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potion
Flask-Potion is a RESTful API framework for Flask and SQLAlchemy, Peewee or MongoEnginecameo
cameo - computer aided metabolic engineering & optimizationshu
Multi-dimensional, trans-omics metabolic maps.Maud
Enzyme models that take into account kinetics, allostery and thermodynamicscroissance
Tool for estimating growth rates from microbial growth curvessnakemake_UmetaFlow
Untargeted metabolomics workflow for large-scale data processing and analysis implemented in SnakemakepyOpenMS_UmetaFlow
Untargeted metabolomics workflow for data processing and analysis written in Jupyter notebooks (Python)ancestry
AngularJS module with interactive lineage chart components based on D3.jsvenom
A transport-agnostic RPC framework for Pythongoodbye-genbank
A Python package for Biopython that gives feature annotations from GenBank records a new and better lifepyrcos
Python wrapper for Circospotion-client
A Python client for APIs written in Flask-Potioncell-factory-design-course
https://biosustain.github.io/cell-factory-design-course/flask-graphql-rest
Flask extension to expose a GraphQL API as REST APIpotion-node
TypeScript client for Flask-Potionmultitfa
Multivariate thermodynamics-based metabolic flux analysis in Python.fermentation-mpc
Model predictive control (MPC) for fermentationsgnomic
A grammar for describing microbial genotypes and phenotypesdata_club
protov
Bounds checking and other validation for Protocol Buffers in PythoniVnat
Draft genome-scale metabolic model of Vibrio natriegensTHG
A protocol for the automatic construction of high quality genome-scale models of human metabolismp-thermo
Genome-scale metabolic model of P. thermoglucosidasius NCIMB 11955trp-scores
Code used for scoring genes as candidates for increased tryptophan productionpseudobatch
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.EcoliKineticBenchmark
This repository contains code to replicate study-benchmark of published E. coli kinetic metabolic modelsgrowth-profiler-align
Growth profiler image analysisGRASP
GRASP allows the user to build kinetic models of cell metabolism and analyse them.flask-venom
A Flask extension for Venom RPCmemote-meta-study
Test metabolic models in the wild and rank them according to popularity and how easily they can be improved.neighbor-joining
Rapid Neighbor-Joining phylogenetic tree creation method implementation for Node.jssanger-sequencing
CO2_fixation_models
Process optimization by combining temperature-dependent mass transfer and metabolic models.genomediff-python
GenomeDiff (*.gd) file parser for Pythonincawrapper
A python wrapper for Metabolic Flux Analysis (MFA) using INCA with additional functionalitiesgenomediff-node
GenomeDiff (*.gd) file parser for Node.jsmemote-meta-models
cameo-notebooks
Example notebooks for Cameoautoprot
The autoprot pipeline allows for absolute quantification of proteins from raw mass-spectrometry files in an automated manner.dgfreg
Regression models of biochemical formation energiesmicroplate
A Node.js package for working with tables and plate layouts loaded from Excel (XLSX).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".2019-08-26-software-carpentry
https://biosustain.github.io/2019-08-26-software-carpentry/Growth-coupling-suite
A constraint-based metabolic model-based workflow for computing and analyzing microbial strain design which couple a target reaction to growthbayesian_statistics_for_computational_biology
A Bayesian statistics course for computational biologistsobo
AutoFlow-HTC
AutoFlow High Throughput CultivationMuSIC-PDO-3HP
Supplementary materials for "Multiscale Analysis of the Sustainable Production of 1,3-PDO and 3HP"co
Make mutated copies of DNA components in BioPythonchemical-tolerance-supplementary
OpentronsCovid19
ec_iYO844
Enzyme constrained B. subtilis model (based on iYO844)polyplot
A wrapper for our favorite python plotting libraries that makes high-quality plots of common data.documentation
documentation of the Biosustain RDM-team's repositorydsp_nf-metagenomics
Shotgun metagenomics pipeline to process microbiome samplesLove Open Source and this site? Check out how you can help us