limiting gpSampler's maxStep

[Delaram]

Hi,

I'm trying to use gpSampler function for a couple of small toy models. when I fix the upper and lower bounds of reactions on a certain flux value, I get  "warning small step", which leads to unreliable results.

In order to fix this problem,I tried changing  gpSampler optional input "maxSteps" from it's default value(1e10) to less values(down to 1e1).

I was wondering how this would effect the uniformity of sample points?

Thanks

[Ronan M.T. Fleming]

Hi Delaram,

this new sampler:

https://academic.oup.com/bioinformatics/article-lookup/doi/10.1093/bioinformatics/btx052

implemented here:

https://github.com/opencobra/cobratoolbox/blob/master/src/sampling/chrrSampler.m

is guaranteed to return a uniform sample.

Regards,

Ronan

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[Delaram]

Dear Ronan,

Thank you for your response.

I downloaded the document and tried sampling with chrrSampler but it gives the following error:

Error using nullSpaceOperator (line 96)
Chrr sampler not compatible with windows OS.

Error in getNullSpace (line 32)
nullS = nullSpaceOperator(S,gmscale,printLevel);        % forms a structure nullS.

Error in preprocess (line 32)
N = getNullSpace(P.A_eq,0);

Error in chrrSampler (line 127)
    [roundedPolytope] = preprocess(P, toRound);

[Laurent Heirendt]

Hi,

As the error states, the chrrSampler is not yet compatible with Windows OS. It can only be used on UNIX systems (macOS or linux) for now.

I hope this helps.

Best,

Laurent

[Ronan M.T. Fleming]

Replace

preprocess (line 32)
N = getNullSpace(P.A_eq,0);

with

archstr = computer('arch');
archstr = lower(archstr);
switch archstr
case {'win32', 'win64'}
N=null(P.A_eq);

case {'glnxa86'}
N = getNullSpace(P.A_eq,0);

end

It will be slower, but should still work.

--

[Delaram]

Unfortunately, It didn't work. This time I got the following errors: 

Error using svd
Use svds for sparse singular values and vectors.

Error in null (line 66)
[~,S,V] = svd(A,0);

Error in preprocess (line 36)
N=null(P.A_eq);

[Ronan M.T. Fleming]

archstr = computer('arch');
archstr = lower(archstr);
switch archstr
case {'win32', 'win64'}

N=null(full(P.A_eq));

case {'glnxa86'}
N = getNullSpace(P.A_eq,0);

end

[Delaram]

It worked this time !!!!!!  THANK YOU!

On Tuesday, May 2, 2017 at 11:42:36 AM UTC+4:30, Ronan M.T. Fleming wrote:

archstr = computer('arch');
archstr = lower(archstr);
switch archstr
case {'win32', 'win64'}
N=null(full(P.A_eq));

case {'glnxa86'}
N = getNullSpace(P.A_eq,0);

end

On 30 April 2017 at 10:44, Delaram <d.pouy...@gmail.com> wrote:

Unfortunately, It didn't work. This time I got the following errors: 

Error using svd
Use svds for sparse singular values and vectors.

Error in null (line 66)
[~,S,V] = svd(A,0);

Error in preprocess (line 36)
N=null(P.A_eq);

Error in chrrSampler (line 127)
[roundedPolytope] = preprocess(P, toRound);

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