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We would like to explore what happens to the model over large numbers of generations, spanning upwards of 106 cells. To make this feasible we would need to drastically reduce the amount of data that i…
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This will not compile in Arduino IDE. i first tried on the current version and had many compile errors. So after reading more about it i saw your mention of needing version 1.8.1. i uninstalled newer…
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### Description
I currently writing a document explaining the main ideas behind the vivarium. Once I will have finished it (by the end of this week) we should integrate part of this text and figures …
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PR #423 adds a temporary monkey-patch to the `unum` units package to fix a bug -- the `Unum` class doesn't implement true-division when the Python 2 caller has `from __future__ import division`.
Se…
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## Current Approach
### Message Passing
When a process has `Process.parallel` set to true, we launch a parallel OS process that runs `vivarium.core.process._run_update()`. `run_update()` contain…
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### Contact Details
_No response_
### Location
runBiosimulations
### What happened?
When running the attached SED-ML file, biosimulations claims there's an error:
```
target /sbml:s…
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Hey! Do you think it would be possible to unlock spells through the save files?
I am on a 2nd character and don't want to go through the tedious process of unlocking all the spells again
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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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https://github.com/ihmeuw/vivarium_census_prl_synth_pop/blob/522f920a35202a98b9c3afa5f99fc91ff623162b/src/vivarium_census_prl_synth_pop/utilities.py#L256
I'm looking for weirdness in the SSN genera…
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## Use Case
As an author for the actin bend/twist coupling micro-publication, I need data to complete the accompanying figure.
## Acceptance Criteria
.simularium trajectories for replicates of al…