Nikolaus Sonnenschein issues

Results 10 issues of


Nikolaus Sonnenschein

Use long-step technique with GLPK to achieve 30-70% reduction in simplex iterations

https://gitter.im/biosustain/optlang?at=5a395187ba39a53f1a7d4d8a ![image](https://user-images.githubusercontent.com/55217/45083921-4378ba00-b0fd-11e8-8328-2b1e419035ae.png)

Fix notebook 9 (vanillin example)

The final OptGene result object is empty.

bug

Add heatmap vis to production envelope visualizations in 3D

enhancement

OptKnock should warn the user if the target rxn cannot carry flux

Otherwise, it will be removed in the process of deleting blocked reactions from the model leading to further problems downstream.

enhancement

OptGene should raise a warning if a model does not contain any genes

enhancement

Adding a reaction from one model to another model should probably raise an exception

because the reaction (still included in the first model) will erroneously point to the second model. Alternatively, model.add_reaction(s) could make a copy first. Maybe this should be solved in cobrapy...

enhancement

Docs missing at https://memote.readthedocs.io/en/latest/test_suite.html

As user I want to rely on memote implementing a comprehensive suite of tests and checks

Epic

Permission issues if admin installed carveme

There is problem with building the diamond db in the first run (I guess new in 1.4.1;https://github.com/cdanielmachado/carveme/commit/fef1ed29495f3a1e6937c68a9df0b16f8e797890) in cases where carveme was installed system wide with the user of carveme...

No `fbc:name` available for `geneProduct`

# Description of the issue Looks like `fbc:name` attributes for geneProducts got lost in a recent update of BiGG? For example now: `` Previous: `` # Page http://bigg.ucsd.edu/models/iJO1366 # Browser...