carveme
CarveMe: genome-scale metabolic model reconstruction (by cdanielmachado)
| carveme | ancient-microbiome-denovo | |
|---|---|---|
| 2 | 1 | |
| 138 | 4 | |
| - | - | |
| 5.0 | 0.0 | |
| 2 months ago | about 3 years ago | |
| Python | Shell | |
| GNU General Public License v3.0 or later | - |
The number of mentions indicates the total number of mentions that we've tracked plus the number of user suggested alternatives.
Stars - the number of stars that a project has on GitHub. Growth - month over month growth in stars.
Activity is a relative number indicating how actively a project is being developed. Recent commits have higher weight than older ones.
For example, an activity of 9.0 indicates that a project is amongst the top 10% of the most actively developed projects that we are tracking.
Stars - the number of stars that a project has on GitHub. Growth - month over month growth in stars.
Activity is a relative number indicating how actively a project is being developed. Recent commits have higher weight than older ones.
For example, an activity of 9.0 indicates that a project is amongst the top 10% of the most actively developed projects that we are tracking.
carveme
Posts with mentions or reviews of carveme.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2021-11-19.
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Advice on how to go about genome scale metabolic model construction
Carveme: https://academic.oup.com/nar/article/46/15/7542/5042022 https://github.com/cdanielmachado/carveme https://carveme.readthedocs.io/en/latest/usage.html
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metaGEM: create your own genome scale metabolic models directly from metagenomes
Thanks sharing, I believe I have seen the github repo/paper before! Looks very interesting, I wonder if mantis could be used for expanding the functional annotation of sequences in the BiGG database (paper). This is the database that is used by CarveMe (paper) for building metabolic models from protein fasta files within the metaGEM workflow. I believe that CarveMe does not actually use the annotations themselves, but simply aligns sequences in a fasta file to the BiGG database, which contains associations between sequences -> genes -> reactions -> metabolites.
ancient-microbiome-denovo
Posts with mentions or reviews of ancient-microbiome-denovo.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2021-07-05.
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metaGEM: create your own genome scale metabolic models directly from metagenomes
In our pre-print, we apply metaGEM to samples from small lab cultures, human gut, plant-associated, bulk soil, and ocean metagenomes. Through pangenome analysis and species metabolic interaction analysis, we showed that the workflow generates phenotype-relevant and context-specific models. I have also applied metaGEM to kefir cultures and fossilized human poop with great success!
What are some alternatives?
When comparing carveme and ancient-microbiome-denovo you can also consider the following projects:
metaGEM - :gem: An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within microbial communities directly from metagenomic data
DECA - DECA: Detailed Expression Capture and Animation (SIGGRAPH 2021)
embl_gems - EMBL GEMs: A collection of GEnome-scale Models for bacterial species
StrayVisualizer - Visualize Data From Stray Scanner https://keke.dev/blog/2021/03/10/Stray-Scanner.html
deepdiff - DeepDiff: Deep Difference and search of any Python object/data. DeepHash: Hash of any object based on its contents. Delta: Use deltas to reconstruct objects by adding deltas together.