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Dear Matt Jenior,
I'm using riptide for transcriptomic-constraint genome scale metabolic model. When I set fraction to a higher value such as 0.9 with samples being the default value 500, I can not…
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Dear Matt Jenior,
I'm using riptide for transcriptomic-constraint genome scale metabolic model. When I use different gene expression datasets, I got similar results, i.e. similar growth rate, flux …
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First, I'd like to thank you for previous help in getting anvi'o working.
However, now that I can use anvi-refine to improve bins, I realized that I am a bit stuck on the deeper issue of when exact…
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Hello,
when I am executing gapseq fill with my model, in the end I get:
> Top 10 produced metabolites:
> NA:NA
> Error in .checkTypos(e, names_x) :
> Object 'ec' not found. Perhaps you int…
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Dear Zorrilla,
In your paper, it is not clear which medium is used in the CarveMe simulation. And it is understood that M11 is used in SMETANA simulation.
However, in Snakefile and config.yaml f…
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Human-GEM.xml=
"
Genome-scale metabolic models are valuable tools to study metabolism and provide a scaffold for the integrative analysis of omics data. This is the lates…
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Dear Matt Jenior,
I'm using riptide for transcriptomic-constraint genome scale metabolic model. When I use different gene expression datasets, I got similar results, i.e. similar growth rate, flux …
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Hi there,
I am trying to run a GSA using Reporter Metabolites using a genome-scale metabolic network reconstruction from the [BiGG Models database](http://bigg.ucsd.edu/).
Unfortunately, when I …
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Hi Daniel,
Hi everyone,
I am a newbie in working with GEMs.
I am trying to figure out how to make sense of the CarveMe output and I have a few (most likely, stupid) questions:
1. Where to find…
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### Description of the issue:
The file in question starts with:
> This document serves as a checklist for creating an open source genome-scale metabolic model (GEM) on GitHub.
I propose the revis…