GitHub repository to support the development of the thesis "Development of microbial community simulation methods to characterize and analyze the effects of metal concentrations on pathogen silencing/promotion".

Collection of scripts for reproduction of simulation results in "Reconstruction of a catalogue of genome-scale metabolic models with enzymatic constraints using GECKO 2.0".

Collection of scripts for enhancing humanGEM based models with kinetic and proteomics constraints and specialized simulation utilities.

Impose constraints on enzyme abundances ratios in enzyme-constraint metabolic models

This project provides a simulation framework for synthetic biology and metabolic engineering, with a focus on the analysis of metabolic models for the production of novel compounds.

KMG060 Systems Biology course - repo for students

PRESTO: Correction of turnover numbers in enzyme-constraint metabolic models

Code and data for in silico strain design for enhanced production of +100 typical bio-products with yeast as a cell-factory. Predictions are based on the ecYeastGEM model avaiable at ecModels.

A constraint-based method for prediction of metabolic engineering targets using ecModels of metabolism

Enzyme-constrained genome-scale models in python

Toolbox for including enzyme constraints on a genome-scale model.

Deep learning and Bayesian approach applied to enzyme turnover number for the improvement of enzyme-constrained genome-scale metabolic models (ecGEMs) reconstruction