Emergent-Behaviors-in-Biology / community-simulator
Simulate microbial community batch culture experiments.
☆42Updated last week
Related projects ⓘ
Alternatives and complementary repositories for community-simulator
- Enumerating biosynthetic pathways in metabolic networks☆12Updated last year
- A COBRApy extension for genome-scale models of metabolism and expression (ME-models)☆34Updated 5 years ago
- Python package for creating, calibrating and simulating RBA models☆11Updated last year
- Dynamic FBA for use with COBRApy metabolic models☆10Updated last year
- Inference of microbial interaction networks from large-scale heterogeneous abundance data☆74Updated 5 months ago
- Python package for building and analyzing models using ModelSEED☆18Updated this week
- Computation of Microbial Ecosystems in Time and Space☆19Updated this week
- Enzyme-constrained genome-scale models in python☆25Updated last year
- Python package simulating artificial selection on microbial communities☆14Updated last year
- A high-fidelity E. coli RNA-seq compendium☆32Updated 3 years ago
- Code depository for papers☆20Updated last week
- ReFramed: metabolic modeling package☆56Updated 2 months ago
- Constraint-Based Reconstruction and EXascale Analysis☆43Updated 2 weeks ago
- Enzyme models that take into account kinetics, allostery and thermodynamics☆26Updated 2 months ago
- Mackinac: A bridge between ModelSEED and COBRApy☆16Updated 6 years ago
- This repository contains the definitive copy of the biochemistry and metadata used to construct models using the ModelSEED/ProbAnno appro…☆56Updated 3 weeks ago
- Repository of tutorials for The COBRA Toolbox☆18Updated this week
- Toolbox for including enzyme constraints on a genome-scale model.☆67Updated 3 weeks ago
- Python toolbox for phenotype analysis of arrayed microbial colonies☆17Updated 9 months ago
- Python package to study microbial communities using metabolic modeling.☆94Updated last week
- From annotated genomes to metabolic screening in large scale microbiotas☆53Updated 2 months ago
- framed: a metabolic modeling package for python☆25Updated 5 years ago
- Efficient random sampling for COBRA models☆13Updated 3 years ago
- Clustering the NCBI nr database with mmseq2 (90% length, 90% identity). Inspired by the NCBI's experimental ClusteredNR database.☆23Updated last year
- EMBL GEMs: A collection of GEnome-scale Models for bacterial species☆25Updated 5 years ago
- CobraMod is a Python 3 open-source package which enables modifying and extending genome-scale metabolic models with metabolic pathway inf…☆12Updated 3 months ago
- CBMPy is a Python based platform for constraint based modelling and analysis.☆19Updated 5 months ago
- Maximum likelihood structural phylogenetics by including Foldseek 3Di characters. Supporting Information for Puente-Lelievre et al. 2023n…☆17Updated 4 months ago
- Online material for the Perspective: "Julia for Biologists" presented at JuliaCon 2021: https://www.youtube.com/watch?v=gRj7E5kYG1I☆96Updated 2 years ago
- Visualize differentially ranked features (taxa, metabolites, ...) and their log-ratios across samples☆32Updated 2 years ago