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Example (12119723):
- Native: https://github.com/virtualcell/vcdb/blob/main/published/biomodel/omex/native/biomodel_12119723.omex
- SBML: https://github.com/virtualcell/vcdb/blob/main/published/biom…
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Frank's [SED-ML Web Tools](http://sysbioapps.dyndns.org/SED-ML_Web_Tools/) allow exporting COMBINE archives with results. When the SED-ML specifies a plot in the output, the archive contains a png. Wh…
0u812 updated
7 years ago
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# Issue
In ticket https://sourceforge.net/p/sed-ml/sed-ml-l1v1/62/ we talked about possibly allowing user defined functions somewhere within SED-ML. This item should remind us about it.
# Examples…
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Often different figures involve different simulations. However, COPASI can only handle 1 simulation at a time. As a result, these SED-ML may have plot that don't reproduce published simulation results…
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Many of the SED-ML classes presume that models and simulation experiments involve float-value attributes.
- UniformTimeCourse.initialTime, UniformTimeCourse.outputStartTime, UniformTimeCourse.output…
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Right now, if you export a simulation to SED-ML (using the `Simulation Experiment` view), OpenCOR will ignore any model parameter which value has been changed by the user during the simulation. Howeve…
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= Description =
- Implementation of the !OneStep class (derived from Simulation).
= Context =
- Simulation is the base-class for running model simulations; in SED-ML level 1 version 2, new Simulation…
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Currently only simple parameter modifications are encoded in SED-ML and element deletions. Need to also include model generator parameter modifications and support for parameter sweeps.
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https://github.com/SED-ML/sed-ml/issues/141
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### Contact Details
lpsmith@uw.edu
### Location
runBiosimulations
### What happened?
Uploaded an omex file that failed, claiming "error uploading the SED-ML specifications to the API."
This...…