borenstein-lab / CoMiDA
The code and distributable for designing minimal microbial communities with specified metabolic functions.
☆11Updated 7 years ago
Related projects ⓘ
Alternatives and complementary repositories for CoMiDA
- Python package to study microbial communities using metabolic modeling.☆94Updated this week
- The aim of this repository is to maintain, refine, and expand the AGORA collection of genome-scale metabolic reconstructions for human gu…☆20Updated 3 years ago
- CBMPy is a Python based platform for constraint based modelling and analysis.☆18Updated 6 months ago
- SMETANA: a tool to analyse interactions in microbial communities☆58Updated 4 years ago
- EMBL GEMs: A collection of GEnome-scale Models for bacterial species☆25Updated 5 years ago
- Mackinac: A bridge between ModelSEED and COBRApy☆16Updated 6 years ago
- From annotated genomes to metabolic screening in large scale microbiotas☆53Updated 3 months ago
- A package to annotate protein sequences☆53Updated 4 months ago
- Automated taxonomy decoration onto a tree☆15Updated last year
- From genomes to phenotypes: Traitar, the microbial trait analyzer☆56Updated 5 years ago
- A toolkit for analyzing and visualizing phylogenetic (placement) data☆57Updated 4 months ago
- ☆16Updated last year
- In this repo you will find demos and tutorials prepared by members of the CBIB. Feel free to use them for non-commercial activities given…☆81Updated 6 years ago
- An imagemagick-like frontend to Biopython SeqIO☆113Updated 8 months ago
- Inference of microbial interaction networks from large-scale heterogeneous abundance data☆74Updated 5 months ago
- Python toolbox for phenotype analysis of arrayed microbial colonies☆17Updated 9 months ago
- Chimera: An easy to use pipeline for Genome based Metabolic Network reconstruction, evaluation and visualization.☆17Updated 2 years ago
- annotation pipeline for microbial genomes and metagenomes☆18Updated 6 years ago
- framed: a metabolic modeling package for python☆25Updated 5 years ago
- an interactive viewer for populations of bacterial genomes linked by a phylogeny☆117Updated 8 months ago
- MetaPathways v2.0: A master-worker model for environmental Pathway/Genome Database construction on grids and clouds☆33Updated 8 years ago
- Repository of tutorials for The COBRA Toolbox☆18Updated 3 weeks ago
- PaperBLAST: find papers about a protein or its homologs☆35Updated last week
- Phylogenetic and taxonomic analysis for genomes and metagenomes☆83Updated 8 years ago
- A tool for agile functional analysis of shotgun metagenomic data☆23Updated 2 months ago
- GraftM - Rapid community profiles from metagenomes☆44Updated 4 months ago
- Sample search by metadata and features☆45Updated last year
- Rapid and scalable homolog identification for bacterial genomes☆32Updated 5 years ago
- ☆17Updated last year
- A scalable bacterial genome assembly, annotation and analysis pipeline☆71Updated 11 months ago