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in the SBML model (e_coli_core), if I set the extracellular species as a boundary species (e.g. for kinetic simulation), and then load the model to cobra, even though the exchange reactions (and bound…
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Hello
I am trying to create a cobra model using sample SBML files downloaded from [KEGG converter](http://www.grissom.gr/keggconverter/). The ``io`` method ``read_sbml_model`` is able to generate m…
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As @matthiaskoenig mentioned during GSoC, it would be nice to restructure ModelPolisher so it can directly annotate model parts without the necessity to parse the complete model.
This would also allo…
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Example (12119723):
- Native: https://github.com/virtualcell/vcdb/blob/main/published/biomodel/omex/native/biomodel_12119723.omex
- SBML: https://github.com/virtualcell/vcdb/blob/main/published/biom…
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To facilitate the use of SED-ML beyond kinetic models encoded in SMBL, I think it would be helpful to add URNs for the SBML-fbc, multi, and qual packages. Because these packages are largely used separ…
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Getting the Antimony from the SBML model "MODEL1303260018 - Smallbone2013 - Glycolysis in S.cerevisiae - Iteration 18" (https://www.ebi.ac.uk/biomodels-main/MODEL1303260018) does not work.
I am on …
NaiaW updated
6 years ago
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= Description =
- Provide the API for adding or removing parameters in SBML models through the Change mechanism in SED-ML.
= Context =
- Parameters are used in reaction nodes in the SBML language; it…
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Hello,
I tried to import ("File" -> "open SBML model") a curated model from Biomodels (SBML level 3 version 1) into MoBi. But opening the SBML file (sometimes) makes MoBi crash.
Curiously, this …
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= Description =
- Provide the API for adding or removing reactions in SBML models through the Change mechanism in SED-ML.
= Context =
- Biochemical reactions are central to the SBML language; it shou…
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A hierarchical SBML file can be broken into multiple SBML files. When an SBML model is selected for simulation, it may have dependencies of other SBML files. The only way to know these dependencies …