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amino_acid

bacterial-exclusion-prediction

Estimating the anti-bacterial property of surfaces based on SEM images

bayesiangem

This repository contains code and data needed to replicate the analysis carried out in the manuscript Li G, et al. 2020.

brainmetabolismmodeling

Modeling of the energy metabolism of the brain

cancerproteinsecretionml

A collection of scripts to analyze cancer transcriptomics data using various statistical and machine-learning approaches.

candia

Canonical Decomposition of Data-Independent-Acquired Spectra

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.

childrengutmicrobialgems

58 GEMs for gut bacterial species from microbiota of healthy and malnourished children.

chipexo_pipeline

Pipeline for analyzing ChIPexo datasets

clpapi

R Interface to C API of COIN-OR Clp

cody

cofactoryeast

Integration of cofactors with proteome-constrained model of Saccharomyces cerevisiae

comparativestudycrabtreeeffect

Collection of data and scripts for the study "Adaptations in metabolism and protein translation give rise to the Crabtree effect in yeast"

cplexapi

R Interface to C API of IBM ILOG CPLEX

depcrpaperutils

Some files needed to run kallisto and bustools in Google Colab

dlkcat

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

dsave-m

Matlab code for the paper "Dissecting Cell-to-Cell Variation in Single-cell RNA-Seq Data"

dsave-r

R Package DSAVE (Down-SAmpling based Variation Estimation). The package operates on single-cell RNA-Seq data and is useful for finding misclassified cells, comparing the outcome of clustering methods, figuring out minimum clustering sizes to get the same variation as for bulk, and comparing the technical variation across datasets. The package is compatible with Seurat.

ecfactory

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

ecm_yeast

Automated pipeline for full kinetic parameterization of a reduced model for Saccharomyces cerevisiae's central carbon metabolism.

ecmodels

A container for all enzyme constrained models created by GECKO.

energy_metabolism_model

Energy metabolism model

enzyme-parameters-analysis

Global analysis of kinetic parameters in the BRENDA database, used by the GECKO toolbox

enzymeconstrained_humanmodels

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

enzymeconstrainedsmallyeast

Enzyme constrained model of intermediary metabolism in S. cerevisiae

epo_gfp

Transcriptome analysis of EPO- and GFP-producing HEK293 Cell-lines

falconet

The FALCONET R package enables to build and visualise metabolic maps of GEM automatically with aid of cellDesigner 4.4 and R platform

fruitfly-gem

Genome scale model for Drosophila melanogaster

gagome-bca

gagome-mced