AuthorsM. Causemann, V. Vinje and M. E. Rognes
TitleSoftware and Data for "Human intracranial pulsatility during the cardiac cycle: a computational modelling framework"
AfilliationScientific Computing
Project(s)Exciting times: Extreme modelling of excitable tissue (EMIx), Department of Numerical Analysis and Scientific Computing
StatusPublished
Publication TypeMiscellaneous
Year of Publication2022
PublisherZenodo
Abstract

This repository contains the code, meshes and data required to reproduce the results of the article "Human intracranial pulsatility during the cardiac cycle: a computational modelling framework", M. Causemann, V. Vinje and M.E. Rognes (2022).

The easiest way of getting the code running is based on snakemake and singularity: Installing both (using .e.g conda:  conda create -c bioconda -c conda-forge -n snakemake snakemake singularity) and running snakemake --cores N will run pull a docker image (mcause/brainsim:openblas) and execute all steps on N cores. Note however, that the required computational resources are quite large and unlikely to be met by a desktop computer. Snakemake also supports submitting jobs on a SLURM cluster via the --profile profile_folder_name option. An example of a profile configuration can be found in the ex3 folder.

The complete workflow is defined in the  Snakefile, which hence also provides documentation of the individual steps.

URL{https://doi.org/10.5281/zenodo.6553790
DOI10.5281/zenodo.6553790
Citation Keymarius_causemann_2022_6553790

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