ModelPolisher
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draeger-lab
ModelPolisher accesses the BiGG Models knowledgebase to annotate SBML models.
My model contains CURIE links for identifiers.org with the pattern `prefix:identifier`. After using ModelPolisher I saw that the BiGG identifiers which had the aforementioned pattern are now duplicated in the...
When reading a model created with ModelPolisher with COBRApy, a series of warnings appear pointed to the fact that the MetaNetX annotations are not added in the desired form using...
The documentation is not very inviting currently. - in the first paragraph we greet the user with a troubleshooting hint -> can be moved to a troubleshooting page in the...
In input files, reactions are usually given in millimole per gram dry weight per hour (mmol / gDW / h). The given unit needs to be decomposed into its parts:...
Suggested enhancement by @tpfau: Look over all present annotations and map every annotation that can be mapped to BiGG. For instance, if there is a KEGG compound annotation that compound...
During a quick look through the models I found that H2O is annotated as hydroxide additionally, among other things. The question here is whether this is correct or this should...
The lack of unit tests makes refactorings of any kind somewhat dangerous. Also there is significant documentation value to be had here. This issue serves to bundle commits that introduce...
From the [spec](https://sbml.org/specifications/sbml-level-3/version-1/fbc/sbml-fbc-version-2-release-1.pdf) section 3.3 page 8 (line numbers at the end): > This is accomplished by defining a set of restrictions which come into effect if strict is set...
Looking over the javadocs #116 revealed that we have a distinct lack of docstrings in the code base. All classes, public constructors and public methods should carry a docstring.
As I forgot about this Parameter when rewriting the RegistryParser and centralizing annotation handling, currently we might get a mix of MIRIAM and non MIRIAM annotations and possibly non MIRIAM...
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ModelPolisher accesses the BiGG Models knowledgebase to annotate SBML models.