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Latest GPML for [pathwayPA165111375](https://www.pharmgkb.org/pathway/PA165111375) is obsolete.
Use this instead: [PA165111375-new.gpml](https://drive.google.com/a/pharmgkb.org/uc?export=download&id=1…
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**[Original report](https://bitbucket.org/mchaput/whoosh/issue/462) by Moritz E. Beber (Bitbucket: [midnighter](https://bitbucket.org/midnighter), GitHub: [midnighter](https://github.com/midnighter)).…
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#### Current behavior:
Suspected duplicated metabolites from Recon3D:
reference ID|met ID|affected rxns| Action for mets|Action for rxns|Comments|
|-----------------|-----------------|-------…
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#### Current behavior:
Suspected duplicated metabolites from MetaNetX:
reference ID|met ID|affected rxns| Action for mets|Action for rxns|Comments|
|-----------------|-----------------|------…
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When I ran "meta.net.gcn=relu(D_hat%*%meta.net%*%D_hat%*%as.matrix(meta.feature))", it produceed this error message"Error in D_hat %*% meta.net %*% D_hat %*% as.matrix(meta.feature) :
non-conforma…
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### Description of the issue:
All metabolites in the model should have chebi-identifiers. This was explicitly mentioned during the Cobra-conference 2018, and seems to be a consensus. The identifier i…
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Hi Daniel,
I have been doing my research with SMETANA as an important tool for deciding the potential metabolic cooperation between species. From Zelezniak's paper, I learned the MIP value is decid…
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* **GO term ID and label for which you request a new superclass**
GO:0006798 polyphosphate catabolic process
* **New superclass (parent) suggested**
generation of precursor metabolites and …
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#### 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…
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I get the following error when running the last chunk of the vignette:
### Plot pathway network
The pathway network is such that it shows metabolites that are connected to different pathways and…