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our simulation is 2d, but users will expect quantities and reaction parameters to be in 3d units
- need to decide how to implement this / present this to the user
- should be some consistency checks…
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I am trying to run ODE_FBA.ipynb notebook and getting following error:
cell:
ode_config = {
'biosimulator_api': 'biosimulators_tellurium',
'model_source': MILLARD2016_PATH,
'mode…
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As new features have been added, SED has grown more capable but also more complex to implement. This compels developers to implement more features, which increases the barrier to entry. This also crea…
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From @matthiaskoenig :
Most of the specification describes how to define the geometries and the domains. I miss a bit the description how this will actually all come together in a simulation of a co…
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There are 5 PROV-O terms that should be supported for SBOL in iBioSim:
1. Activity
2. Association
3. Usage
4. Plan
5. Agent
Refer to SBOL[ specification 2.1.0](http://sbolstandard.org/wp-conte…
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Hi, I am using the code below to make my bifurcation diagram for many random parameter sets, and I want to know which set can have oscillation, can we do this? Thanks!
auto = Plugin("tel_auto2000")
…
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Currently `test_biosimulators` runs tests on the following biosimulators: biosimulators_tellurium, biosimulators_cobrapy, biosimulators_cbmpy, biosimulators_bionetgen, biosimulators_gillespy2, biosimu…
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As pointed out by @matthiaskoenig [here](https://github.com/sys-bio/roadrunner/issues/898#issuecomment-950869708) and @luciansmith [here](https://github.com/sys-bio/roadrunner/issues/146#issuecomment-…
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Parameter changes which affect compartment volumes must update the concentrations of the species in the compartments. This is currently not done in AMICI resulting in incorrect initial concentrations/…