CobraMod is a Python 3 open-source package which enables modifying and extending genome-scale metabolic models with metabolic pathway information from various metabolic pathways databases or user-curated data sets.
☆18May 11, 2026Updated 4 months ago
Alternatives and similar repositories for cobramod
Users that are interested in cobramod are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- refineGEMs is a python package inteded to help with the curation of genome-scale metabolic models (GEMS).☆22Sep 7, 2026Updated last week
- StrainDesign is a python package for the computational design of metabolic networks and based on COBRApy☆53Sep 12, 2026Updated last week
- Uncover organisms' metabolic blueprints☆18Jun 18, 2024Updated 2 years ago
- An integrated visual environment for metabolic modeling methods such as FBA, FVA and Elementary Flux Modes, and advanced features such as…☆70Updated this week
- Python package for building and analyzing models using ModelSEED☆31Feb 11, 2026Updated 7 months ago
- 1-Click AI Models by DigitalOcean Gradient • AdDeploy popular AI models on DigitalOcean Gradient GPU virtual machines with just a single click. Zero configuration with optimized deployments.
- ReFramed: metabolic modeling package☆64Jun 26, 2026Updated 2 months ago
- mergem is a python package and command-line tool for merging, comparing, and translating genome-scale metabolic models☆15Aug 20, 2025Updated last year
- FLYCOP (FLexible sYnthetic Consortium OPtimization)☆12Sep 24, 2018Updated 7 years ago
- ☆20Aug 29, 2025Updated last year
- Metabolic Engineering Workbench☆43Jun 9, 2024Updated 2 years ago
- EMBL GEMs: A collection of GEnome-scale Models for bacterial species☆34Mar 5, 2019Updated 7 years ago
- COnstraint Based Reconstruction and EXascale Analysis (in Julia)☆19Sep 26, 2025Updated 11 months ago
- This repository contains all source code in the reconstructor python package, installation instructions, important file dependencies, and…☆26Feb 6, 2026Updated 7 months ago
- Retrieves kcat data and adds protein allocation constraints to stoichiometric metabolic models according to the sMOMENT method. Also chec…☆17Feb 28, 2025Updated last year
- AI Agents on DigitalOcean Gradient AI Platform • AdBuild production-ready AI agents using customizable tools or access multiple LLMs through a single endpoint. Create custom knowledge bases or connect external data.
- cameo - computer aided metabolic engineering & optimization☆129Nov 7, 2022Updated 3 years ago
- Pathway-based and phylogenetically adjusted quantification of competition and cooperation between microbial species☆20Mar 17, 2021Updated 5 years ago
- ☆24Oct 19, 2023Updated 2 years ago
- Curation and analysis of metabolic models☆37Aug 8, 2023Updated 3 years ago
- SMETANA: a tool to analyse interactions in microbial communities☆74May 6, 2025Updated last year
- Protocol for finding informative protein families and then using them to score metagenomic sets.☆10Oct 11, 2021Updated 4 years ago
- Constraint-Based Reconstruction and EXascale Analysis☆46Oct 23, 2024Updated last year
- Package that facilitates pulling database entries from KEGG via its REST API☆14Aug 12, 2026Updated last month
- Pathway-Guided Pruning Reconstruction of Genome-Scale Metabolic Models☆13Nov 28, 2023Updated 2 years ago
- AI Agents on DigitalOcean Gradient AI Platform • AdBuild production-ready AI agents using customizable tools or access multiple LLMs through a single endpoint. Create custom knowledge bases or connect external data.
- Constraint-based Metabolic Modeling Course☆12Jul 25, 2022Updated 4 years ago
- Scripts to build high-quality genome-scale metabolic model by using a deep neural network to guide gapfilling☆19May 26, 2026Updated 3 months ago
- A simple python web app to visualise google location history☆16Jul 16, 2024Updated 2 years ago
- The sources of the web LFortran GUI interface☆15May 6, 2026Updated 4 months ago
- An implementation of genome-scale model reconstruction using Cost Optimization Reaction Dependency Assessment by Schultz et. al☆26Jul 15, 2024Updated 2 years ago
- C++ lossless and lossy mass spectrometry compression☆15Sep 16, 2021Updated 5 years ago
- A two-phase (water + gas) reactive transport model, written in Julia, that also simulates geochemical reactions between water-gas-mineral…☆13May 8, 2017Updated 9 years ago
- Python package for creating, calibrating and simulating RBA models☆14Aug 19, 2026Updated last month
- CarveMe: genome-scale metabolic model reconstruction☆222Sep 12, 2025Updated last year
- Managed Database hosting by DigitalOcean • AdPostgreSQL, MySQL, MongoDB, Kafka, Valkey, and OpenSearch available. Automatically scale up storage and focus on building your apps.
- An alternative approach to capture the breadth of cellular functions by performing a functional analysis of existing biological networks.☆16Oct 19, 2022Updated 3 years ago
- A tutorial on cobrapy☆10Sep 1, 2026Updated 2 weeks ago
- The funny insult device for everyday use.☆16May 10, 2026Updated 4 months ago
- Need a quick way to make sure your design/diagram/figure is color blind-friendly? Use this simulator to check out if your colors will ret…☆12Oct 31, 2020Updated 5 years ago
- Visualization of metabolic models in Makie.☆21Feb 15, 2025Updated last year
- A pipeline to identify BLAST hits and perform phylogenetic analysis across multiple queries and local genome databases☆28Sep 11, 2026Updated last week
- Whole cell model of E. coli implemented with Vivarium☆32Updated this week