345284
constant: true
units: dimensionless
value: 0.0
name: heat
type: Parameter

949593
stoichiometry: 1.0
species: metaid utp
type: SpeciesReference

metaid glc
initial amount: NaN
in compartment: metaid cell
name: glucose
boundary condition: false
has only substance units: false
is: SBO:0000247
is: CHEBI:17925
constant: false
initial concentration: 0.09675
type: Species

metaid g1p
is: CHEBI:16077
name: glucose 1-phosphate
has only substance units: false
type: Species
initial concentration: 0.1
initial amount: NaN
in compartment: metaid cell
constant: false
is: SBO:0000247
boundary condition: false

metaid shock tpp
units: dimensionless
value: 18.0
type: LocalParameter

345297
constant: false
units: dimensionless
value: NaN
name: log10 change in trehalose
type: Parameter

metaid g6p
is: SBO:0000247
in compartment: metaid cell
type: Species
constant: false
has only substance units: false
boundary condition: false
is: CHEBI:17665
name: glucose 6-phosphate
initial amount: NaN
initial concentration: 2.675

metaid Kf6p pgi
units: 949062
value: 0.29
type: LocalParameter

345302
constant: false
units: dimensionless
value: NaN
name: log10 change in UDP glucose
type: Parameter

345185
kinetic law: metaid kineticLaw hxt
product: 949279
reactant: 949267
is: SBO:0000185
fast: false
reversible: true
name: glucose transport
type: Reaction

metaid trh 0
constant: true
units: 949062
value: 0.05
type: Parameter

metaid shock hxt
units: dimensionless
value: 8.0
type: LocalParameter

949267
stoichiometry: 1.0
species: metaid glx
type: SpeciesReference

949087
exponent: -1.0
scale: 0
multipler: 1.0
kind: LITRE
type: SBMLUnit

949062
unit: 949087
unit: 949075
name: mM
type: SBMLUnitsDef

metaid medium
is: GO:0005576
constant: true
size: 1.0
spatial dimensions: 3.0
name: medium
type: Compartment

949569
stoichiometry: 2.0
species: metaid glc
type: SpeciesReference

949135
exponent: 1.0
scale: -3
multipler: 1.0
kind: MOLE
type: SBMLUnit

metaid tpp
reactant: 949424
product: 949436
kinetic law: 949460
name: T6P phosphatase
reversible: false
fast: false
is: SBO:0000176
is version of: http://identifiers.org/ec-code/3.1.3.12
product: 949448
type: Reaction
reactant: 949412

949436
stoichiometry: 1.0
species: metaid trh
type: SpeciesReference

metaid glc 0
constant: true
units: 949062
value: 0.09765
type: Parameter

345258
units: 949062
value: 3.8
type: LocalParameter

345263
units: 949123
value: 15.2
type: LocalParameter

metaid Kadp hxk
units: 949062
value: 0.23
type: LocalParameter

metaid adp
in compartment: metaid cell
is: CHEBI:16761
initial concentration: 1.282
type: Species
name: ADP
initial amount: NaN
constant: false
boundary condition: true
is: SBO:0000247
has only substance units: false

metaid Kiudg ugp
units: 949062
value: 0.0035
type: LocalParameter

949304
stoichiometry: 1.0
species: metaid atp
type: SpeciesReference

949111
exponent: -1.0
scale: 0
multipler: 60.0
kind: SECOND
type: SBMLUnit

metaid pgi
kinetic law: metaid kineticLaw pgi
product: 949255
reactant: 949243
is version of: http://identifiers.org/ec-code/5.3.1.9
is: SBO:0000176
fast: false
reversible: true
name: G6P isomerase
type: Reaction

949581
stoichiometry: 1.0
species: metaid g1p
type: SpeciesReference

metaid t6p
constant: false
initial concentration: 0.02
is: SBO:0000247
initial amount: NaN
is: CHEBI:18283
type: Species
has only substance units: false
in compartment: metaid cell
name: trehalose 6-phosphate
boundary condition: false

metaid Kg1p ugp
units: 949062
value: 0.32
type: LocalParameter

metaid nth
product: 949569
reactant: 949545
is: SBO:0000176
fast: false
name: trehalase
is version of: http://identifiers.org/ec-code/3.2.1.28
reactant: 949557
reversible: false
kinetic law: metaid kineticLaw nth
type: Reaction

metaid trh
type: Species
initial concentration: 0.05
initial amount: NaN
has only substance units: false
boundary condition: false
is: SBO:0000247
constant: false
name: trehalose
in compartment: metaid cell
is: CHEBI:16551

