ginkgobioworks / geckopy
Enzyme-constrained genome-scale models in python
☆26Updated last year
Alternatives and similar repositories for geckopy:
Users that are interested in geckopy are comparing it to the libraries listed below
- Dynamic FBA for use with COBRApy metabolic models☆10Updated last year
- A COBRApy extension for genome-scale models of metabolism and expression (ME-models)☆36Updated 6 years ago
- StrainDesign is a python package for the computational design of metabolic networks and based on COBRApy☆42Updated last month
- D3.js based visualizations of cobrapy metabolic models☆45Updated 5 years ago
- Generate biomass objective function stoichiometric coefficients for genome-scale models from experimental data☆27Updated last year
- CBMPy is a Python based platform for constraint based modelling and analysis.☆19Updated 11 months ago
- Enumerating biosynthetic pathways in metabolic networks☆12Updated 2 months ago
- An integrated visual environment for metabolic modeling with common methods such as FBA, FVA and Elementary Flux Modes, and advanced feat…☆54Updated last month
- Computation of Microbial Ecosystems in Time and Space☆23Updated last week
- Python package for building and analyzing models using ModelSEED☆22Updated last week
- This repository contains the definitive copy of the biochemistry and metadata used to construct models using the ModelSEED/ProbAnno appro…☆60Updated 2 months ago
- Python package for creating, calibrating and simulating RBA models☆12Updated last year
- Toolbox for including enzyme constraints on a genome-scale model.☆70Updated this week
- ReFramed: metabolic modeling package☆58Updated this week
- ETFL: A formulation for flux balance models accounting for expression, thermodynamics, and resource allocation constraints☆16Updated 7 months ago
- Repository of tutorials for The COBRA Toolbox☆21Updated this week
- The BiGG Models website server☆82Updated 5 years ago
- GPRuler, an open-source computational framework to automate the reconstruction process of Gene-Protein-Reaction (GPR) rules within metabo…☆11Updated 2 years ago
- CobraMod is a Python 3 open-source package which enables modifying and extending genome-scale metabolic models with metabolic pathway inf…☆14Updated 8 months ago
- Mackinac: A bridge between ModelSEED and COBRApy☆19Updated 6 years ago
- A python implementation of flux balance analysis to model microbial metabolism☆27Updated 2 years ago
- Retrieves kcat data and adds protein allocation constraints to stoichiometric metabolic models according to the sMOMENT method☆14Updated last month
- Metabolic Engineering Workbench☆40Updated 10 months ago
- Python package to study microbial communities using metabolic modeling.☆97Updated last week
- A Python 3 implementation of Thermodynamics-based Flux Analysis☆39Updated 2 months ago
- Pathway-Guided Pruning Reconstruction of Genome-Scale Metabolic Models☆12Updated last year
- A collection of M models downloaded from published studies☆16Updated 9 years ago
- BiGMeC - Biosynthetic Gene cluster Metabolic pathway Constructor☆14Updated last year
- A high-fidelity E. coli RNA-seq compendium☆32Updated 4 years ago
- ☆22Updated 4 years ago