The standard for open-source GEMs on GitHub
☆22Oct 5, 2026Updated last month
Alternatives and similar repositories for standard-GEM
Users that are interested in standard-GEM are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Generate biomass objective function stoichiometric coefficients for genome-scale models from experimental data☆28Jul 6, 2023Updated 3 years ago
- The aim of this repository is to maintain, refine, and expand the AGORA collection of genome-scale metabolic reconstructions for human gu…☆25Dec 10, 2020Updated 5 years ago
- Genome-scale model for Mus musculus☆14Oct 6, 2026Updated last month
- Scripts to build high-quality genome-scale metabolic model by using a deep neural network to guide gapfilling☆19Oct 14, 2026Updated 3 weeks ago
- Enzyme-constrained genome-scale models in python☆39Oct 25, 2023Updated 3 years ago
- Deploy on Railway without the complexity - Free Credits Offer • AdConnect your repo and Railway handles the rest with instant previews. Quickly provision container image services, databases, and storage volumes.
- ModelPolisher accesses the BiGG Models knowledgebase to annotate SBML models.☆24Jan 28, 2025Updated last year
- memote – the genome-scale metabolic model test suite☆152Aug 14, 2025Updated last year
- Constraint-Based Reconstruction and EXascale Analysis☆46Oct 23, 2024Updated 2 years ago
- The BiGG Models website server☆93Nov 7, 2019Updated 7 years ago
- The consensus GEM for Saccharomyces cerevisiae☆137Updated this week
- ☆27Dec 9, 2022Updated 3 years ago
- A collection of M models downloaded from published studies☆18Feb 18, 2016Updated 10 years ago
- Genome-scale model of Yarrowia lipolytica.☆13Jul 8, 2026Updated 3 months ago
- refineGEMs is a python package inteded to help with the curation of genome-scale metabolic models (GEMS).☆22Updated this week
- Open source password manager - Proton Pass • AdSecurely store, share, and autofill your credentials with Proton Pass, the end-to-end encrypted password manager trusted by millions.
- The COnstraint-Based Reconstruction and Analysis Toolbox. Documentation:☆293Updated this week
- The generic genome-scale metabolic model of Homo sapiens☆176Updated this week
- GPRuler, an open-source computational framework to automate the reconstruction process of Gene-Protein-Reaction (GPR) rules within metabo…☆13Oct 11, 2022Updated 4 years ago
- The RAVEN Toolbox for genome scale model reconstruction, curation and analysis. This repository holds RAVEN 2.x; RAVEN 3 is developed in …☆135Oct 15, 2026Updated 3 weeks ago
- BiGMeC - Biosynthetic Gene cluster Metabolic pathway Constructor☆18May 14, 2023Updated 3 years ago
- A snakemake workflow for benchmarking variant calling approaches with Genome in a Bottle (GIAB), CHM (syndip) or other custom datasets☆13Nov 1, 2026Updated last week
- pymCADRE enables the reconstruction of tissue-specific metabolic models in Python using transcriptomic data and information of the networ…☆14Mar 20, 2024Updated 2 years ago
- This repository contains the definitive copy of the biochemistry and metadata used to construct models using the ModelSEED/ProbAnno appro…☆71Oct 6, 2026Updated last month
- A Java-based software for visualizing and translating the KEGG PATHWAY database. Conversion of KGML files into BioPAX, SBML, GraphML, GML…☆22Jun 26, 2023Updated 3 years ago
- GPUs on demand by Runpod - Special Offer Available • AdRun AI, ML, and HPC workloads on powerful cloud GPUs—without limits or wasted spend. Deploy GPUs in under a minute and pay by the second.
- Python package for building and analyzing models using ModelSEED☆31Feb 11, 2026Updated 8 months ago
- Open source genome-scale metabolic models of human and model animals☆28Updated this week
- ReFramed: metabolic modeling package☆63Jun 26, 2026Updated 4 months ago
- Differentiable constraint-based metabolic models☆14Oct 15, 2026Updated 3 weeks ago
- cameo - computer aided metabolic engineering & optimization☆129Nov 7, 2022Updated 4 years ago
- ☆52Jun 11, 2025Updated last year
- A compact metabolic model of Escherichia Coli core and biosynthetic metabolism☆14Mar 17, 2026Updated 7 months ago
- FLYCOP (FLexible sYnthetic Consortium OPtimization)☆12Sep 24, 2018Updated 8 years ago
- Mass Action Stoichiometric Simulation (MASS) Toolbox☆13Aug 1, 2017Updated 9 years ago
- Simple, predictable pricing with DigitalOcean hosting • AdAlways know what you'll pay with monthly caps and flat pricing. Enterprise-grade infrastructure trusted by 600k+ customers.
- MATLAB Development Tools☆28Sep 27, 2024Updated 2 years ago
- A yFiles-based editor for SBGN diagrams written in Kotlin☆13Apr 2, 2020Updated 6 years ago
- The Systems Biology Ontology (SBO) is a set of controlled, relational vocabularies of terms commonly used in Systems Biology, and in part…☆14May 16, 2023Updated 3 years ago
- High-level, high-performance, constraint-based reconstruction and analysis in Julia☆63Apr 26, 2023Updated 3 years ago
- ☆11Oct 28, 2026Updated last week
- COBRApy is a package for constraint-based modeling of metabolic networks.☆596Updated this week
- SBGN User Website and Developer Wiki (outdated version of the website)☆13Jan 20, 2023Updated 3 years ago