README.md

CuFluxSampler.jl

Documentation

Flux samplers for COBREXA.jl, accelerated on GPUs via CUDA.jl.

The repository contains the following modules with samplers:

• Affine-combination-directed Hit&Run (module CuFluxSampler.AffineHR)
• Artificially-Centered Hit&Run (module CuFluxSampler.ACHR)

Both modules export a specific function for running the sampler atop COBREXA.jl MetabolicModel structure, typically called sample. See the code comments and documentation for details.

Samplers support many options that can be turned on and off, in general:

• Number of points used for mixing the new run directions in AffineHR may be changed by mix_points parameter, and you can alternatively supply your own mixing matrix in mix_mtx.
• You can turn on/off the stoichiometry checks with check_stoichiometry and tune it with epsilon (in both ACHR and AffineHR)
• You can add tolerance bounds on stoichiometry in order to expand the feasible region a little to allow randomized runs to succeed; see check_stoichiometry and direction_noise_max parameters.
• You can set a seed for the GPU-generated random numbers using seed

Running the package code and tests requires a CUDA-capable GPU.

Acknowledgements

CuFluxSampler.jl was developed at the Luxembourg Centre for Systems Biomedicine of the University of Luxembourg (uni.lu/lcsb). The development was supported by European Union's Horizon 2020 Programme under PerMedCoE project (permedcoe.eu), agreement no. 951773.