DTU Biosustain

shu

Multi-dimensional, trans-omics metabolic maps.

Maud

Enzyme models that take into account kinetics, allostery and thermodynamics

snakemake_UmetaFlow

Untargeted metabolomics workflow for large-scale data processing and analysis implemented in Snakemake

pyOpenMS_UmetaFlow

Untargeted metabolomics workflow for data processing and analysis written in Jupyter notebooks (Python)

multitfa

Multivariate thermodynamics-based metabolic flux analysis in Python.

data_club

pseudobatch

The Pseudobatch transformation is a method to easy analysis of measurement from a fed-batch fermentation process. After transformation, the data can be analysed as if it was obtained from a batch fermentation process. The Pseudobatch transformation is especially useful for fed-batch processes where samples where drawn from the bioreactor.

THG

A protocol for the automatic construction of high quality genome-scale models of human metabolism

CO2_fixation_models

Process optimization by combining temperature-dependent mass transfer and metabolic models.

autoprot

The autoprot pipeline allows for absolute quantification of proteins from raw mass-spectrometry files in an automated manner.

bayesian_statistics_for_computational_biology

A Bayesian statistics course for computational biologists

dgfreg

Regression models of biochemical formation energies

Growth-coupling-suite

A constraint-based metabolic model-based workflow for computing and analyzing microbial strain design which couple a target reaction to growth

incawrapper

A python wrapper for Metabolic Flux Analysis (MFA) using INCA with additional functionalities

dsp_nf-metagenomics

Shotgun metagenomics pipeline to process microbiome samples

lifelike

Turning big data into contextualized knowledge. Lifelike is a modern application platform for data extraction, analysis and visualization.

.github

cmfa

Compositional Metabolic Flux analysis

code-quality-check

consortia_synthetic_anaerobe

Supporting material for "CRISPRi-mediated metabolic switch enables concurrent aerobic and synthetic anaerobic fermentations in engineered consortium" manuscript

GEM-Exometabolome

Pipeline for the integration of exometabolomic data into GEM analysis and interpretation

growtho

Statistical growthometer

maud-debugging

A repository that details a list of common issues encountered within Maud and associated ways to solve them.

maudtools

Tools for working with Maud

Methionine_model

msdap

MS-DAP: downstream analysis pipeline for quantitative proteomics

pankb

The Pangenome Knowledge Base (PanKB) serves as an up-to-date resource for pangenomics research methods and the dissemination of results and currently offers basic pangenome characteristics and advanced pangenome analytics for six major biotech bacteria families.

QconCATquantSTAR

QconCAT protein quantification accompanying STAR protocol for QconCATs

salb_imodulons

shu_case_studies

Shu case study figures.