Python package for creating, calibrating and simulating RBA models
☆13Jun 5, 2023Updated 2 years ago
Alternatives and similar repositories for RBApy
Users that are interested in RBApy are comparing it to the libraries listed below
Sorting:
- ETFL: A formulation for flux balance models accounting for expression, thermodynamics, and resource allocation constraints☆16Jul 8, 2025Updated 8 months ago
- Enzyme models that take into account kinetics, allostery and thermodynamics☆28Sep 3, 2024Updated last year
- Python interface for running COMETS simulations and analyzing the results☆15Feb 24, 2026Updated 3 weeks ago
- ReFramed: metabolic modeling package☆63Sep 16, 2025Updated 6 months ago
- Python package for building and analyzing models using ModelSEED☆26Feb 11, 2026Updated last month
- Retrieves kcat data and adds protein allocation constraints to stoichiometric metabolic models according to the sMOMENT method. Also chec…☆17Feb 28, 2025Updated last year
- Efficient random sampling for COBRA models☆14Oct 14, 2021Updated 4 years ago
- An integrated visual environment for metabolic modeling methods such as FBA, FVA and Elementary Flux Modes, and advanced features such as…☆63Mar 13, 2026Updated last week
- cameo - computer aided metabolic engineering & optimization☆123Nov 7, 2022Updated 3 years ago
- CBMPy is a Python based platform for constraint based modelling and analysis.☆20May 12, 2024Updated last year
- Registry of containerized biosimulation tools that support a standard command-line interface☆15Updated this week
- An alternative approach to capture the breadth of cellular functions by performing a functional analysis of existing biological networks.☆15Oct 19, 2022Updated 3 years ago
- Compute strain abundance in a defined microbial community☆10Jul 27, 2023Updated 2 years ago
- EMBL GEMs: A collection of GEnome-scale Models for bacterial species☆30Mar 5, 2019Updated 7 years ago
- agent based modelling☆35Aug 28, 2024Updated last year
- General low-level API☆50Jul 18, 2022Updated 3 years ago
- A cookiecutter template that reflects my favored structure for setting up Snakemake-based analysis pipelines.☆16Jul 25, 2016Updated 9 years ago
- Metabolic Engineering Workbench☆41Jun 9, 2024Updated last year
- Genome scale metabolic models in SBML format☆10Nov 16, 2021Updated 4 years ago
- A snakemake workflow for benchmarking variant calling approaches with Genome in a Bottle (GIAB), CHM (syndip) or other custom datasets☆13Mar 12, 2026Updated last week
- memote – the genome-scale metabolic model test suite☆145Aug 14, 2025Updated 7 months ago
- Causal and probabilistic reasoning with continuous time dynamical systems☆20Aug 29, 2025Updated 6 months ago
- Reproducible Research in Finse☆10Aug 5, 2020Updated 5 years ago
- the toolbox for Microbial and personalized GEM, REactiobiome and community NEtwork modelling☆11Feb 3, 2024Updated 2 years ago
- A machine learning-based tool for predicting metabolic modules in incomplete bacterial genomes.☆23Aug 14, 2025Updated 7 months ago
- CobraMod is a Python 3 open-source package which enables modifying and extending genome-scale metabolic models with metabolic pathway inf…☆16Mar 12, 2026Updated last week
- A collection of tools to work with Illumina's basespace☆13Apr 10, 2019Updated 6 years ago
- Higher-Order Co-occurrence☆12Nov 9, 2021Updated 4 years ago
- A Python 3 implementation of Thermodynamics-based Flux Analysis☆43Jul 9, 2025Updated 8 months ago
- Whole cell model of E. coli implemented with Vivarium☆30Updated this week
- ☆10Oct 21, 2023Updated 2 years ago
- Procedural world game based on raycast rendering and sparse voxel octree technologies with using Vulkan API☆12Updated this week
- Muller diagrams excel at visualizing evolutionary dynamics of a population over time. A common use case, and the intended use case durin…☆13Oct 13, 2020Updated 5 years ago
- Microsoft Azure HPC & Big Compute☆15Aug 18, 2019Updated 6 years ago
- Predict All Links In Ecological Networks☆13Dec 9, 2021Updated 4 years ago
- ☆15Sep 8, 2021Updated 4 years ago
- An online database of variants functionally demonstrated to affect (or not affect) splicing.☆11Mar 20, 2025Updated last year
- A tool for semantics-based annotation and composition of biosimulation models☆20Jan 6, 2023Updated 3 years ago
- Protein common interface databases☆10Apr 13, 2019Updated 6 years ago