Re: [sbml-distrib] Another new version (0.23) of distrib!

[Nicolas Rodriguez]

Hi Chris,

I have just pushed some changes to JSBML to be able to support the new csymbol elements (not the rest of the specs).

You can either build a new jar from the master branch or use the 1.5-SNAPSHOT maven target.

The new csymbol nodes will have the type FUNCTION_CSYMBOL so you have to use it to create new node or read existing file.

Later on, we might have a specific node type for each distribution declared in the specs like libsbml is doing.

cheers,

Nico

On 26/02/2019 15:30, Chris Myers wrote:

Any progress on JSBML support?

Chris

On Feb 25, 2019, at 5:15 PM, Lucian Smith <luciano...@gmail.com> wrote:

A new version of distrib can now be found at

https://drive.google.com/file/d/17RttI-dgfW8jGIVJigUCU7AamJ8Y9LCS/view?usp=sharing

It does the following:

* The old Distributions are now gone, replaced by a 'distribution' child of Uncertainty with a Math child, which should have a distrib-defined csymbol in it.

* The UncertStatistics class is now gone, and its children moved to Uncertainty

* Various edits for clarity added by Mike Hucka (thanks, Mike!)

None of these changes affect the basic use of distrib to compute distributions using csymbols; the current version of libsbml can still be used for that.  Any questions/opinions, let me know!

I'll be working on getting the libsbml source updated to the above code, and then will try to implement a few of the Uncertainty features in Antimony; in the meantime, let me know if you have any issues with the basic csymbol use!

-Lucian

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[Matthias König]

Hi all,

it would be great if JSBML could be updated to support the latest version of the distrib specification (v0.24).

Then I could read and use distrib models I write with libsbml-5.18.0-experimental also with JSBML.

I would like to implement distrib support in Cy3SBML, but depend on an updated JSBML for that.

Best Matthias

[Nicolas Rodriguez]

Hi Matthias,

Can you provide some of the files you generated that contain the new uncertainties elements.

Thanks,

Nico

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[Matthias König]

Hi Nico,

please find attached the examples.

I basically created two files which try to cover all features of distrib, i.e. distributions and uncertainty called distrib.xml and uncertainty.xml respectively.

If you need more fine grained-files I could create smaller uncertainty examples.

Best Matthias

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[Nicolas Rodriguez]

something with everything is perfect, thanks,

Nico

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[Nicolas Rodriguez]

Hi Matthias,

Forgot to mention it when I have done it. I have updated the 1.5 maven snapshot of jsbml and it should be able to support all of distrib.

Nico

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[Matthias König]

Hi Nico,

thanks so much.

Best Matthias

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Matthias König, PhD.
Junior Group Leader LiSyM - Systems Medicine of the Liver
Humboldt Universität zu Berlin, Institute of Biology, Institute for Theoretical Biology
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