SysBioChalmers/RAVEN

The RAVEN Toolbox for genome scale model reconstruction, curation and analysis.

Language: MATLAB - Size: 1010 MB - Last synced: 3 days ago - Pushed: 3 days ago - Stars: 97 - Forks: 52

mauriceling/advancesyntoolkit

Toolkit for Modelling and Simulation of Gene Expressions and Metabolism

Language: Python - Size: 15.3 MB - Last synced: 9 days ago - Pushed: 9 days ago - Stars: 12 - Forks: 40

opencobra/cobratoolbox

The COnstraint-Based Reconstruction and Analysis Toolbox. Documentation:

Language: MATLAB - Size: 1.02 GB - Last synced: 14 days ago - Pushed: 15 days ago - Stars: 237 - Forks: 303

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!

Language: Python - Size: 6.92 MB - Last synced: 15 days ago - Pushed: 16 days ago - Stars: 41 - Forks: 7

brsynth/straindesign

Library to perform metabolic engineering tasks

Language: Python - Size: 10.4 MB - Last synced: 17 days ago - Pushed: 17 days ago - Stars: 4 - Forks: 0

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!

Language: Jupyter Notebook - Size: 97.9 MB - Last synced: 6 days ago - Pushed: about 1 month ago - Stars: 32 - Forks: 3

brsynth/RetroPathRL

Reinforcement Learning based bioretrosynthesis tool

Language: Python - Size: 40.1 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 46 - Forks: 16

modsim/FluxML

A Universal Modeling Language for Metabolic Flux Analysis

Language: C++ - Size: 1.98 MB - Last synced: 28 days ago - Pushed: 2 months ago - Stars: 9 - Forks: 6

brsynth/rptools

Suite of tools that work on rpSBML format

Language: HTML - Size: 22 MB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 6 - Forks: 2

tubanlee/MM

Infer metabolic directions from moment differences of mass-weighted intensity distributions

Language: R - Size: 4.17 MB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 186 - Forks: 14

cnapy-org/optlang_enumerator

Language: Python - Size: 101 KB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 2 - Forks: 1

brsynth/RetroPath2-wrapper

Python wrapper for Retropath2.0 Knime workflow

Language: JavaScript - Size: 73.2 MB - Last synced: 24 days ago - Pushed: 5 months ago - Stars: 7 - Forks: 1

bebop/ark

Go REST API to replace Genbank, Uniprot, Rhea, and CHEMBL

Language: Go - Size: 17 MB - Last synced: 5 months ago - Pushed: 5 months ago - Stars: 19 - Forks: 5

pwendering/RENZO_paper

Impose constraints on enzyme abundances ratios in enzyme-constraint metabolic models

Language: MATLAB - Size: 1.71 MB - Last synced: 8 months ago - Pushed: 8 months ago - Stars: 1 - Forks: 0

jcapels/jupyterhub_metabolic_modelling

A jupyter hub docker app for metabolic modelling using mewpy, troppo, cobra, etfl and cplex.

Language: Shell - Size: 26.4 KB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

xlxs4/constraint-based-metabolic-modeling

An exploration of using FBA to engineer E. coli's metabolism in Julia

Language: Julia - Size: 2.04 MB - Last synced: 4 months ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

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

Language: Java - Size: 10.7 KB - Last synced: about 1 year ago - Pushed: about 2 years ago - Stars: 0 - Forks: 0

SysBioChalmers/Yarrowia_lipolytica_W29-GEM

Genome-scale model of Yarrowia lipolytica.

Language: MATLAB - Size: 3.61 MB - Last synced: 7 months ago - Pushed: almost 3 years ago - Stars: 7 - Forks: 7

MetExplore/dexom

Diversity-based enumeration of optimal context-specific metabolic networks

Language: MATLAB - Size: 2.32 MB - Last synced: 7 months ago - Pushed: almost 3 years ago - Stars: 5 - Forks: 1

r2rahul/sybilMosek

A RMosek optimization interface for the Sybil package

Language: R - Size: 277 KB - Last synced: 7 months ago - Pushed: almost 3 years ago - Stars: 1 - Forks: 0

juanvillada/iJV803

iJV803: a genome-scale metabolic model for Methylomicrobium album BG8

Size: 8.54 MB - Last synced: 9 months ago - Pushed: about 3 years ago - Stars: 1 - Forks: 0

draeger-lab/SBMLsqueezer

Context-sensitive creation of kinetic equations in biochemical networks

Language: HTML - Size: 608 MB - Last synced: 7 months ago - Pushed: about 3 years ago - Stars: 3 - Forks: 0

HassounLab/ELP

Enzymatic Link Prediction

Language: Python - Size: 117 KB - Last synced: 11 days ago - Pushed: over 3 years ago - Stars: 4 - Forks: 0

LMSE/emilio Fork of shyamsrinivasan/emilio

Source code for EMILiO: A fast algorithm for genome-scale strain design.

Language: MATLAB - Size: 1.63 MB - Last synced: 10 months ago - Pushed: about 4 years ago - Stars: 0 - Forks: 0

SysBioChalmers/rhto-GEM

Genome-scale metabolic model of Rhodotorula toruloides

Language: MATLAB - Size: 22.7 MB - Last synced: 3 months ago - Pushed: about 4 years ago - Stars: 1 - Forks: 2

sysbiomics/Cordyceps_militaris-GEM

Genome-scale metabolic model of Cordyceps militaris

Language: MATLAB - Size: 41.6 MB - Last synced: 7 months ago - Pushed: about 4 years ago - Stars: 1 - Forks: 1

Spherotob/gcOpt

Determination of product-growth-coupled strain designs employing stoichiometric metabolic models.

Language: MATLAB - Size: 45.9 KB - Last synced: 7 months ago - Pushed: over 4 years ago - Stars: 2 - Forks: 0

shyamsrinivasan/emilio

EMILiO

Language: Matlab - Size: 1.63 MB - Last synced: 12 months ago - Pushed: over 6 years ago - Stars: 1 - Forks: 1

LMSE/kbistable

Code for Model-based Design of Bistable Cell Factories for Metabolic Engineering

Language: Matlab - Size: 93.3 MB - Last synced: 10 months ago - Pushed: over 6 years ago - Stars: 0 - Forks: 0

dbkgroup/reaction-balancer

Chemical reaction balancing web service

Language: Python - Size: 45.9 KB - Last synced: about 1 year ago - Pushed: over 6 years ago - Stars: 2 - Forks: 0