Constraint-Based Reconstruction and EXascale Analysis

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COBREXA is a toolkit for working with large constraint-based metabolic models, and running very large numbers 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.

Development history of COBREXA.jl.

Quick start guide

A dedicated quick start guide is available for quickly trying out the analysis with COBREXA.jl.

Example notebooks and workflows

Detailed example listing is available here. All examples are also avaialble as JuPyteR notebooks.

• Loading models
• Converting, modifying and saving models
• Exploring model contents
• Generic accessors
• CoreModel usage
• Basic usage of StandardModel
• Model construction and modification
• Flux balance analysis (FBA)
• Extending FBA with modifications
• Flux variability analysis (FVA)
• Gene knockouts
• Restricting and disabling individual reactions
• Parsimonious flux balance analysis (pFBA)
• Loopless FBA
• FBA with crowding
• Growth media analysis
• Maximum-minimum driving force analysis
• Minimization of metabolic adjustment (MOMA)
• sMOMENT
• GECKO
• Hit and run sampling
• Production envelopes

Core concept documentation

Detailed concept guide listing is available here.

• Screening many model variants
• Writing custom optimizer modifications
• Working with custom models
• Extending the models

Functions and types API reference

Detailed table of contents of the API documentation is available here.

• Analysis functions
• Base functions
• Input and output
• Model construction functions
• Types
• Utilities

Contribution guide

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

Acknowledgements

COBREXA.jl is developed at the Luxembourg Centre for Systems Biomedicine of the University of Luxembourg (uni.lu/lcsb), cooperating with the Institute for Quantitative and Theoretical Biology at the Heinrich Heine University in Düsseldorf (qtb.hhu.de).

The development was supported by European Union's Horizon 2020 Programme under PerMedCoE project (permedcoe.eu) agreement no. 951773.