readSBML and writeSBML are very slow on Matlab 2017Rb and Mac OS 13.12 (High Sierra)

[Uri David Akavia]

Hi.

I'm working with RECON 2.2. 

Reading the SBML or writing the SBML (as distributed by BioModels website http://www.ebi.ac.uk/biomodels-main/MODEL1603150001) takes about 20 minutes. Is this the same amount of time it takes for everybody, or is this another one of the features I have to "thank" Apple for?

If it takes this amount of time just for me, I'm wondering if that can be fixed. Especially since I'm trying to work with people who use cobrapy, and prefer reading/writing SBML. If it is everybody, maybe SBML processing is just slow.

Thanks,

Uri David

[Thomas Pfau]

Hi Uri David,

I can confirm this behaviour on a linux machine with 2016b. The COBRA Toolbox code (after libSBMLs translateSBML) takes about 80 seconds on my machine, while translateSBML takes ~1000 second on recon2.2.
We are currently trying to investigate this with the libsbml team to see, why this takes so long (given, that the online Validator parses the file withinhalf a minute).

Best

Thomas

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[Uri David Akavia]

Hi Thomas,

Thanks for letting me know!

If I can help in fixing this, feel free to ask.

Cheers,

Uri David

On Mon, Feb 5, 2018 at 1:41 AM, Thomas Pfau <thoma...@uni.lu> wrote:

Hi Uri David,

I can confirm this behaviour on a linux machine with 2016b. The COBRA Toolbox code (after libSBMLs translateSBML) takes about 80 seconds on my machine, while translateSBML takes ~1000 second on recon2.2.
We are currently trying to investigate this with the libsbml team to see, why this takes so long (given, that the online Validator parses the file withinhalf a minute).

Best

Thomas

On 2018-02-05 00:40, Uri David Akavia wrote:

Hi.

I'm working with RECON 2.2. 

Reading the SBML or writing the SBML (as distributed by BioModels website http://www.ebi.ac.uk/biomodels-main/MODEL1603150001) takes about 20 minutes. Is this the same amount of time it takes for everybody, or is this another one of the features I have to "thank" Apple for?

If it takes this amount of time just for me, I'm wondering if that can be fixed. Especially since I'm trying to work with people who use cobrapy, and prefer reading/writing SBML. If it is everybody, maybe SBML processing is just slow.

Thanks,

Uri David

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[Sarah Keating]

Hi Guys

I am aware of the issue and will look into asap. My first thought that
it is not the read that is the problem, but the creation of the matlab
structure but I haven't confirmed that yet.

Hopefully I will get time later this week.

Sarah

On 05/02/2018 13:15, Uri David Akavia wrote:
> Hi Thomas,
>
> Thanks for letting me know!
> If I can help in fixing this, feel free to ask.
>
> Cheers,
>
> Uri David
>
> On Mon, Feb 5, 2018 at 1:41 AM, Thomas Pfau <thoma...@uni.lu
> <mailto:thoma...@uni.lu>> wrote:
>
> Hi Uri David,
>
> I can confirm this behaviour on a linux machine with 2016b. The
> COBRA Toolbox code (after libSBMLs translateSBML) takes about 80
> seconds on my machine, while translateSBML takes ~1000 second on
> recon2.2.
> We are currently trying to investigate this with the libsbml team to
> see, why this takes so long (given, that the online Validator parses
> the file withinhalf a minute).
>
> Best
>
> Thomas
>
>
> On 2018-02-05 00:40, Uri David Akavia wrote:
>> Hi.
>>
>> I'm working with RECON 2.2.
>> Reading the SBML or writing the SBML (as distributed by BioModels
>> website http://www.ebi.ac.uk/biomodels-main/MODEL1603150001

>> <http://www.ebi.ac.uk/biomodels-main/MODEL1603150001>) takes about

>> 20 minutes. Is this the same amount of time it takes for
>> everybody, or is this another one of the features I have to
>> "thank" Apple for?
>>
>> If it takes this amount of time just for me, I'm wondering if that
>> can be fixed. Especially since I'm trying to work with people who
>> use cobrapy, and prefer reading/writing SBML. If it is everybody,
>> maybe SBML processing is just slow.
>>
>> Thanks,
>>
>> Uri David
>> --
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[Uri David Akavia]

Hi Everybody,

Any progress on this? Anything I can help with?

Yours,

Uri David

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[Thomas Pfau]

Hi Uri,

Yes, there was progress, and it will come in with the next release of libsbml, which should come some time this month.

Best

Thomas

On 2018-04-15 19:10, Uri David Akavia wrote:

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[Thomas Pfau]

Hi Uri David,

Could you give this a try again with the new libSBML binaries (came into the develop branch yesterday)?

Best

Thomas

[Uri David Akavia]

Hi Thomas,

This version (libSBML 5.17) is much faster. Thanks!

Uri David

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[Thomas Pfau]

Don't thank me, thank Sarah for the awesome work :)

Best

Thomas

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