Embl_gems Alternatives

Similar projects and alternatives to embl_gems

metaGEM

14 165 6.3 Python embl_gems VS 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
carveme

2 138 5.0 Python embl_gems VS carveme

CarveMe: genome-scale metabolic model reconstruction
InfluxDB

www.influxdata.com sponsored

Power Real-Time Data Analytics at Scale. Get real-time insights from all types of time series data with InfluxDB. Ingest, query, and analyze billions of data points in real-time with unbounded cardinality.

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embl_gems reviews and mentions

Posts with mentions or reviews of embl_gems. We have used some of these posts to build our list of alternatives and similar projects. The last one was on 2021-11-19.

Advice on how to go about genome scale metabolic model construction
3 projects | /r/bioinformatics | 19 Nov 2021

Hi OP, what is your organism? Is it possible that a model already exists for that organism here (https://github.com/cdanielmachado/embl_gems)? If you are interested in reconstructing metabolic models directly from metagenomic samples then I can recommend the metaGEM pipeline, which uses CarveMe. In the paper we argue that metagenome-based metabolic models capture strain and context specific pangenomic variation that is missed by using reference genomes as a starting point of metabolic models 💎
metaGEM: metagenomes -> genomes -> metabolic models
2 projects | /r/bioinformatics | 8 Oct 2021

Regarding your question about a reference database, we have deposited the models in a zenodo repository for now (https://zenodo.org/record/4407746#.YWFXFBbRYWM), but I do plan on making them more accessible (e.g. https://github.com/cdanielmachado/embl_gems) and also providing the underlying genomes + taxonomic annotation and other info/metadata generated by metaGEM.