cobrapy

cobrapy copied to clipboard

Adding reactions from another model does not reset the reactions their metabolites refer to

8

From the mailing list: > Thank you! That is very helpful. If I add a reaction, the metabolites are also added (good!) but all reactions from the universal model associated...

Midnighter

I am trying to read the mini_cobra.xml file but i am getting the below error. Please help me with this

1

### Checklist    - [ ] I searched the [documentation](https://cobrapy.readthedocs.io). - [ ] I looked through [similar issues on...

Kunalpinnelli

### Checklist - [ x] There are [no similar issues or pull requests](https://github.com/opencobra/cobrapy/issues) for this yet. ### Is your feature related to a problem? Please describe it. There are three...

lptolik

Update storage of annotations

24

Hi all, there are currently some issues with how annotations are stored in cobrapy. [1] MIRIAM qualifiers are dropped RDF annotations are triples of the form (subject - predicate -...

matthiaskoenig

Switch SBML parser defaults to not rewriting IDs

20

#### Problem description Reading a SBML model with ASCII codes in the IDs may generate invalid cobrapy IDs during parsing (for instance names including spaces). #### Code Sample That one...

cdiener

Support compression on file import and export

7

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...

matthiaskoenig

Constraint upper bound overwritten when copying model

8

#### Problem description Using the `model.copy()` with the gurobi interface causes the upper bound of constraints to be overwritten. #### Code Sample ```python import cobra model = cobra.Model() model.add_metabolites(cobra.Metabolite('a')) model.metabolites.a.constraint.lb...

coltonlloyd

The file cannot save formula after assigning a model formula

3

### Checklist - [ ] I searched the [documentation](https://cobrapy.readthedocs.io). - [ ] I looked through [similar issues on GitHub](https://github.com/opencobra/cobrapy/issues). - [ ] I looked up "How to do ... in...

dengxiao01

Solution fluxes are different from model summary fluxes

5

#### Problem description Please explain: I am trying to study the FBA output of a model, changing different growth substrates in the media. To do this, I'm mapping the solution...

danolson1

cobra.io.write_sbml_file ignoring default upper bound from cobra.Configuration()

1

Starting with [the Recon3D model straight from BiGG](http://bigg.ucsd.edu/static/models/Recon3D.xml), which has all reactions set to a default upper bound of 1000, I changed some reactions to have upper bounds larger than...

Devlin-Moyer