345299
constant: false
units: dimensionless
value: NaN
name: log10 change in trehalose 6-phosphate
type: Parameter

metaid ugp
is version of: http://identifiers.org/ec-code/2.7.7.9
reactant: 949581
type: Reaction
kinetic law: metaid kineticLaw ugp
name: UDP glucose phosphorylase
product: 949629
fast: false
reactant: 949593
reactant: 949605
is: SBO:0000176
product: 949617
reversible: false

metaid g6p 0
constant: true
units: 949062
value: 2.675
type: Parameter

949376
stoichiometry: 1.0
species: metaid g6p
type: SpeciesReference

metaid ppi
constant: false
boundary condition: true
initial amount: NaN
name: diphosphate
type: Species
in compartment: metaid cell
initial concentration: NaN
is: SBO:0000247
is: CHEBI:18361
has only substance units: false

metaid t6p 0
constant: true
units: 949062
value: 0.02
type: Parameter

949521
stoichiometry: 1.0
species: metaid h
type: SpeciesReference

949038
unit: 949050
name: min
type: SBMLUnitsDef

949243
stoichiometry: 1.0
species: metaid g6p
type: SpeciesReference

345262
units: dimensionless
value: 1.0
type: LocalParameter

949255
stoichiometry: 1.0
species: metaid f6p
type: SpeciesReference

949496
stoichiometry: 1.0
species: metaid t6p
type: SpeciesReference

metaid Keq pgm
units: dimensionless
value: 0.1667
type: LocalParameter

metaid Kg6p pgm
units: 949062
value: 0.05
type: LocalParameter

949050
exponent: 1.0
scale: 0
multipler: 60.0
kind: SECOND
type: SBMLUnit

949075
exponent: 1.0
scale: -3
multipler: 1.0
kind: MOLE
type: SBMLUnit

345220
units: 949123
value: 289.6
type: LocalParameter

949388
stoichiometry: 1.0
species: metaid g1p
type: SpeciesReference

metaid shock pgm
units: dimensionless
value: 16.0
type: LocalParameter

949424
stoichiometry: 1.0
species: metaid h2o
type: SpeciesReference

metaid g1p 0
constant: true
units: 949062
value: 0.1
type: Parameter

345209
units: dimensionless
value: 1.0
type: LocalParameter

metaid Katp hxk
units: 949062
value: 0.15
type: LocalParameter

949123
unit: 949159
unit: 949147
unit: 949135
name: mM per min
type: SBMLUnitsDef

949557
stoichiometry: 1.0
species: metaid h2o
type: SpeciesReference

metaid h
constant: false
type: Species
initial concentration: NaN
name: H+
initial amount: NaN
is: CHEBI:24636
in compartment: metaid cell
boundary condition: true
has only substance units: false
is: SBO:0000247

metaid Kiutp ugp
units: 949062
value: 0.11
type: LocalParameter

metaid udg
name: UDP glucose
in compartment: metaid cell
constant: false
is: SBO:0000247
is: CHEBI:18066
type: Species
has only substance units: false
initial concentration: 0.7
boundary condition: false
initial amount: NaN

949340
stoichiometry: 1.0
species: metaid h
type: SpeciesReference

metaid Kutp ugp
units: 949062
value: 0.11
type: LocalParameter

metaid hxk
type: Reaction
modifier: 949352
product: 949316
reversible: false
kinetic law: 949364
name: hexokinase
is version of: http://identifiers.org/ec-code/2.7.1.1
reactant: 949304
reactant: 949292
fast: false
product: 949340
product: 949328
is: SBO:0000176

345260
units: 949062
value: 0.886
type: LocalParameter

metaid Ki hxt
units: dimensionless
value: 0.91
type: LocalParameter

345202
units: 949123
value: 1071.0
type: LocalParameter

metaid h2o
constant: false
is: CHEBI:15377
initial amount: NaN
has only substance units: false
boundary condition: true
type: Species
initial concentration: NaN
in compartment: metaid cell
is: SBO:0000247
name: water

