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sys-bio / tellurium

Python Environment for Modeling and Simulating Biological Systems
http://tellurium.analogmachine.org/
Apache License 2.0
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SED-ML L1V3 data support (csv & numl) #225

Closed matthiaskoenig closed 7 years ago

matthiaskoenig commented 7 years ago

Support for data based on L1V3 spec.

See also https://github.com/SED-ML/sed-ml/issues/12 https://github.com/SED-ML/sed-ml/issues/41

matthiaskoenig commented 7 years ago

The following test archives have been added to test implementation. JWS must save their non-standard data after this is implemented.

    # data not supported: FIXME: https://github.com/sys-bio/tellurium/issues/225
    'specification/L1V3/L1V3_plotting-data.omex',
    'specification/L1V3/L1V3_reading-data-numl.omex',
    'specification/L1V3/L1V3_reading-data-csv.omex',

    # non-standard data implementation: FIXME: https://github.com/matthiaskoenig/tellurium-web/issues/53
    'jws/omex/adlung2017_fig2g.sedx',
    'jws/omex/adlung2017_fig2bto2e.sedx',
    'jws/omex/adlung2017_fig2f.sedx',
    'jws/omex/bachmann2011.sedx',
    'jws/omex/kouril3_experiment-user.sedx',
    'jws/omex/penkler2aa_experiment-user.sedx',
    'jws/omex/perelson1996_fig1b_top.sedx',
    'jws/omex/stafford2000_fig2.sedx',
matthiaskoenig commented 7 years ago

I finished the implementation, i.e., we have full SED-ML L1V3 support in tellurium. But to be able to merge this with master and bring this in the next release I would need the latest libsedml and libnuml releases as tesedml( #231 ) and tenuml ( #189 ).

We will release the L1V3 SED-ML spec at the end of next week, i.e. before COMBINE. It would be great if we can make a release of tellurium which supports the new spec until than.

hsauro commented 7 years ago

This is excellent news. Yes we should do a release before combine.

Herbert

On Thu, Sep 28, 2017 at 11:06 PM Matthias König notifications@github.com wrote:

I finished the implementation, i.e., we have full SED-ML L1V3 support in tellurium. But to be able to merge this with master and bring this in the next release I would need the latest libsedml and libnuml releases as tesedml(

231 https://github.com/sys-bio/tellurium/issues/231 ) and tenuml ( #189

https://github.com/sys-bio/tellurium/issues/189 ).

We will release the L1V3 SED-ML spec at the end of next week, i.e. before COMBINE. It would be great if we can make a release of tellurium which supports the new spec until than.

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