04 PM
    • Submitted by: Nicolas Le Novère
    • With comment: Original import of Rohwer2001_Sucrose

(*) You might be seeing discontinuous revisions as only public revisions are displayed here. Any private revisions unpublished model revision of this model will only be shown to the submitter and their collaborators.

: Variable used inside SBML models

Reactions Rate Parameters
Suc => Sucvac compartment*Vmax11*Suc/(Km11Suc+Suc) Km11Suc=100.0; Vmax11=1.0
Fru + ATP => HexP + ADP compartment*Vmax5/(1+Fru/Ki5Fru)*Fru/Km5Fru*ATP/Km5ATP/(1+Fru/Km5Fru+ATP/Km5ATP+Fru*ATP/(Km5Fru*Km5ATP)+ADP/Ki5ADP) Ki5Fru=12.0; Km5Fru=0.1; Vmax5=0.164; Km5ATP=0.085; Ki5ADP=2.0
Fru + ATP => HexP + ADP; Glc compartment*Vmax4*Fru/Km4Fru*ATP/Km4ATP/((1+ATP/Km4ATP)*(1+Glc/Km3Glc+Fru/Km4Fru+0.113*HexP/Ki3G6P+0.0575*HexP/Ki4F6P)) Vmax4=0.197; Ki3G6P=0.1; Km3Glc=0.07; Km4Fru=10.0; Km4ATP=0.25; Ki4F6P=10.0
ATP + Glc => HexP + ADP; Fru compartment*Vmax3*Glc/Km3Glc*ATP/Km3ATP/((1+ATP/Km3ATP)*(1+Glc/Km3Glc+Fru/Km4Fru+0.113*HexP/Ki3G6P+0.0575*HexP/Ki4F6P)) Km3ATP=0.25; Ki3G6P=0.1; Km3Glc=0.07; Km4Fru=10.0; Vmax3=0.197; Ki4F6P=10.0
HexP + Fru => Suc + UDP compartment*(-Vmax8f)*(Suc*UDP-Fru*0.8231*HexP/Keq8)/(Suc*UDP*(1+Fru/Ki8Fru)+Km8Suc*(UDP+Ki8UDP)+Km8UDP*Suc+Vmax8f/(Vmax8r*Keq8)*(Km8UDPGlc*Fru*(1+UDP/Ki8UDP)+0.8231*HexP*(Km8Fru*(1+Km8UDP*Suc/(Ki8UDP*Km8Suc))+Fru*(1+Suc/Ki8Suc)))) Ki8Suc=40.0; Vmax8f=0.677; Km8Suc=50.0; Keq8=5.0; Ki8Fru=4.0; Ki8UDP=0.3; Km8UDP=0.3; Km8UDPGlc=0.3; Vmax8r=0.3; Km8Fru=4.0
Suc6P => Suc + phos compartment*Vmax7*Suc6P/(Km7Suc6P+Suc6P) Vmax7=0.5; Km7Suc6P=0.1
Glcex => Glc compartment*Vmax2*Glcex/(Km2Glcex*(1+Glc/Ki2Glc)+Glcex) Vmax2=0.286; Ki2Glc=1.0; Km2Glcex=0.2
Curator's comment:
(added: 18 Jan 2010, 12:55:48, updated: 18 Jan 2010, 12:55:48)
Dependence of the reaction flux J11 (v11 in the model) on the maximal velocities of Fructose uptake (Vmax1) and Hexokinase (Vmax3). As in the original article in fig. 3 A and B, Vmax1 was increased and Vmax3 decreased 5 fold. The calculations were performed using Copasi 4.5.