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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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Place into `biosimulators_utils.model_lang.bngl.utils`
Can be done once RuleWorld/PyBioNetGen#10 is addressed.
- [x] Time course settings
- [x] Algorithm parameters e.g., seed
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### _**Abstract**_
I have been using [biosimulators.org](https://www.biosimulators.org/) as the perspective for our “landing page” as it is our own unique little section of the internet. I am also …
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Presently, NEURON and PySCeS cannot be used together a single Python memory space, likely due to their shared dependency on SUNDIALS.
The Dockerfile below illustrates the problem. Building this res…
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I see LibSBMLsim only has a compiled versions for Python 2.7. BioSimulators-utils is tested to work with Python 3.7 and higher. This will likely need a LibSBMLsim version for Python 3.7 or higher.
- …
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### Simulation tool
---
id: smoldyn
version: 2.73
specificationsUrl: https://raw.githubusercontent.com/ssandrews/Smoldyn/master/biosimulators.json
specificationsPatch:
version: 2.73
image:
u…
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After fixing issues with the [create_omex](https://github.com/robertvi/SBMLShowcase/blob/2c38d1abe0542196ed51e45f3e1f24b4c73e2e1e/utils/__init__.py#L44) function [#3](https://github.com/robertvi/SBMLS…
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Example: https://github.com/biosimulators/Biosimulators_test_suite/blob/0.1.84/examples/bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ/Dolan2015.bngl
- This works with BioNetGen < 2.8.0
- 2.8.0 produced th…
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## Use Case
As a developer, I want to be able to get plot metrics data from the BioSimulations API in order to visualize more data in the viewer.
## Acceptance Criteria
A front end prototype (on …
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Many of the errors in importing the Physiome CellMl models are are due to the attribute "id" being present in the equation element, which is flagged by the schema as incorrect. However, the CellML pr…