COBREXA.jl: COnstraint-Based Reconstruction & EXa-scale Analysis

COBREXA.jl is a Julia package for high-performance huge-scale constraint-based reconstruction and analysis of biological models at the exa-scale. This package allows billions of individual genome-scale metabolic models to be constructed simultaneously, and makes analysis of the resulting trillions of reactions straightforward and efficient. We will show the functionality of COBREXA.jl on biological datasets, demonstrate the user interface, and highlight where and how COBREXA.jl addresses current

The primary purpose of the newly developed COBREXA.jl package is to facilitate the construction and analysis of community-sized, genome-scale metabolic models in high-performance computing (HPC) environments. By taking advantage of Julia's rich ecosystem of high-performance computational tools, as well as many language features unique to Julia, we enable the massively parallel processing of constrained-based metabolic models. This unlocks the ability to screen vast amounts of organism variants and generate novel biological insights about large-scale communities of microorganisms. We will demonstrate the flexible user interface and the scalability of the package, utilizing an HPC cluster for demonstration. Additionally, we will showcase the new SBML.jl package for loading and working with the models stored in the community standard Systems Biology Markup Language (SBML). Finally, we will highlight some easily achievable results on concrete multi-organism models using this interface.

See also: The poster PDF (2.0 MB)