Discover biosustain/croissance Open Source project

cameo - computer aided metabolic engineering & optimization

489

cameo

Multi-dimensional, trans-omics metabolic maps.

112

shu

Rust

swiglpk

Simple swig bindings for the GNU Linear Programming Kit

Enzyme models that take into account kinetics, allostery and thermodynamics

Maud

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

snakemake_UmetaFlow

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

pyOpenMS_UmetaFlow

AngularJS module with interactive lineage chart components based on D3.js

ancestry

JavaScript

venom

A transport-agnostic RPC framework for Python

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

goodbye-genbank

Python wrapper for Circos

pyrcos

A Python client for APIs written in Flask-Potion

potion-client

https://biosustain.github.io/cell-factory-design-course/

cell-factory-design-course

Flask extension to expose a GraphQL API as REST API

flask-graphql-rest

TypeScript client for Flask-Potion

potion-node

TypeScript

multitfa

Multivariate thermodynamics-based metabolic flux analysis in Python.

Model predictive control (MPC) for fermentations

fermentation-mpc

A grammar for describing microbial genotypes and phenotypes

gnomic

data_club

Bounds checking and other validation for Protocol Buffers in Python

protov

Draft genome-scale metabolic model of Vibrio natriegens

iVnat

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

THG

Genome-scale metabolic model of P. thermoglucosidasius NCIMB 11955

p-thermo

Code used for scoring genes as candidates for increased tryptophan production

trp-scores

MATLAB

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.

This repository contains code to replicate study-benchmark of published E. coli kinetic metabolic models

EcoliKineticBenchmark

Growth profiler image analysis

growth-profiler-align

GRASP allows the user to build kinetic models of cell metabolism and analyse them.

GRASP

A Flask extension for Venom RPC

flask-venom

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

memote-meta-study

Rapid Neighbor-Joining phylogenetic tree creation method implementation for Node.js

neighbor-joining

JavaScript

sanger-sequencing

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

CO2_fixation_models

GenomeDiff (*.gd) file parser for Python

genomediff-python

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

incawrapper

GenomeDiff (*.gd) file parser for Node.js

genomediff-node

TypeScript

memote-meta-models

cameo-notebooks

Example notebooks for Cameo

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

autoprot

PowerShell

dgfreg

Regression models of biochemical formation energies

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

microplate

JavaScript

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".

https://biosustain.github.io/2019-08-26-software-carpentry/

2019-08-26-software-carpentry

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

Growth-coupling-suite

A Bayesian statistics course for computational biologists

bayesian_statistics_for_computational_biology

obo

AutoFlow High Throughput Cultivation

AutoFlow-HTC

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

MuSIC-PDO-3HP

Make mutated copies of DNA components in BioPython

chemical-tolerance-supplementary

OpentronsCovid19

Enzyme constrained B. subtilis model (based on iYO844)

ec_iYO844

MATLAB

polyplot

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