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A hierarchical SBML file can be broken into multiple SBML files. When an SBML model is selected for simulation, it may have dependencies of other SBML files. The only way to know these dependencies …
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Hi, just found your library! Very exciting.
Were you planning to add support for ODE simulation with diffrax?
I use diffrax to simulate my models and optimistix to fit them, and more generally wo…
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If we take Herbert's HARMONY 2017 example where a reaction with product A is extracted from an SBML model and then inserted into another model where A is a reactant in a different reaction, the conser…
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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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Running simulations with synchronous updating produces the same results from SBML files with different initialLevels.
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Following the discussion today at HARMONY I was trying a few examples to see where I had issues with models with negative start times.
One example are events which are triggered based on `time>=0`. B…
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For enforcing the `wall_time_sim` for SBML models, we use a hack where the simulation is actually run in the separate script sbml-runner.py . If installing through PyPI, sbml-runner.py is not installe…
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## SBML test suite report
SBMLtoolkit.jl is regularly tested against the [SBML test suite](https://github.com/sbmlteam/sbml-test-suite/tree/master/cases/semantic). The last test was run on October 24…
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### Simulation tool
### Simulation tool
---
id: vcell
version: 7.5.0.27
specificationsUrl: https://github.com/virtualcell/vcell/releases/download/7.6.0.27/biosimulators.json
specificationsPa…
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To facilitate the use of SED-ML beyond kinetic models encoded in SMBL, I think it would be helpful to add URNs for the SBML-fbc, multi, and qual packages. Because these packages are largely used separ…