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### Simulation tool
---
id: vcell
version: 7.7.0.9
specificationsUrl: https://github.com/virtualcell/vcell/releases/download/7.7.0.9/biosimulators.json
specificationsPatch:
version: 7.7.0.9
…
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**Which problem would you like to address? Please describe.**
I often have simulation experiments where I not only have to change initial values but also values after a certain time. I.e. the conditi…
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- [x] Is the class an entity or a process? Is it an information entity about a material entity/process, or a pure information entity/process?
- [x] Specify the ontology URI for class. Is there a hier…
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@matthiaskoenig and others have suggested we make our tables more [normalized](https://en.wikipedia.org/wiki/Database_normalization).
Instead of a timecourses table (#581), I would suggest an exper…
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Version 4.4.0 (Windows 11)
When using SBML and the Gillespie solver all replicates are synchronized. There is no method to set a seed for each model instance or to otherwise knock the simulator out o…
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# Issue
Currently it is not possible to access variables in models based on model composition.
This is a general problem of composed models where part of the model XML definition is in external fil…
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### Background
Expressions with discontinuities pose a difficult problem for numerical testing of expression equivalence.
for example
exp1 = 3 * a^2/(b-c) * ((t >200)*(*t200)*(*t
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Hi, I am trying several tooling options and I thought JSim is the most universal man-in-the-middle between SBML, CellMl and other languages. I tried to import CellMl model ( https://models.cellml.org/…
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Hi, I've a problem simulating this model [BIOMD0000000005](https://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000005.3?filename=BIOMD0000000005_url.xml) using the cupsoda simulator. I wrote this …
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The version of libsbml in SVN right now, and which will be part of the next release, changes how ASTNodes are handled in such a way that it might slow things down in roadrunner. The developers are in…