Emergent-Behaviors-in-Biology / community-simulatorLinks
Simulate microbial community batch culture experiments.
☆43Updated last year
Alternatives and similar repositories for community-simulator
Users that are interested in community-simulator are comparing it to the libraries listed below
Sorting:
- A COBRApy extension for genome-scale models of metabolism and expression (ME-models)☆35Updated 6 years ago
- Mackinac: A bridge between ModelSEED and COBRApy☆19Updated 7 years ago
- Computation of Microbial Ecosystems in Time and Space☆26Updated last month
- Python package for creating, calibrating and simulating RBA models☆13Updated 2 years ago
- ReFramed: metabolic modeling package☆62Updated 2 months ago
- A high-fidelity E. coli RNA-seq compendium☆33Updated 4 years ago
- Pyro models of SARS-CoV-2 variants☆77Updated last year
- D3.js based visualizations of cobrapy metabolic models☆49Updated 5 years ago
- An integrated visual environment for metabolic modeling with common methods such as FBA, FVA and Elementary Flux Modes, and advanced feat…☆58Updated last month
- Repository of tutorials for The COBRA Toolbox☆23Updated this week
- This repository contains the definitive copy of the biochemistry and metadata used to construct models using the ModelSEED/ProbAnno appro…☆64Updated this week
- Code depository for papers☆26Updated last month
- Dynamic FBA for use with COBRApy metabolic models☆10Updated 2 years ago
- Enzyme-constrained genome-scale models in python☆29Updated 2 years ago
- Enumerating biosynthetic pathways in metabolic networks☆12Updated 10 months ago
- SARS-CoV-2 RBD antibody escape calculator☆12Updated last year
- Maximum likelihood structural phylogenetics by including Foldseek 3Di characters. Supporting Information for Puente-Lelievre et al. 2023n…☆22Updated 7 months ago
- Python package simulating artificial selection on microbial communities☆14Updated 2 years ago
- Python library to simulate evolutionary sequence data☆80Updated 3 years ago
- ☆10Updated 6 years ago
- framed: a metabolic modeling package for python☆26Updated 6 years ago
- Toolbox for including enzyme constraints on a genome-scale model.☆79Updated 2 weeks ago
- Inference of microbial interaction networks from large-scale heterogeneous abundance data☆90Updated 2 months ago
- Python package for building and analyzing models using ModelSEED☆24Updated 7 months ago
- The BiGG Models website server☆85Updated 6 years ago
- Epidemiological modeling framework for pathogen population genetics and evolution.☆18Updated last year
- agent based modelling☆34Updated last year
- StrainDesign is a python package for the computational design of metabolic networks and based on COBRApy☆46Updated last month
- ☆25Updated 3 years ago
- Online material for the Perspective: "Julia for Biologists" presented at JuliaCon 2021: https://www.youtube.com/watch?v=gRj7E5kYG1I☆101Updated 3 years ago