SysBioChalmers/GECKO

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

Language: MATLAB - Size: 107 MB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 70 - Forks: 52

SysBioChalmers/DLKcat

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

Language: Python - Size: 46.2 MB - Last synced at: about 1 month ago - Pushed at: almost 2 years ago - Stars: 151 - Forks: 57

ginkgobioworks/geckopy

Enzyme-constrained genome-scale models in python

Language: Python - Size: 4.84 MB - Last synced at: about 1 month ago - Pushed at: over 1 year ago - Stars: 26 - Forks: 7

SysBioChalmers/ecFactory

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

Language: MATLAB - Size: 524 KB - Last synced at: about 1 month ago - Pushed at: 3 months ago - Stars: 8 - Forks: 4

SysBioChalmers/CellFactory-ecYeastGEM

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.

Language: MATLAB - Size: 138 MB - Last synced at: about 1 month ago - Pushed at: 3 months ago - Stars: 2 - Forks: 2

SysBioChalmers/EnzymeConstrained_humanModels

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

Language: MATLAB - Size: 464 MB - Last synced at: about 2 months ago - Pushed at: about 5 years ago - Stars: 2 - Forks: 0

SysBioChalmers/KMG060-Systems-Biology-course

KMG060 Systems Biology course - repo for students

Language: MATLAB - Size: 25.9 MB - Last synced at: about 1 month ago - Pushed at: over 1 year ago - Stars: 2 - Forks: 7

IVANDOMENZAIN/diverseYeasts_metabolism

Language: MATLAB - Size: 111 MB - Last synced at: about 1 month ago - Pushed at: 9 months ago - Stars: 1 - Forks: 1

areias03/tmCOM

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".

Language: Jupyter Notebook - Size: 107 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

pwendering/RENZO_paper

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

Language: MATLAB - Size: 1.71 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 1 - Forks: 0

pwendering/PRESTO

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

Language: MATLAB - Size: 92.2 MB - Last synced at: over 1 year ago - Pushed at: about 2 years ago - Stars: 2 - Forks: 0

SysBioChalmers/GECKO2_simulations

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".

Language: MATLAB - Size: 17 MB - Last synced at: about 2 months ago - Pushed at: almost 3 years ago - Stars: 1 - Forks: 0