metabolic-engineering
There are 36 repositories under metabolic-engineering topic.
opencobra/cobratoolbox
The COnstraint-Based Reconstruction and Analysis Toolbox. Documentation:
SysBioChalmers/RAVEN
The RAVEN Toolbox for genome scale model reconstruction, curation and analysis.
20n/act
Computational synthetic biology: Predicting DNA edits for bioengineering
johon-lituobang/MM
Infer metabolic directions from moment differences of mass-weighted intensity distributions
brsynth/RetroPathRL
Reinforcement Learning based bioretrosynthesis tool
cnapy-org/CNApy
An integrated visual environment for metabolic modeling with common methods such as FBA, FVA and Elementary Flux Modes, and advanced features such as thermodynamic methods, extended Minimal Cut Sets, OptKnock, RobustKnock, OptCouple and more!
hiyama341/teemi
teemi: A Python package for reproducible and FAIR microbial strain construction. Simulate the entire dbtl-cycle, generate genetic parts, design libraries, and track samples. Open-source Python platform for workflow flexibility and automated tasks, accelerating metabolic engineering. Try teemi with our Google Colab notebooks!
bebop/ark
Go REST API to replace Genbank, Uniprot, Rhea, and CHEMBL
mauriceling/advancesyntoolkit
Toolkit for Modelling and Simulation of Gene Expressions and Metabolism
COBREXA/COBREXA.jl
COnstraint Based Reconstruction and EXascale Analysis (in Julia)
modsim/FluxML
A Universal Modeling Language for Metabolic Flux Analysis
SysBioChalmers/Yarrowia_lipolytica_W29-GEM
Genome-scale model of Yarrowia lipolytica.
brsynth/RetroPath2-wrapper
Python wrapper for Retropath2.0 Knime workflow
brsynth/rptools
Suite of tools that work on rpSBML format
brsynth/straindesign
Library to perform metabolic engineering tasks
HassounLab/ELP
Enzymatic Link Prediction
MetExplore/dexom
Diversity-based enumeration of optimal context-specific metabolic networks
draeger-lab/SBMLsqueezer
Context-sensitive creation of kinetic equations in biochemical networks
Spherotob/gcOpt
Determination of product-growth-coupled strain designs employing stoichiometric metabolic models.
dbkgroup/reaction-balancer
Chemical reaction balancing web service
pwendering/RENZO_paper
Impose constraints on enzyme abundances ratios in enzyme-constraint metabolic models
Fabian11lrg/CobraPy-Model-Photosynthesis
CobraPy - Chlorella vulgaris iFR947 GSM model - Programming Documentation - Python, pandas, Jupyter Notebooks
juanvillada/iJV803
iJV803: a genome-scale metabolic model for Methylomicrobium album BG8
r2rahul/sybilMosek
A RMosek optimization interface for the Sybil package
shyamsrinivasan/emilio
EMILiO
SysBioChalmers/rhto-GEM
Genome-scale metabolic model of Rhodotorula toruloides
sysbiomics/Cordyceps_militaris-GEM
Genome-scale metabolic model of Cordyceps militaris
xlxs4/constraint-based-metabolic-modeling
An exploration of using FBA to engineer E. coli's metabolism in Julia
yaoguangluo/DataCatalytic_DNAMetabolic
DNA微分催化与肽计算， 元基花计算，进化计算，遗传计算，智慧计算，索引计算，元基编码，肽展公式，大数据计算分析, 数据加密
hiyama341/G8H_CPR_library
This repository is used in relation with the Python package teemi for constructing microbial strains to de-bottleneck the strictosidine pathway.
willchenko/EAStrainDesign
Uses an evolutionary algorithm to design hundreds of microbial strains for overproduction of a desired chemical, while minimizing the number of required designs
jcapels/jupyterhub_metabolic_modelling
A jupyter hub docker app for metabolic modelling using mewpy, troppo, cobra, etfl and cplex.
LMSE/emilio
Source code for EMILiO: A fast algorithm for genome-scale strain design.
LMSE/kbistable
Code for Model-based Design of Bistable Cell Factories for Metabolic Engineering
pinmarin/LS_pputida_ma
Large-scale Kinetic Models of Pseudomonas putida KT2440 for Muconic Acid Production from Lignin-based Aromatics