sbioconsmoiety
Find conserved moieties in SimBiology model
Syntax
[
G
, Sp
]
= sbioconsmoiety(modelObj
)
[G, Sp
] = sbioconsmoiety(modelObj
, alg
)
H
= sbioconsmoiety(modelObj
, alg
,'p')
H
= sbioconsmoiety(modelObj
, alg
,'p', FormatArg
)
[SI, SD, L0, NR, ND
]
= sbioconsmoiety(modelObj
,'link')
Arguments
G | An m-by-n matrix, where m is
the number of conserved quantities found and n is
the number of species in the model. Each row of G specifies
a linear combination of species whose rate of change over time is
zero. |
Sp | Cell array of species names that labels the columns of . If
the species are in multiple compartments, species names are qualified
with the compartment name in the form |
modelObj | Model object to be evaluated for conserved moieties. |
alg | Specify algorithm to use during evaluation of conserved moieties.
Valid values are 'qr' , 'rreduce' ,
or 'semipos' . |
H | Cell array of character vectors containing the conserved moieties. |
p | Prints the output according to the format defined by
FormatArg . |
FormatArg | Specifies formatting for the output H .
FormatArg must either be a character
vector or string specifying a C-style format, or a
positive integer specifying the maximum number of digits of precision
used. |
SI | Cell array containing the names of independent species in the model. |
SD | Cell array containing the names of dependent species in the model. |
L0 | Link matrix relating
|
NR | Reduced stoichiometry matrices containing one row for
each independent species. The concatenated matrix
|
ND | Reduced stoichiometry matrices containing one row for
each dependent species. The concatenated matrix
|
Description
[
calculates
a complete set of linear conservation relations for the species in
the SimBiology® model object G
, Sp
]
= sbioconsmoiety(modelObj
)
.
modelObj
sbioconsmoiety
computes conservation relations
by analyzing the structure of the model object's stoichiometry matrix.
Thus, sbioconsmoiety
does not include species that
are governed by algebraic or rate rules.
[
provides
an algorithm specification. For G, Sp
] = sbioconsmoiety(modelObj
, alg
)
,
specify alg
'qr'
, 'rreduce'
, or 'semipos'
.
When you specify
'qr'
,sbioconsmoiety
uses an algorithm based onQR
factorization. From a numerical standpoint, this is the most efficient and reliable approach.When you specify
'rreduce'
,sbioconsmoiety
uses an algorithm based on row reduction, which yields better numbers for smaller models. This is the default.When you specify
'semipos'
,sbioconsmoiety
returns conservation relations in which all the coefficients are greater than or equal to 0, permitting a more transparent interpretation in terms of physical quantities.
For larger models, the QR
-based method is
recommended. For smaller models, row reduction or the semipositive
algorithm may be preferable. For row reduction and QR
factorization,
the number of conservation relations returned equals the row rank
degeneracy of the model object's stoichiometry matrix. The semipositive
algorithm may return a different number of relations. Mathematically
speaking, this algorithm returns a generating set of vectors for the
space of semipositive conservation relations.
returns
a cell array of character vectors H
= sbioconsmoiety(modelObj
, alg
,'p')
containing
the conserved quantities inH
.
modelObj
specifies
formatting for the output H
= sbioconsmoiety(modelObj
, alg
,'p', FormatArg
)H
.
should
either be a FormatArg
C-style
format string, or a positive
integer specifying the maximum number of digits of precision used.
[
uses
a SI, SD, L0, NR, ND
]
= sbioconsmoiety(modelObj
,'link')QR
-based algorithm to compute information relevant
to the dimensional reduction, via conservation relations, of the reaction
network in
.modelObj
Examples
Example 1
This example shows conserved moieties in a cycle.
Create a model with a cycle. For convenience use arbitrary reaction rates, as this will not affect the result.
Look for conserved moieties.
g = 1 1 1 sp = 'a' 'b' 'c'
Explore Conservation Relations in SimBiology Oscillator Model
Load the model.
sbioloadproject("oscillator.sbproj");
Return semipositive conservation relations in the model in which all the coefficients are greater than or equal to 0 and print the output.
sbioconsmoiety(m1,"semipos","p")
ans = 4x1 cell
{'pol + pol_OpA + pol_OpB + pol_OpC' }
{'OpB + pol_OpB + pA_OpB1 + pA_OpB_pA + pA_OpB2'}
{'OpA + pol_OpA + pC_OpA1 + pC_OpA2 + pC_OpA_pC'}
{'OpC + pol_OpC + pB_OpC1 + pB_OpC2 + pB_OpC_pB'}
Version History
Introduced in R2006a