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Hi Joshua,
I was wondering if you could update the `sf.processSBMLforRE`/`sf.pruneCurrencyMetabs`/`modelStatArray` functions to handle community models as well. Right now it only seems to work for …
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Working with @nmarkari, a basic table of GO-CAM to gene data should be generated as an input to enrichment test.
Some detail from @nmarkari:
> I'd like a table that for all causal models in prod…
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Carsten Zengler confirmed consumption of metabolites in S. elongatus. We can use this to confirm nonzero uptake flux (but not growth).
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**Is your feature request related to a problem? Please describe.**
At the moment the `animal` model tracks energy directly, while the `soil` and `litter` models track carbon, which is an imperfect p…
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#### Problem description
>A related one is the need for ATP production to be lower than the thermodynamically feasible limit. Typically 60-80% of the limit
- Radhakrishnan Mahadevan
> Hi Krishna,…
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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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Hello @vvvieira, @jorgemlferreira and the MEWpy team,
First, I'd like to express my appreciation for the tool your group has developed for in-silico metabolic modeling and engineering. It appears …
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One of the things that will happen as we work with teams in manually curating their metabolic models, is that we will find compounds that are erroneously merged, or not. Sugars are a culprit here bec…
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**Workflow for Kolokotrones _et al_ 2010:**
_hffung, ronghao94, raecv_
1. Load raw data (as a tibble)
- skip the citation, metadata in first 5 rows
2. Add the fits to the plot: 2 functions to…
raecv updated
2 years ago
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We want to gap fill for a whole bunch of carbon sources, how should we do it?