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https://issues.apache.org/jira/browse/MATH-1108?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=13920708#comment-13920708
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Buharov Alexander commented on MATH-1108:
-----------------------------------------
This problem is related with systems biology. This models are saved in
SBML-format. And there are special Matlab TOOLBOX (COBRA) for solving this
problem (http://opencobra.sourceforge.net/openCOBRA/Welcome.html).
If you want to test this toolbox. I attached file AdipocyteModel.xml with model
(this model have same non-bounds constraints and object function like previous
example). You can instal COBRA toolbox and make next calculation in Matlab:
model = readCbModel('AdipocyteModel.xml'); % read model
changeCobraSolver('glpk'); % choose
solver
FBAsolution = optimizeCbModel(model,'max'); % solve
As I understand this solver use modification of simplex method (But I could be
wrong). Calculation time is around 1s.
> SimplexSolver returns TooManyIterationsException
> ------------------------------------------------
>
> Key: MATH-1108
> URL: https://issues.apache.org/jira/browse/MATH-1108
> Project: Commons Math
> Issue Type: Bug
> Affects Versions: 3.2, 3.1.1
> Reporter: Buharov Alexander
> Attachments: AdipocyteModel.xml, Problem.zip
>
>
> We have vector v and matrix s (from file S.txt)
> v - vector ( size: 1*649 )
> s - matrix ( size: 554*649 )
> We want solve linear problem:
> * max (v[31])
> * Bounds:
> * s*v = 0
> * -1 <= v[i] <= 1 for i=0,..., 648
> We changed MaxIter parameter (from 100 to 1e+6). And we changed epsilon (
> set default value and 1e-3). But solver always throws
> TooManyIterationsException (and work very slow).
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