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Hi,
I am currently trying to implement the metaGEM pipeline for the assembly and metabolic reconstruction of eukaryotic (particularly fungal) genomes. I was wondering if EukRep has been integrated …
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Hi,In the reported paper "Reconstruction and analysis of a Kluyveromyces marxianus genome-scale metabolic model", ``r_1912`` is the biomass production reaction in which the protein coefficient is the …
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I have this error message:
`######### Running metabolic network reconstruction with Pathway Tools #########
Remove genomes temporary datas.
mpwt could not find the version of Pathway Tools.
It i…
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**Is your feature request related to a problem? Please describe.**
I have used A. thaliana models from the specialized literature, but they do not work with Metaboverse.
**Describe the solution yo…
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Hi, I have been trying to execute the software metage2metabo, using the command recon which uses pathway tools. I have the following error message:
****lib/python3.9/site-packages/mpwt/pwt_wrappe…
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I generated a metabolic reconstruction using Mackinac and found that the objective values obtained between Mackinac (mackinac.optimize_modelseed_model) and Cobra (model.optimize()) are different. The …
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Hi Francisco,
Thanks so much for taking the time to develop these great tutorials.
In my project I am comparing two groups of species (Entero co-colonizers vs co-excluders) and have identified a…
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### Description of the issue:
Richelle et al., in a recent [research article](https://www.sciencedirect.com/science/article/pii/S2667237521000850#!) suggested an approach for interpretation of omics …
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I noticed recently that the models generated via all of the modelseed services have explicitly-represented boundary metabolites rather than the standard use of a true boundary (e.g., standard is extra…
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A reaction in an SBML in a metabolic reconstruction is annotated as:
Although this runs counter to:
id abbreviation name …