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Hi,
when using a Gram-positive universe in the carving process, the draft contains the reaction: 'R_HSLGTHLK' which is not a known identifer in BiGG. When not explicitely selecting the gram-positive…
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Running Smetana (master branch, commit d2b10434d) with 4 models and with parameters ` --solver cplex -v --flavor bigg --detailed ` returns `segmentation fault`. Models were generated using carve…
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ATM when I do `Model.seach(undefined_field_in: [123]).result` it issues `SELECT models.* from models`. I think it should throw an exception.
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# Issue
SED-ML can currently not perform typical fbc simulations.
These would include things like
* optimization
* setting boundaries
* adding LP constraints
Typical simulation experiments ar…
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Sehr geehrter Herr Gumbel,
ich habe gerade nochmals Ihre LyX-Vorlage für meine Bachelorarbeit heruntergeladen. Wenn ich Jedoch das Dokument "thesis.lyx" kompilieren will und die PDF-Ausgabe mir ans…
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Hi Daniel
I'm having some issues with building alternative universal models using CARVEME (such as with the alternative biomass reactions). If i run
``` build_universe --curated```
I get th…
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### Description of the issue:
I have discovered a couple of bugs in the annotation /ids of the metabolites including:
- "_c or _e" appended to BiGG annotations (e.g bigg.metabolite: actACPmmy_c)
- …
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We expect to move Metaboverse out of the `beta` designation with the release of `v0.6.0`, slated for release by the end of March 2021.
- `v0.6.0` will include the ability to overlay data on [BiGG]…
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Hi Daniel,
I could not find a changelog for v1.5.0, so this is rather a question on that.
With the latest version, some reactions that used to be in the bacterial universe disappeared (for examp…
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Hi Daniel,
I was wondering if it would be possible for CarveMe to output more detailed info regarding the metabolties/reactions that were introduced by gapfilling. For example, shown below is the o…