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A work-in-progress list of things required to support 3d models:
- [x] dune-copasi should already support 3d simulation
- presumably membrane reactions go from a flux across a 1d edge between el…
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Hi all,
I just read the LASSIE paper and wanted to compare the results to libroadrunner I was involved with
See:
https://www.ncbi.nlm.nih.gov/pubmed/26085503
which achieves in my own experience ~5…
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iBioSim Version 3.0.0
Operating system: Windows 10
Bug reported by: micotner9@gmail.com
Description:
When trying to preform a reaction-based abstraction on my model using the SSA-Direct (Dynamic) s…
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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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It would be really nice if it would be possible to change the initial concentration of molecules during the workflow in the analysis window. Here is what I had in mind. In the second step during the s…
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Currently, whenever the rateOf is defined inside the delay tag for any of the SBML model then it does not take that delay into account and just provides the rateOf values as the time proceeds.
Issu…
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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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The current toolbox is a frontend for the MATLAB SimBiology toolbox. It might be useful to create a Python version of the toolbox that could serve as a front end for some similar Python SBML-compatib…
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Currently users need to provide strings and file parameters in the annotation spreadsheet with surrounding quotes. For example:
| ID | Value |
-- | --
Input_conc | "conc_inputs3.csv"
Input_EGR …
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Could look into supporting import & simulation of 3d parametric geometry.
- read only geometry
- output from DUNE as paraview files
- would need converter from SBML parametric geometry to gmsh / DU…