DTU Biosustain (@biosustain)
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biosustain

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Top repositories

1

potion

Flask-Potion is a RESTful API framework for Flask and SQLAlchemy, Peewee or MongoEngine
Python
489
star
2

cameo

cameo - computer aided metabolic engineering & optimization
Python
112
star
3

shu

Multi-dimensional, trans-omics metabolic maps.
Rust
37
star
4

swiglpk

Simple swig bindings for the GNU Linear Programming Kit
Python
26
star
5

Maud

Enzyme models that take into account kinetics, allostery and thermodynamics
Python
25
star
6

croissance

Tool for estimating growth rates from microbial growth curves
Python
24
star
7

snakemake_UmetaFlow

Untargeted metabolomics workflow for large-scale data processing and analysis implemented in Snakemake
Python
22
star
8

pyOpenMS_UmetaFlow

Untargeted metabolomics workflow for data processing and analysis written in Jupyter notebooks (Python)
Jupyter Notebook
15
star
9

venom

A transport-agnostic RPC framework for Python
Python
15
star
10

ancestry

AngularJS module with interactive lineage chart components based on D3.js
JavaScript
14
star
11

goodbye-genbank

A Python package for Biopython that gives feature annotations from GenBank records a new and better life
Python
14
star
12

pyrcos

Python wrapper for Circos
Python
12
star
13

potion-client

A Python client for APIs written in Flask-Potion
Python
11
star
14

cell-factory-design-course

https://biosustain.github.io/cell-factory-design-course/
Jupyter Notebook
11
star
15

flask-graphql-rest

Flask extension to expose a GraphQL API as REST API
Python
10
star
16

potion-node

TypeScript client for Flask-Potion
TypeScript
8
star
17

multitfa

Multivariate thermodynamics-based metabolic flux analysis in Python.
Python
8
star
18

fermentation-mpc

Model predictive control (MPC) for fermentations
Jupyter Notebook
8
star
19

gnomic

A grammar for describing microbial genotypes and phenotypes
Python
6
star
20

data_club

HTML
6
star
21

protov

Bounds checking and other validation for Protocol Buffers in Python
Python
5
star
22

iVnat

Draft genome-scale metabolic model of Vibrio natriegens
Jupyter Notebook
4
star
23

THG

A protocol for the automatic construction of high quality genome-scale models of human metabolism
Python
4
star
24

p-thermo

Genome-scale metabolic model of P. thermoglucosidasius NCIMB 11955
HTML
4
star
25

trp-scores

Code used for scoring genes as candidates for increased tryptophan production
MATLAB
4
star
26

EcoliKineticBenchmark

This repository contains code to replicate study-benchmark of published E. coli kinetic metabolic models
Jupyter Notebook
4
star
27

growth-profiler-align

Growth profiler image analysis
Python
3
star
28

GRASP

GRASP allows the user to build kinetic models of cell metabolism and analyse them.
HTML
3
star
29

memote-meta-study

Test metabolic models in the wild and rank them according to popularity and how easily they can be improved.
HTML
3
star
30

neighbor-joining

Rapid Neighbor-Joining phylogenetic tree creation method implementation for Node.js
JavaScript
3
star
31

sanger-sequencing

Python
3
star
32

CO2_fixation_models

Process optimization by combining temperature-dependent mass transfer and metabolic models.
Jupyter Notebook
3
star
33

genomediff-python

GenomeDiff (*.gd) file parser for Python
Python
2
star
34

incawrapper

A python wrapper for Metabolic Flux Analysis (MFA) using INCA with additional functionalities
Python
2
star
35

genomediff-node

GenomeDiff (*.gd) file parser for Node.js
TypeScript
2
star
36

memote-meta-models

2
star
37

cameo-notebooks

Example notebooks for Cameo
Jupyter Notebook
2
star
38

autoprot

The autoprot pipeline allows for absolute quantification of proteins from raw mass-spectrometry files in an automated manner.
PowerShell
2
star
39

dgfreg

Regression models of biochemical formation energies
Python
2
star
40

microplate

A Node.js package for working with tables and plate layouts loaded from Excel (XLSX).
JavaScript
2
star
41

apoptosis

Data and code related to the draft paper "Modelling Classical Apoptosis Resistance in CHO cells with CRISPR-Mediated Knock-outs of BAK1, BAX, and BOK Reveals both delayed onset and decreased rates of cell death".
Python
2
star
42

2019-08-26-software-carpentry

https://biosustain.github.io/2019-08-26-software-carpentry/
Python
2
star
43

Growth-coupling-suite

A constraint-based metabolic model-based workflow for computing and analyzing microbial strain design which couple a target reaction to growth
Python
2
star
44

obo

Python
1
star
45

AutoFlow-HTC

AutoFlow High Throughput Cultivation
Python
1
star
46

flask-venom

A Flask extension for Venom RPC
Python
1
star
47

MuSIC-PDO-3HP

Supplementary materials for "Multiscale Analysis of the Sustainable Production of 1,3-PDO and 3HP"
Python
1
star
48

co

Make mutated copies of DNA components in BioPython
Python
1
star
49

chemical-tolerance-supplementary

Jupyter Notebook
1
star
50

OpentronsCovid19

Python
1
star
51

ec_iYO844

Enzyme constrained B. subtilis model (based on iYO844)
MATLAB
1
star
52

polyplot

A wrapper for our favorite python plotting libraries that makes high-quality plots of common data.
Python
1
star
53

documentation

documentation of the Biosustain RDM-team's repository
1
star
54

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.
Jupyter Notebook
1
star
55

dsp_nf-metagenomics

Shotgun metagenomics pipeline to process microbiome samples
Shell
1
star
56

bayesian_statistics_for_computational_biology

A Bayesian statistics course for computational biologists
HTML
1
star