Pinned Repositories
ancestry
AngularJS module with interactive lineage chart components based on D3.js
cameo
cameo - computer aided metabolic engineering & optimization
croissance
Tool for estimating growth rates from microbial growth curves
goodbye-genbank
A Python package for Biopython that gives feature annotations from GenBank records a new and better life
Maud
Enzyme models that take into account kinetics, allostery and thermodynamics
potion
Flask-Potion is a RESTful API framework for Flask and SQLAlchemy, Peewee or MongoEngine
pyOpenMS_UmetaFlow
Untargeted metabolomics workflow for data processing and analysis written in Jupyter notebooks (Python)
shu
Multi-dimensional, trans-omics metabolic maps.
snakemake_UmetaFlow
Untargeted metabolomics workflow for large-scale data processing and analysis implemented in Snakemake
venom
A transport-agnostic RPC framework for Python
DTU Biosustain's Repositories
biosustain/shu
Multi-dimensional, trans-omics metabolic maps.
biosustain/Maud
Enzyme models that take into account kinetics, allostery and thermodynamics
biosustain/snakemake_UmetaFlow
Untargeted metabolomics workflow for large-scale data processing and analysis implemented in Snakemake
biosustain/pyOpenMS_UmetaFlow
Untargeted metabolomics workflow for data processing and analysis written in Jupyter notebooks (Python)
biosustain/multitfa
Multivariate thermodynamics-based metabolic flux analysis in Python.
biosustain/data_club
biosustain/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.
biosustain/bayesian_statistics_for_computational_biology
A Bayesian statistics course for computational biologists
biosustain/autoprot
The autoprot pipeline allows for absolute quantification of proteins from raw mass-spectrometry files in an automated manner.
biosustain/datacatalog-documentation
biosustain/dgfreg
Regression models of biochemical formation energies
biosustain/Growth-coupling-suite
A constraint-based metabolic model-based workflow for computing and analyzing microbial strain design which couple a target reaction to growth
biosustain/incawrapper
A python wrapper for Metabolic Flux Analysis (MFA) using INCA with additional functionalities
biosustain/dsp_nf-metagenomics
Shotgun metagenomics pipeline to process microbiome samples
biosustain/lifelike
Turning big data into contextualized knowledge. Lifelike is a modern application platform for data extraction, analysis and visualization.
biosustain/.github
biosustain/cmfa
Compositional Metabolic Flux analysis
biosustain/code-quality-check
biosustain/consortia_synthetic_anaerobe
Supporting material for "CRISPRi-mediated metabolic switch enables concurrent aerobic and synthetic anaerobic fermentations in engineered consortium" manuscript
biosustain/dsp_nf-msdap
Nextflow pipeline for MS-DAP, a downstream pipeline to generate statistical reports for MS data
biosustain/dsp_nfcore_taxprofiler
Taxonomica profiling using nf-core/taxprofiler pipeline
biosustain/GEM-Exometabolome
Pipeline for the integration of exometabolomic data into GEM analysis and interpretation
biosustain/Methionine_model
biosustain/msdap
MS-DAP: downstream analysis pipeline for quantitative proteomics
biosustain/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.
biosustain/pankb_db
biosustain/QconCATquantSTAR
QconCAT protein quantification accompanying STAR protocol for QconCATs
biosustain/rdm-self_learning
This is a course template forked from hds-sandbox
biosustain/salb_imodulons
biosustain/shu_case_studies
Shu case study figures.