MODEL1105180000#
type: SpeciesReference
initial amount: NaN
constant: false
boundary condition: false
in compartment: meta cell
name: v5
name: v4
stoichiometry: 1.0
name: v2
exponent: 1.0
reversible: true
kind: DIMENSIONLESS
is: SBO:0000176
type: Reaction
is: SBO:0000185
name: A
scale: 0
value: 0.333333333333333
multipler: 1.0
is: SBO:0000247
type: KineticLaw
initial concentration: NaN
name: v1
type: LocalParameter
name: B
value: -Infinity
value: Infinity
value: 1.0
value: 0.0
type: SBMLUnit
name: v3
has only substance units: false
units: dimensionless
type: Species
fast: false
type: SBMLUnitsDef

meta cell
type: Compartment
is: GO:0005622
is: SBO:0000290
constant: true
size: 1.0
spatial dimensions: 3.0
name: cell

MODEL1105180000
type: SBMLModel
name: Smallbone2009 - FBA model-Geometric Perspective
substance units: MODEL1105180000#
reaction: MODEL1105180000#
volume units: MODEL1105180000#
modified:
  W3 CDTF: Thu Jun 13 12:00:38 BST 2013
length unit: 076567
notes: This model is from the article: Flux balance analysis: a geometric perspective. Smallbone K, Simeonidis E. J Theor Biol. 2009 May 21;258(2):315-5 19490860 , Abstract: Advances in the field of bioinformatics have led to reconstruction of genome-scale networks for a number of key organisms. The application of physicochemical constraints to these stoichiometric networks allows researchers, through methods such as flux balance analysis, to highlight key sets of reactions necessary to achieve particular objectives. The key benefits of constraint-based analysis lie in the minimal knowledge required to infer systemic properties. However, network degeneracy leads to a large number of flux distributions that satisfy any objective; moreover, these distributions may be dominated by biologically irrelevant internal cycles. By examining the geometry underlying the problem, we define two methods for finding a unique solution within the space of all possible flux distributions; such a solution contains no internal cycles, and is representative of the space as a whole. The first method draws on typical geometric knowledge, but cannot be applied to large networks because of the high computational complexity of the problem. Thus a second method, an iteration of linear programs which scales easily to the genome scale, is defined. The algorithm is run on four recent genome-scale models, and unique flux solutions are found. The algorithm set out here will allow researchers in flux balance analysis to exchange typical solutions to their models in a reproducible format. Moreover, having found a single solution, statistical analyses such as correlations may be performed.
species: MODEL1105180000#
compartment: meta cell
curated: false
creator:
  ORG:
    orgname: University of Manchester
  n:
    given: Kieran
    family: Smallbone
is described by: http://identifiers.org/pubmed/19490860
area units: 076543
units def: MODEL1105180000#
created:
  W3 CDTF: Mon Oct 20 01:00:00 BST 2008
time units: MODEL1105180000#