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Hello there,
It seems line 24 in utils.py is using a file that's missing from the pools, is it the same as bigg_universe? Thanks!
```python
biomass_rxns = np.array(pd.read_csv('./data/…
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# Description of the issue
The compounds have the identical annotation but different IDs. This can then also lead to the problem of having different reaction IDs for identical reactions (examples c…
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Hi,
I tried to download bigg_models following the instructions in [INSTALL.md](https://github.com/draeger-lab/SBSCL/blob/master/INSTALL.md), but the Dropbox link seems to be invalid.
Any help?
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In this issue all current gap-filling tools implemented in refineGEMs are summarised and possible enhancements explored.
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**Current gap-filling modules:**
- `genecomp` (now: `kegg_analysis`):
…
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Hello, I am trying to create a model of Macaca Mulatta (mmul) using MetaDraft. I have the `.faa` file for mmul, along with a Homo Sapien `.gbff` file and an SBML file (Recon3D from the BiGG database).…
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The command ```\big\Vert``` command produces output which is the same size as ```\Big\Vert```, which results in output inconsistent with other delimiters like ```\vert```, as shown below:
![\vert a…
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Thank you for developing eggnog-mapper, I've been including it in my pipelines to generate CarveMe metabolic models for a couple of years now.
The current eggnog-mapper outputs a .tsv file that inc…
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`\big`, `\bigg`, `\Big`, and `\Bigg` can be quite useful to tweak the size of symbols. It would be nice to have them
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Our metabolomics data does not contain the compartment in the bigg ID.
We need to modify `build.py` to append `_e` to the metabolite names.
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Hi.
I would like to learn about the possibility to run CHESHIRE with xml models reconstructed from Kbase.
It is known that Kbase provides ModelSEED-based pipelines for construction, but I am not …