GitHub topics: cobrapy
ModelSEED/ModelSEEDpy
Python package for building and analyzing models using ModelSEED
Language: Python - Size: 7.78 MB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 22 - Forks: 18
MetExplore/dexom-python
diversity-based enumeration of optimal context-specific metabolic networks using the cobrapy library
Language: Python - Size: 1.93 MB - Last synced at: 9 days ago - Pushed at: 12 days ago - Stars: 1 - Forks: 0
klamt-lab/straindesign
StrainDesign is a python package for the computational design of metabolic networks and based on COBRApy
Language: Python - Size: 39.3 MB - Last synced at: 19 days ago - Pushed at: about 2 months ago - Stars: 42 - Forks: 7
BeeAnka/EFMlrs
Python package and workflow for EFM calculation via (mp)lrs and efmtool
Language: Python - Size: 5.37 MB - Last synced at: 1 day ago - Pushed at: over 2 years ago - Stars: 5 - Forks: 1
SBRG/ssbio
A Python framework for structural systems biology
Language: Python - Size: 38.2 MB - Last synced at: 17 days ago - Pushed at: over 4 years ago - Stars: 107 - Forks: 28
COBREXA/JSONFBCModels.jl
Reader and writer for JSON metabolic models
Language: Julia - Size: 104 KB - Last synced at: 21 days ago - Pushed at: 8 months ago - Stars: 0 - Forks: 1
mjenior/riptide
Reaction Inclusion by Parsimony and Transcript Distribution
Language: Python - Size: 4.53 MB - Last synced at: 11 days ago - Pushed at: about 2 years ago - Stars: 11 - Forks: 3
biosustain/multitfa
Multivariate thermodynamics-based metabolic flux analysis in Python.
Language: Python - Size: 70.9 MB - Last synced at: 11 days ago - Pushed at: over 1 year ago - Stars: 9 - Forks: 2
MetExplore/miom
Constraint-based modeling of metabolism using Mixed Integer Optimization
Language: Python - Size: 1020 KB - Last synced at: 16 days ago - Pushed at: 7 months ago - Stars: 11 - Forks: 2
micom-dev/micom
Python package to study microbial communities using metabolic modeling.
Language: Python - Size: 39.3 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 77 - Forks: 17
openCONTRABASS/CONTRABASS
Constraint-based model vulnerabilities analysis - Python analysis tool http://contrabass.unizar.es
Language: HTML - Size: 5.61 MB - Last synced at: 11 days ago - Pushed at: over 1 year ago - Stars: 3 - Forks: 0
vjz3qz/cancer-metabolic-analysis
Bioinformatics project analyzing cancer metabolism using computational modeling and analysis. The project was awarded the GIDI-UP: Summer Research Award and includes data, models, and scripts.
Language: Jupyter Notebook - Size: 23.4 KB - Last synced at: 12 months ago - Pushed at: over 1 year ago - Stars: 1 - Forks: 0
c-mayer/ECMproject
ECMproject is a standalone python program, which enumerates Elementary Conversion Modes (ECMs) of metabolic models.
Language: Jupyter Notebook - Size: 4.68 MB - Last synced at: 12 months ago - Pushed at: 12 months ago - Stars: 0 - Forks: 0
SBRG/cobrame
A COBRApy extension for genome-scale models of metabolism and expression (ME-models)
Language: Python - Size: 1.61 MB - Last synced at: 11 months ago - Pushed at: over 6 years ago - Stars: 33 - Forks: 17
Fxe/kb_escher
Escher Service for KBase
Language: JavaScript - Size: 22.5 MB - Last synced at: about 1 year ago - Pushed at: over 3 years ago - Stars: 0 - Forks: 1
resendislab/corda
An implementation of genome-scale model reconstruction using Cost Optimization Reaction Dependency Assessment by Schultz et. al
Language: Python - Size: 1.6 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 21 - Forks: 8
duartebred/fba-Flux-Balance-Analysis
Repositório para apresentação de código e posterior análise, desenvolvido pelo grupo 1 para a UC Biologia de Sistemas, do Mestraddo em Bioinformática, ano lectivo 23-24.
