Carveme Alternatives
Similar projects and alternatives to carveme based on common topics and language
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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
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WorkOS
The modern identity platform for B2B SaaS. The APIs are flexible and easy-to-use, supporting authentication, user identity, and complex enterprise features like SSO and SCIM provisioning.
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StrayVisualizer
Visualize Data From Stray Scanner https://keke.dev/blog/2021/03/10/Stray-Scanner.html
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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. (by seperman)
carveme reviews and mentions
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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.
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cdanielmachado/carveme is an open source project licensed under GNU General Public License v3.0 or later which is an OSI approved license.
The primary programming language of carveme is Python.
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