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Implement the Pure variant: http://www.vdiplomacy.com/variants.php?variantID=11
This isn't a particularly fun or popular variant, but it's one step harder than "France vs Austria". It shares the sa…
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**Suggestion:**
* Let solution not be lazy but its contained values are determined by a parameter to `model.optimize` which returns the solution.
* The attribute `model.solution` will be ~~depreca…
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Currently on devel-2:
```python
import cobra.test
model = cobra.test.create_test_model('textbook')
print('Before:\t{}'.format(model.objective.expression))
with model:
with model:
…
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Right now dycone uses asolver already contained in the rcdd package. However, it is based on converting everything to fractions and using an exact solver based on rational arithmetic. This is great fo…
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I've been looking at detectDeadEnds, and when setting removeExternalMets to 1, the behavior seems to be buggy.
All examples are from human RECON 2 website.
Right now, setting it to true would remove a…
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I'm totally new to GIM3E, so I tried the examples from the examples folder. I changed the solver to gurobi as I don't have a cplex license and sadle both examples give errors concerning turnover metab…
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The following improvements would be useful:
- [x] FVA only runs for reactions which might be displayed (input/output/biomass)
- [x] solver options should be accepted (and the ability to specify a solv…
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There are some weird results in the docs for the summary functions.
Looking at [section 4.3.1](http://cobrapy.readthedocs.org/en/latest/simulating.html#Running-FVA-in-summary-methods) the FVA flux fo…
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As discussed there should be a revamp of the website soon in order to promote cobrapy and packages that use it. The following features were recommended/requested:
- better info about the project (m…