949629
stoichiometry: 1.0
species: metaid ppi
type: SpeciesReference

metaid pho
initial amount: NaN
constant: false
in compartment: metaid cell
has only substance units: false
boundary condition: true
is: CHEBI:43474
initial concentration: NaN
is: SBO:0000247
type: Species
name: phosphate

949316
stoichiometry: 1.0
species: metaid g6p
type: SpeciesReference

metaid cell
is: GO:0005622
constant: true
size: 1.0
spatial dimensions: 3.0
name: cell
type: Compartment

345253
units: 949123
value: 6.5
type: LocalParameter

metaid f6p
is: CHEBI:16084
type: Species
is: SBO:0000247
initial concentration: 0.625
initial amount: NaN
boundary condition: true
constant: false
name: fructose 6-phosphate
in compartment: metaid cell
has only substance units: false

949026
exponent: 1.0
scale: -3
multipler: 1.0
kind: MOLE
type: SBMLUnit

949508
stoichiometry: 1.0
species: metaid udp
type: SpeciesReference

949159
exponent: -1.0
scale: 0
multipler: 60.0
kind: SECOND
type: SBMLUnit

345287
constant: false
units: dimensionless
value: NaN
name: log10 change in glucose
type: Parameter

949617
stoichiometry: 1.0
species: metaid udg
type: SpeciesReference

metaid Keq hxk
units: dimensionless
value: 2000.0
type: LocalParameter

metaid udp
constant: false
name: UDP
type: Species
in compartment: metaid cell
boundary condition: true
is: SBO:0000247
initial concentration: 0.2815
initial amount: NaN
has only substance units: false
is: CHEBI:17659

metaid udg 0
constant: true
units: 949062
value: 0.7
type: Parameter

949484
stoichiometry: 1.0
species: metaid udg
type: SpeciesReference

345294
constant: false
units: dimensionless
value: NaN
name: log10 change in glucose 6-phosphate
type: Parameter

949545
stoichiometry: 1.0
species: metaid trh
type: SpeciesReference

metaid Kt6p tpp
units: 949062
value: 0.5
type: LocalParameter

949292
stoichiometry: 1.0
species: metaid glc
type: SpeciesReference

metaid Kitrh hxk
units: 949062
value: 0.04
type: LocalParameter

949412
stoichiometry: 1.0
species: metaid t6p
type: SpeciesReference

metaid Kglc hxt
units: 949062
value: 1.1918
type: LocalParameter

345257
units: 949123
value: 1.371
type: LocalParameter

949328
stoichiometry: 1.0
species: metaid adp
type: SpeciesReference

metaid pgm
kinetic law: 949400
product: 949388
reactant: 949376
is version of: http://identifiers.org/ec-code/5.4.2.2
is: SBO:0000176
fast: false
reversible: true
name: phosphoglucomutase
type: Reaction

metaid Kg1p pgm
units: 949062
value: 0.023
type: LocalParameter

345243
units: 949123
value: 0.3545
type: LocalParameter

metaid tps
product: 949521
type: Reaction
reactant: 949472
name: T6P synthase
product: 949496
is version of: http://identifiers.org/ec-code/2.4.1.15
product: 949508
reactant: 949484
fast: false
is: SBO:0000176
kinetic law: 949533
reversible: false

345267
units: 949123
value: 36.82
type: LocalParameter

949448
stoichiometry: 1.0
species: metaid pho
type: SpeciesReference

949014
unit: 949026
name: mmol
type: SBMLUnitsDef

345265
units: 949062
value: 2.99
type: LocalParameter

metaid Keq pgi
units: dimensionless
value: 0.3
type: LocalParameter

metaid Kglc hxk
units: 949062
value: 0.08
type: LocalParameter

949147
exponent: -1.0
scale: 0
multipler: 1.0
kind: LITRE
type: SBMLUnit

metaid shock ugp
units: dimensionless
value: 16.0
type: LocalParameter

345210
units: 949123
value: 97.24
type: LocalParameter

metaid Kg6p pgi
units: 949062
value: 1.4
type: LocalParameter

metaid glx
initial concentration: 100.0
has only substance units: false
initial amount: NaN
in compartment: metaid medium
constant: false
is: CHEBI:17925
name: glucose
type: Species
boundary condition: true
is: SBO:0000247

metaid atp
boundary condition: true
is: SBO:0000247
has only substance units: false
name: ATP
in compartment: metaid cell
is: CHEBI:15422
initial amount: NaN
initial concentration: 2.525
constant: false
type: Species

