Ecosyste.ms: Awesome

https://github.com/sysbiochalmers/gecko

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

data-integration enzyme-constraints kinetics matlab proteomics systems-biology toolbox

Last synced: 18 Dec 2024

https://github.com/sysbiochalmers/dlkcat

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

bayesian deep-learning enzyme-constraints enzyme-turnover-number kcat kinetics

Last synced: 03 Dec 2024

https://github.com/ginkgobioworks/geckopy

Enzyme-constrained genome-scale models in python

data-integration enzyme-constraints kinetics omics proteomics systems-biology thermodynamics

Last synced: 05 Nov 2024

https://github.com/sysbiochalmers/ecfactory

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

cell-factory enzyme-constraints metabolic-models microbes

Last synced: 03 Dec 2024

https://github.com/sysbiochalmers/kmg060-systems-biology-course

KMG060 Systems Biology course - repo for students

enzyme-constraints flux-balance-analysis metabolic-models rna-seq-analysis systems-biology

Last synced: 03 Dec 2024

https://github.com/ivandomenzain/diverseyeasts_metabolism

enzyme-constraints gem metabolism systems-biology

Last synced: 02 Nov 2024

https://github.com/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".

constraint-based-modeling enzyme-constraints metabolism

Last synced: 03 Dec 2024

https://github.com/sysbiochalmers/enzymeconstrained_humanmodels

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

enzyme-constraints genome-scale-models kinetics proteomics-data-integration systems-biology

Last synced: 03 Dec 2024

https://github.com/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.

cell-factory constraint-based-modeling enzyme-constraints yeast

Last synced: 03 Dec 2024