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If we take Herbert's HARMONY 2017 example where a reaction with product A is extracted from an SBML model and then inserted into another model where A is a reactant in a different reaction, the conser…
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**Background**
JSBML is a Java library for reading, manipulating and writing SBML files. SBML (Systems Biology Markup Language) is a representation format for computational models of biological pro…
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Atomizer fails with the following error when I try to run it on a small SBML level 3 model:
```
Traceback (most recent call last):
File "", line 68, in
File "", line 58, in main
File "/U…
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```python
from pyomexmeta import RDF
import lxml.etree
import os
model_filename = 'toy-model.xml'
# verify file exists, is a syntactically-valid XML
assert os.path.isfile(model_filename)
lx…
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MoBi-Import of [BIOMD0000000528](http://www.ebi.ac.uk/biomodels-main/BIOMD0000000528) and [BIOMD0000000489](http://www.ebi.ac.uk/biomodels-main/BIOMD0000000489) Biomodels fails due to wrong import of …
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## Minimal code example to reproduce the problem
It looks like for some file formats the subsystem field might not be parsed. I've spotted this from two different models in SBML format, so I checke…
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**Is your feature request related to a problem? Please describe.**
Sometimes when parameter estimating ODE-models, or when importing a model in the SBML format, event time-points are dependent on m…
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How best to annotate models and components here? See https://tellurium.readthedocs.io/en/latest/antimony.html for tool used for annotation for SBML?
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#### Problem description
> I don't believe this framework is general enough to be appropriate for the wide range of modeling tools that the community will develop. For example, Pathway Tools uses a…
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In the discussion with @Midnighter it came up that there should be a generic support for compressed files for the various io modules. I.e. cobrapy should support the reading and writing of compressed …