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- [ ] Set up a [Virtuoso server](https://github.com/openlink/virtuoso-opensource) open source edition on Google cloud
- Docker images available here: https://hub.docker.com/r/openlink/virtuoso-ope…
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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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### Contact Details
_No response_
### Location
runBiosimulations
### What happened?
Everything ran though and looked fine, but it then claimed it failed and quit, because there was no RDF file in…
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### Background
- Previously, the java codebase in the VCell CLI project interacted with the biosimulators_utils python library through starting a new system process to call and execute a specific pyt…
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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...…
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Hi,
I'm running MacOS 10.15.6 and I'm using pyenv to manage python distributions.
when I run the following in python:
\>import tellurium as te
\>te.loadSBMLModel("rubrum_all_reactions.sbml")
I …
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### Simulation tool
---
id: vcell
version: 7.7.0.10
specificationsUrl: https://github.com/virtualcell/vcell/releases/download/7.7.0.10/biosimulators.json
specificationsPatch:
version: 7.7.0.10…
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### Description of the issue:
The [SBML](http://sbml.org) is a declarative file format that specifies model components, structure, and interaction of those components. But it does not directly specif…
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Typos can result in namespace URIs that lack trailing `#` or `/`. It would be helpful to catch these mistakes.