Language: Jupyter Notebook - Size: 353 KB - Last synced at: 14 days ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0
ModelSEED/KB-ModelSEEDCOBRA
KBase SDK module for model analysis apps created and managed by the ModelSEED team
Language: Python - Size: 2.55 MB - Last synced at: about 1 year ago - Pushed at: over 2 years ago - Stars: 1 - Forks: 0
tracykuper/mimics
Multi-scale model of Metabolism In Cellular Systems
Language: Java - Size: 8.66 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0
OSS-Lab/FBAhv
FBAhv: FBA analysis of host-virus metabolic model (read related publication at: https://www.life-science-alliance.org/content/4/1/e202000869)
Language: Python - Size: 32.2 KB - Last synced at: over 1 year ago - Pushed at: over 4 years ago - Stars: 0 - Forks: 0
SBRG/ecolime
Data and tools necessary to construct iJL1678b-ME, a genome-scale model of E. coli K-12 MG1655 metabolism and expression
Language: Python - Size: 13.3 MB - Last synced at: 11 months ago - Pushed at: almost 6 years ago - Stars: 4 - Forks: 12
stolarczyk/metaboLITE
Shiny app for visualization of the toy GENREs
Language: R - Size: 19.2 MB - Last synced at: 2 months ago - Pushed at: almost 4 years ago - Stars: 1 - Forks: 1
CompBtBs/FalseDiscoveriesAnalysis
Adjusting for false discoveries in constraint- and sampling-based differential metabolic flux analysis
Language: Jupyter Notebook - Size: 24.1 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 2 - Forks: 0
pyubero/quantitative_mutations
A class based on COBRApy to handle quantitative mutations on metabolic models.
Language: Jupyter Notebook - Size: 1.18 MB - Last synced at: almost 2 years ago - Pushed at: almost 3 years ago - Stars: 0 - Forks: 0
findCP/findCPcli
findCP CLI package - find ChokePoint reactions in genome-scale metabolic models
Language: Python - Size: 5.6 MB - Last synced at: 5 days ago - Pushed at: over 3 years ago - Stars: 3 - Forks: 0
ElshaymaaAhmed/Computational-Biology-Techniques2-Final-Project
Pathways That Harvest Chemical Reactions
Language: Jupyter Notebook - Size: 8.32 MB - Last synced at: about 2 years ago - Pushed at: almost 3 years ago - Stars: 0 - Forks: 0
ElshaymaaAhmed/Build-Model-Task-One
Computational Biology Techniques 2, Glucose Pathway
Language: Jupyter Notebook - Size: 64.5 KB - Last synced at: about 2 years ago - Pushed at: about 3 years ago - Stars: 0 - Forks: 0
biosimulators/Biosimulators_COBRApy
COBRApy biochemical network simulation program via BioSimulators-compliant command-line interface and Docker container
Language: Python - Size: 2.26 MB - Last synced at: 1 day ago - Pushed at: about 3 years ago - Stars: 2 - Forks: 0
Cognition-Flux/NAMU2021b_old
Proyecto para las redes metabolicas humanas.
Language: HTML - Size: 317 MB - Last synced at: about 2 months ago - Pushed at: almost 4 years ago - Stars: 0 - Forks: 0
findCP/findCPcore
findCP core package - find ChokePoint reactions in genome-scale metabolic models
Language: HTML - Size: 8.97 MB - Last synced at: 29 days ago - Pushed at: over 3 years ago - Stars: 1 - Forks: 0
earmingol/cobra_utils
Utility to simplify obtaining information from genome-scale models as well as their manipulation. This implementation is available only for working with COBRApy.
Language: Jupyter Notebook - Size: 1.66 MB - Last synced at: 29 days ago - Pushed at: about 5 years ago - Stars: 1 - Forks: 1
gulermalaria/iPfal17_curation
iPfal17 genome-scale metabolic reconstruction; lipid metabolism curation
Language: Python - Size: 155 MB - Last synced at: about 2 years ago - Pushed at: almost 7 years ago - Stars: 0 - Forks: 0
jackmeersman/ComputationalBiologyResearch
Repository of code and information developed for computational biology research at UGA
Language: Matlab - Size: 1.36 MB - Last synced at: about 2 years ago - Pushed at: over 6 years ago - Stars: 0 - Forks: 0
resendislab/cobrame-docker
Docker image for a full ME model stack.
Language: Jupyter Notebook - Size: 8.53 MB - Last synced at: almost 2 years ago - Pushed at: almost 8 years ago - Stars: 0 - Forks: 0