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Dear Francisco,
Thank you so much for quick response and detailed instructions!
Actually I would like to run carveme, memote, and SMETNAN part of this pipeline and start with carveme. I have mov…
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Dear Gapseq developer,
I am super excited about this software. It does improve CarveMe and ModelSeed draft models a lot and it provides a long list of tentative reactions, which provides transparen…
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Dear gapseq team,
I have been exploring starch/oligosaccharides degradation reactions present in my models and have noticed that certain reactions are labeled as 'good_blast' in the *Reactions.tbl …
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Hi,
First, thank you for gapseq, it is really useful.
I have a small issue with options given to the sub command `doall` of `gapseq` on Ubuntu 22.04.
When calling `./gapseq -v`, I have an exp…
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I am tryng to compute the gene KOs for a large network, Human-GEM, but it is stucked in preprocessing.
Is this normal?
Strain design computation progress:
Preparing strain design computation.
Us…
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Hi all,
I followed the workflow of metaGEM (except using metaspades and das_tool instead of megahit and metawrap). when I used gtdbtk to classify the bins determined by das_tool based on binning res…
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Hello,
I am trying to create context-specific GEM models for my transcriptomic data using the Cobra toolbox and gurobi solver in Matlab. I have created models before using the same Human-GEM guide. N…
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@brynnz22 submitted a JSON file to the `/metadata/json:submit` endpoint.
The corresponding run on Dagit failed:
![image](https://github.com/microbiomedata/nmdc-runtime/assets/134325062/2c643da2-…
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Hi @JamesPino
According to [Santos-Merino 2023](https://doi.org/10.3389/fmicb.2023.1126030), they reported the following confusion matrix:
![Screen Shot 2023-05-30 at 7 55 54 PM](https://github…
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Creation of network should not only be possible for C. elegans, but also for other species.
Therefore a generic input is required. An important factor is the order of reactions, because reactions dep…