carveme
deepdiff
| carveme | deepdiff | |
|---|---|---|
| 2 | 1 | |
| 138 | 1,902 | |
| - | - | |
| 5.0 | 8.7 | |
| 2 months ago | 25 days ago | |
| Python | Python | |
| GNU General Public License v3.0 or later | GNU General Public License v3.0 or later |
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carveme
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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.
deepdiff
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JSON Crack – Seamlessly visualize your JSON data instantly into graphs
Python's deepdiff [0] is your friend (more or less).
[0] https://github.com/seperman/deepdiff
What are some alternatives?
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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ancient-microbiome-denovo
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primediffex - Prime Difference Explorer (primediffex.py) is a Python project that explores the properties of prime numbers. It generates prime numbers, calculates their second differences and second ratios, identifies specific sets of primes (such as twin primes, cousin primes, and others), and writes these results to various output files.
password-generator - Generate passwords with Images 🐱💻, Truly random password
TextDistance - 📐 Compute distance between sequences. 30+ algorithms, pure python implementation, common interface, optional external libs usage.