949279
stoichiometry: 1.0
species: metaid glc
type: SpeciesReference

metaid shock nth
units: dimensionless
value: 6.0
type: LocalParameter

BIOMD0000000380
species: metaid ppi
parameter: metaid trh 0
rule: 259078
modified:
  W3 CDTF: Wed May 16 15:48:51 BST 2012
parameter: 345302
occurs in: http://identifiers.org/taxonomy/4932
species: metaid pho
parameter: 345290
reaction: metaid tps
parameter: metaid udg 0
parameter: 345297
species: metaid g1p
type: SBMLModel
volume units: 498095
species: metaid glx
parameter: 345287
rule: 259080
reaction: metaid tpp
reaction: metaid nth
created:
  W3 CDTF: Mon Jul 12 01:00:00 BST 2010
parameter: 345284
substance units: 949014
units def: 949038
reaction: metaid ugp
species: metaid trh
units def: 949123
rule: 259073
species: metaid g6p
name: Smallbone2011_TrehaloseBiosynthesis
is: MODEL1010010000
species: metaid utp
species: metaid t6p
species: metaid glc
species: metaid f6p
parameter: 345299
time units: 949038
species: metaid atp
reaction: metaid pgm
reaction: 345185
compartment: metaid medium
parameter: metaid g6p 0
reaction: metaid pgi
species: metaid h2o
creator:
  ORG:
    orgname: EMBL-EBI
  n:
    given: Vijayalakshmi
    family: Chelliah
rule: 259074
parameter: metaid t6p 0
compartment: metaid cell
species: metaid udg
units def: 949014
parameter: metaid g1p 0
creator:
  ORG:
    orgname: University of Manchester
  n:
    given: Kieran
    family: Smallbone
parameter: metaid glc 0
species: metaid udp
units def: 949062
rule: 259077
area units: 498119
species: metaid h
length unit: length
reaction: metaid hxk
notes: This model is from the article: Building a Kinetic Model of Trehalose Biosynthesis in Saccharomyces cerevisiae. Smallbone K, Malys N, Messiha HL, Wishart JA, Simeonidis E. Methods Enzymol. 2011;500:355-70. 21943906 , Abstract: In this chapter, we describe the steps needed to create a kinetic model of a metabolic pathway based on kinetic data from experimental measurements and literature review. Our methodology is presented by utilizing the example of trehalose metabolism in yeast. The biology of the trehalose cycle is briefly reviewed and discussed. This SBML model is made available under the Creative Commons Attribution-Share Alike 3.0 Unported Licence (see www.creativecommons.org ). This model originates from BioModels Database: A Database of Annotated Published Models (http://www.ebi.ac.uk/biomodels/). It is copyright (c) 2005-2012 The BioModels.net Team. For more information see the terms of use . 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 Novère N, Laibe C (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol., 4:92.
rule: 259083
is version of: GO:0005992
curated: true
parameter: 345294
is described by: http://identifiers.org/pubmed/21943906
units def: 949099
initial assignment: BIOMD0000000380#
species: metaid adp

345290
constant: false
units: dimensionless
value: NaN
name: log10 change in glucose 1-phosphate
type: Parameter

949099
unit: 949111
name: per min
type: SBMLUnitsDef

metaid Kg6p hxk
units: 949062
value: 30.0
type: LocalParameter

949472
stoichiometry: 1.0
species: metaid g6p
type: SpeciesReference

metaid utp
initial concentration: 0.6491
is: SBO:0000247
constant: false
name: UTP
has only substance units: false
boundary condition: true
type: Species
is: CHEBI:46398
in compartment: metaid cell
initial amount: NaN

metaid shock hxk
units: dimensionless
value: 8.0
type: LocalParameter

949605
stoichiometry: 1.0
species: metaid h
type: SpeciesReference

metaid shock tps
units: dimensionless
value: 12.0
type: LocalParameter