Chronological Thread 

< Chronological >      < Thread >

---

Hi Michael,
thanks. This looks great and exactly what I was looking for.
I will give it a try.
Best Matthias

On Wed, Jul 6, 2022 at 12:11 PM Michael Clerx
<work AT michaelclerx.com>
wrote:

> On 7/6/22 10:09, Matthias König wrote:
>
> Is there a python library with which I can generate CellML 1.0/1.1?
>
>
> Hi Matthias,
>
> Myokit is a Python library that can import and export CellML 1.0 and 1.1
> (with exceptions, see here:
> https://protect-au.mimecast.com/s/FbW1CANpL9H27XOGFG1Ki5?domain=github.com,
> the main one being imports)
>
> Since April 2020 it can also import and export CellML 2.0 (without imports
> or resets)
>
> It can import SBML (with some serious improvements in support in the last
> 2 years: it is now being used for PKPD modelling with SBML models)
>
> It can export to C with euler or CVODES, matlab, html, latex and python,
> and various formats specifically for cardiac cell modelling (EasyML, OpenCL
> and CUDA multi-cell simulations, plus import of ephys data from ABF and
> WCP)
>
> So yeah it's called "import" and "export" and there's an intermediate
> representation which users can read (like OpenCOR has too) so some
> structure & names won't get carried over, but apart from those cosmetic
> issues... You can definitely import SBML and export CellML 1.0, 1.1, or 2.0
> with Myokit :D
>
> Myokit's main goal is to simulate stuff with CVODES, so you can do that
> too.
>
> Cheers,
> Michael
>
>
>
>
>
>
> On 7/6/22 10:09, Matthias König wrote:
>
> Hi Alan,
> thanks for the answer.
>
> So do I understand correctly,
> - the main library libcellml (corresponding to the python package
> libcellml) only generates cellml 2.0
> - the main simulator OpenCOR only supports CellML version 1.0/1.1
> This seems like a major bottleneck in CellML support at the moment.
>
> Is there a python library with which I can generate CellML 1.0/1.1?
>
> As part of a google summer of code project we working on a showcase of the
> COMBINE standards with jupyter notebooks. Currently we are working on the
> CellML repressilator model, i.e. we want to create & simulate the model
> using CellML python libraries.
>
> Is there a simple workflow to create and simulate CellML with python
> (preferable using OpenCOR)?
> Are there any good converters? I know of antimony which uses the old
> cellml library. Is there anything else for CellML -> SBML or other ODE
> format (e.g. writing CVODE code or similar things).
> As I understand cellml most of the things should be convertable to SBML
> with exception of models not using time as a dependent variable and likely
> some strange event syntax? Is this true or are there other conversion
> issues?
>
> Best Matthias
>
>
>
>
>
>
>
> On Wed, Jul 6, 2022 at 1:09 AM Alan Garny
> <a.garny AT auckland.ac.nz>
> wrote:
>
>> No, only from CellML 1.0/1.1 to CellML 2.0.
>>
>> We use XSLT for that conversion and I am not sure we could do something
>> similar for CellML 2.0 to CellML 1.0/1.1. Indeed, in CellML 2.0,
>> connections don't hold any directionality information. So, to convert
>> CellML 2.0 to CellML 1.0/1.1 would require analysing the model to determine
>> that directionality information. So, yes, it wouldn't be as straightforward
>> as converting from CellML 1.0/1.1 to CellML 2.0.
>>
>> Alan
>> ------------------------------
>> *From:*
>> cellml-discussion-request AT lists.cellml.org
>> <
>> cellml-discussion-request AT lists.cellml.org>
>> on behalf of Lucian Smith <
>> lucianoelsmitho AT gmail.com>
>> *Sent:* Wednesday, 6 July 2022 9:15 am
>> *To:* CellML Discussion List
>> <cellml-discussion AT cellml.org>
>> *Subject:* Re: [cellml-discussion] CellML model not rendered in OpenCOR
>>
>> 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/6XxTCBNqMRHBErKzT6BuFo?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 libcellmlfrom 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/LjtwCD1vOJH0gzADTAESHv?domain=livermetabolism.com
>> konigmatt AT googlemail.com
>> https://protect-au.mimecast.com/s/eK_vCE8wg6HMR2xkuPpvJd?domain=twitter.com
>> https://protect-au.mimecast.com/s/22BlCGv0kQtGjR42Fk3BB6?domain=github.com
>>
>>
>
> --
> 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/LjtwCD1vOJH0gzADTAESHv?domain=livermetabolism.com
> konigmatt AT googlemail.com
> https://protect-au.mimecast.com/s/eK_vCE8wg6HMR2xkuPpvJd?domain=twitter.com
> https://protect-au.mimecast.com/s/22BlCGv0kQtGjR42Fk3BB6?domain=github.com
>
>

--
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/LjtwCD1vOJH0gzADTAESHv?domain=livermetabolism.com
konigmatt AT googlemail.com
https://protect-au.mimecast.com/s/eK_vCE8wg6HMR2xkuPpvJd?domain=twitter.com
https://protect-au.mimecast.com/s/22BlCGv0kQtGjR42Fk3BB6?domain=github.com

---

• [cellml-discussion] CellML model not rendered in OpenCOR, Matthias König, 07/06/2022
  • Re: [cellml-discussion] CellML model not rendered in OpenCOR, Alan Garny, 07/06/2022
    • Re: [cellml-discussion] CellML model not rendered in OpenCOR, Lucian Smith, 07/06/2022
      • Re: [cellml-discussion] CellML model not rendered in OpenCOR, Alan Garny, 07/06/2022
        • Re: [cellml-discussion] CellML model not rendered in OpenCOR, Matthias König, 07/06/2022
          • Re: [cellml-discussion] CellML model not rendered in OpenCOR, Michael Clerx, 07/06/2022
            • Re: [cellml-discussion] CellML model not rendered in OpenCOR, Matthias König, 07/07/2022
              • Re: [cellml-discussion] CellML model not rendered in OpenCOR, Alan Garny, 07/07/2022

---

Archive powered by MHonArc 2.6.18.