Constraint-Based Reconstruction and EXascale Analysis

COBREXA is a toolkit for working with large constraint-based metabolic models, and a running very large number of analysis tasks on these models in parallel. Its main purpose is to make the methods of Constraint-based Reconstruction and Analysis (COBRA) scale to problem sizes that require the use of huge computer clusters and HPC environments, which allows them to be realistically applied to pre-exascale-sized models.

In this package, you will find the usual COBRA-like functions that interface to underlying linear programming solvers. We use JuMP.jl as the unified interface for many solvers; you can plug in whichever compatible solver you want, including the popular Tulip.jl, GLPK.jl, OSQP.jl, and Gurobi.jl.

history
Development history of COBREXA.jl.

Quick start guide

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Tutorials

Detailed tutorial content is available here.

Example notebooks and workflows

Detailed notebook content is available here.

Functions reference

Contribution guide

If you wish to contribute code, patches or improvements to COBREXA.jl, please read the basic contribution guidelines and hints..