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Re: [cellml-discussion] CellML model not rendered in OpenCOR


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  • From: Lucian Smith <lucianoelsmitho AT gmail.com>
  • To: CellML Discussion List <cellml-discussion AT cellml.org>
  • Subject: Re: [cellml-discussion] CellML model not rendered in OpenCOR
  • Date: Tue, 5 Jul 2022 14:15:20 -0700
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Is there a converter from CellML 2.0 to 1.1?

On Tue, Jul 5, 2022 at 1:55 PM Alan Garny
<a.garny AT auckland.ac.nz>
wrote:

> Hi Matthias,
>
> Sorry, but libCellML generates CellML 2.0 models while OpenCOR "only"
> supports CellML 1.0/1.1 at this stage. So, yes, using OpenCOR, you won't be
> able to edit/run any model generated by libCellML.
>
> Support for CellML 2.0 in OpenCOR is planned, but it is still some time
> away. This will be done through libOpenCOR, OpenCOR's new backend which
> will be using libCellML rather than the original CellML API. (The reason
> for going the libOpenCOR route is that libOpenCOR will greatly improve our
> Python bindings.)
>
> Hopefully, I will have more information to share at COMBINE in October.
>
> Alan
> ------------------------------
> *From:*
> cellml-discussion-request AT lists.cellml.org
> <
> cellml-discussion-request AT lists.cellml.org>
> on behalf of Matthias König <
> konigmatt AT googlemail.com>
> *Sent:* Wednesday, 6 July 2022 3:17 am
> *To:*
> cellml-discussion AT lists.cellml.org
> <
> cellml-discussion AT lists.cellml.org>
> *Subject:* [cellml-discussion] CellML model not rendered in OpenCOR
>
> Hi all,
> I am trying to create the repressilator in CellML as part of a project via
> the python binding.
> Unfortunately, the created models (cellml v2.0) are not rendered in
> OpenCOR. I.e. normally I see nice CellML Text in the editor, but for the
> attached model nothing is displayed.
>
> ```
>
> <?xml version="1.0" encoding="UTF-8"?>
> <model
> xmlns="https://protect-au.mimecast.com/s/doOqCP7Lw5FMD1Apfzp-zw?domain=cellml.org";
> name="repressilator">
> <component name="parameters">
> <variable name="n" units="dimensionless" initial_value="2"/>
> </component>
> </model>
>
> ```
> Model was created using libcellml via
>
> ```
>
> import libcellml
> from cellml_utilities import print_model
>
>
> def create_model(cellml_path: Path) -> libcellml.Model:
> """Create CellML repressilator and save to Path."""
> model = libcellml.Model()
> model.setName("repressilator")
>
> comp_parameters = libcellml.Component()
> comp_parameters.setName("parameters")
> model.addComponent(comp_parameters)
>
> # var n: dimensionless {init: 2, pub: out};
> var_n = libcellml.Variable()
> var_n.setName("n")
> var_n.setInitialValue(2.0)
> var_n.setUnits("dimensionless")
> # var_n.setInterfaceType()
> comp_parameters.addVariable(var_n)
>
> # Checking that it worked
> print_model(model)
>
> # Save model
> printer = libcellml.Printer()
> serialised_model: str = printer.printModel(model)
>
> with open(cellml_path, "w") as f_cellml:
> f_cellml.write(serialised_model)
>
> return model
>
> ```
>
> How can I create models with python libcellml which I can use/edit/view in
> OpenCOR?
> Best Matthias
>
> --
> Matthias König, PhD.
> Junior Group Leader Systems Medicine of the Liver Lab
> Humboldt-Universität zu Berlin,
> Institute of Biology, Institute for Theoretical Biology
> Philippstraße 13, Haus 20, 10115 Berlin
> Tel: +49 30 2093 98435
> https://protect-au.mimecast.com/s/mJLCCQnMx5CrD140fPKLTd?domain=livermetabolism.com
> konigmatt AT googlemail.com
> https://protect-au.mimecast.com/s/K3u-CRONy5uBKDP2IP78YT?domain=twitter.com
> https://protect-au.mimecast.com/s/OSf5CVARD0T94njGHJ-1N7?domain=github.com
>

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