openBF.jl

openBF is an open-source 1D blood flow solver based on MUSCL finite-volume numerical scheme, written in Julia and released under Apache 2.0 free software license.

Docs

• openBF ≦v0.6.3 check this website for documentation and tutorials.
• openBF v0.7+ docs can be built as julia make.jl inside the docs/ folder (this requires Documenter package).

Installation

Provided you already have a Julia v1.x installation (all platforms download and Windows instructions), you can add openBF as

julia> ]
(v1.x) pkg> add https://github.com/INSIGNEO/openBF

test it as

julia> ]
(v1.x) pkg> test openBF

and use it as

julia> using openBF
julia> openBF.runSimulation("<input file name>.yml")

You can also create (MacOSX/Linux only) an openBF alias as

$ echo "alias openBF='cp ~/.julia/v1.x/openBF/main.jl ./main.jl && julia main.jl $1'" >> ~/.bashrc
$ source ~/.bashrc
$ openBF -h
usage: main.jl [-v] [-f] [-h] input_filename

positional arguments:
  input_filename   .yml input file name

optional arguments:
  -v, --verbose    Print STDOUT - default false
  -f, --out_files  Save complete results story rather than only the
                   last cardiac cycle
  -h, --help       show this help message and exit

How to dev

$ git clone https://github.com/INSIGNEO/openBF.git
$ cd openBF
$ julia
julia> ]
(v1.x) pkg> add Revise
(v1.x) pkg> activate .
(openBF) <backspace>
julia> using Revise
julia> using openBF

Ecosystem

• A collection of 1D networks (from literature) solved by means of openBF can be found in the openBF-hub repository.
• The scripts to generate a virtual population of ADAN56s can be found in openBF-db repository.
• openBF badge

Publications

openBF has been used in the following works:

• Melis A. Gaussian process emulators for 1D vascular models. PhD Thesis, 2017.
• Melis A, Clayton RH, Marzo A. Bayesian sensitivity analysis of a 1D vascular model with Gaussian process emulators. International Journal for Numerical Methods in Biomedical Engineering, 2017. DOI: 10.1002/cnm.2882
• Melis A, Clayton RH, Marzo A. A more efficient approach to perform sensitivity analyses in 0D/1D cardiovascular models, CMBE July 2015, Cachan, FR. In proceedings

Have you used openBF for your research? Let us know!

Citation

@misc{openBF.jl-2018,
title={openBF: Julia software for 1D blood flow modelling}, 
url={https://figshare.com/articles/openBF_Julia_software_for_1D_blood_flow_modelling/7166183/1}, 
DOI={10.15131/shef.data.7166183}, 
abstractNote={
openBF is an open-source 1D blood flow solver based on MUSCL finite-volume numerical scheme, written in Julia and released under Apache 2.0 free software license.

See https://github.com/INSIGNEO/openBF for the git repository and https://insigneo.github.io/openBF/ for the documentation.
}, 
publisher={figshare}, 
author={Melis, Alessandro}, 
year={2018}, 
month={Oct}}