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**What did you expect to happen?**
AMICI should support events which trigger at time 0. Often one wants to change values at time zero via events, for instance to set dosing protocols.
**To Reprod…
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Currently, the matlab parser creates some issues with java updates. Also library is no longer maintained. The matlabparser `com.jmatio` is only used in `cobra.COBRAparser`.
There are two options to…
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## Issue description
The full model:
[SbmlWithComp.log](https://github.com/sbmlteam/libsbml/files/8519941/SbmlWithComp.log) (change the extension from `.log` to `.xml` to reproduce, github does no…
eltix updated
2 years ago
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Hi,
I'm trying to use d2d on my SBML model with my own experimental dataset.
I loaded the sbml model using arParseSBML then arLoadModel, which created the model's .def file.
In my model's .def …
sl6zq updated
2 years ago
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### Background
[Newt](http://newteditor.org) [1] is a [Cytoscape.js](http://js.cytoscape.org/) based viewer and editor for biological maps in Systems Biology Graphical Notation (SBGN) notation [2] to…
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### Description of the issue:
In the .xml file and when loaded in MATLAB, metabolite identifiers and names are suffixed with compartment information. This is absent in the .yml, .txt and .xlsx files.…
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#### Problem description
#### Code Sample
Create a [minimal, complete, ver…
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### Description of the issue:
Dear Z-GEM developers,
I am trying to parse the `.xml` files from all your '?-GEM' model. I found that in Zebrafish-GEM, the identifiers showed in the `metabolites.t…
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I executed the example doc [sampling_diagnostics](https://github.com/ICB-DCM/pyPESTO/blob/master/doc/example/sampling_diagnostics.ipynb) from PyPesto and the first code cell did not work as intended.
…
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Hello,
I downloaded Pathvisio a couple of weeks ago and am encountering a couple of errors. I know Pathvisio connects to the wikipathways database, but I want to import REACTOME and PANTHER pathway…