memote – the genome-scale metabolic model test suite

Minimal Microbial Consortia creation tools

COBRApy is a package for constraint-based modeling of metabolic networks.

Rembg is a tool to remove images background

SMETANA: a tool to analyse interactions in microbial communities

💎 An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within microbial communities directly from metagenomic data

The COnstraint-Based Reconstruction and Analysis Toolbox. Documentation:

From annotated genomes to metabolic screening in large scale microbiotas

Python package to study microbial communities using metabolic modeling.

Computation of Microbial Ecosystems in Time and Space

microbiome engineering through prescriptive perturbations

Python interface for running COMETS simulations and analyzing the results

Pathway-Guided Pruning Reconstruction of Genome-Scale Metabolic Models

This is µbialSim, a dynamic Flux-Balance-Analysis-based simulator for complex microbial communities.

This repository contains all source code in the reconstructor python package, installation instructions, important file dependencies, and benchmarking scores for reconstructor models. Reconstructor…

A latent text-to-image diffusion model

Dynamic FBA for use with COBRApy metabolic models

MMODES (Metabolic Models based Ordinary Differential Equations Simulation)

Informed prediction and analysis of bacterial metabolic pathways and genome-scale networks

MinPath (Minimal set of Pathways) is a parsimony approach for biological pathway reconstructions using protein family predictions, achieving a more conservative, yet more faithful, estimation of th…

Implementation of Dreambooth (https://arxiv.org/abs/2208.12242) by way of Textual Inversion (https://arxiv.org/abs/2208.01618) for Stable Diffusion (https://arxiv.org/abs/2112.10752). Tweaks focuse…

CarveMe: genome-scale metabolic model reconstruction

Code files for Poshmark webinar.