COBREXA.jl
- Summary
- COBREXA.jl is an HPC-capable metabolic modeling toolbox, with advanced functionality for simulating microbiomes and bacterial communities.
A separate website is maintained at https://github.com/COBREXA/.
COBREXA.jl was originally produced by PerMedCoE project at LCSB between 2021 and 2024; the maintenance now continues at DSE since the main author moved back to Prague. The software uses a dedicated constraint-based modeling toolkit called ConstraintTrees.jl, Julia language for gaining a combination of user accessibility and performance, and runs large analyses quite effortlessly by leveraging the current HPC technologies.
Documentation and tutorials are available from https://cobrexa.github.io/COBREXA.jl/.
Maintained by
Latest publications
- Multi-omic data fusion reveals the in vivo enzyme kinetics of Vibrio natriegens at the genome-scale (2026)
- COBREXA 2: tidy and scalable construction of complex metabolic models (2025)
- Algebraic differentiation for fast sensitivity analysis of optimal flux modes in metabolic models (2025)
- Interrogating the effect of enzyme kinetics on metabolism using differentiable constraint-based models (2022)
- COBREXA.jl: constraint-based reconstruction and exascale analysis (2022)
Research topics
Bioinformatics
Bioinformatics sits on the interface of computer science and molecular biology where it helps to manage, understand and analyze biological and biomedical data. Our research in bioinformatics focuses on the development of software tools applicable mainly in the domain of structural bioinformatics and visualization. These include tools for protein binding site detection, with the application in computational drug discovery, or tools for visualization of the structure of macromolecules. All our methods are implemented as software solutions used by thousands of users all over the world. Most of our tools were first implemented as bachelor or master thesis in our department.
Research Software Engineering
Optimization of scientific code to allow scientific breakthroughs.