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

update it as

julia> ]
(v1.x) pkg> update 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] [-c] [-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
  -c, --conv_ceil  Ceil convergence value to 100 mmHg (default true)
  -h, --help       show this help message and exit

Example

project name: <project name>
results folder: <path/to/your/results/directory>

blood:
  rho: 1060.0 # density
  mu: 4.e-3   # kinematic viscosity

solver:
  Ccfl: 0.9   # Courant number
  cycles: 100 # max number of cardiac cycles
  jump: 100
  convergence tolerance: 15.0 # convergence min error threshold

network:
  - label: <vessel name>
	sn: 1
    tn: 2
    E: 400000 # Young's modulus
    L: 0.04   # length
    R0: 0.012 # lumen radius
    inlet number: 1
    inlet: Q
    inlet file: <inlet filename>
  - label: <vessel name>
  	sn: 2
    tn: 3
    E: 400000
    L: 0.103
    R0: 0.010
    outlet: wk2
  	Cc: 8.2e-11      # peripheral compliance
    R1: 8480000000.0 # peripheral resistance

Plotting

Install Plots.jl

julia> ]
(v1.x) pkg> add Plots
(v1.x) pkg> <backspace>
julia> using Plots

(the first time you run this, the library will be compiled and it may takes several minutes)

plot something

using DelimitedFiles

# open the result files
v1 = DelimitedFiles.readdlm("v1_P.last")
v2 = DelimitedFiles.readdlm("v2_P.last")

plot(v1[:,1], v1[:,end]/133.332, label="v1")
plot(v2[:,1], v2[:,end]/133.332, label="v2")

xlabel!("time (s)")
ylabel!("pressure (mmHg)")

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.
The scripts to generate aged versions of a template openBF model can be found in openBF_ageing.
openBF badge

Publications

openBF has been used in the following works:

Journal Papers

Benemerito I, Mustafa A, Wang N, Narata AP, Narracott A, Marzo A. A multiscale computational framework to evaluate flow alterations during mechanical thrombectomy for treatment of ischaemic stroke. Frontiers in Cardiovascular Medicine, 2023. DOI: 10.3389/fcvm.2023.1117749
Benemerito I, Narata AP, Narracott A, Marzo A. Determining clinically-viable biomarkers for ischaemic stroke through a mechanistic and machine learning approach. Annals of Biomedical Engineering, 2022. DOI: 10.1007/s10439-022-02956-7
Melis A, Moura F, Larrabide I, Janot K, Clayton RH, Marzo A. Improved biomechanical metrics of cerebral vasospasm identified via sensitivity analysis of a 1D cerebral circulation model. Journal of Biomechanics, 2019. DOI: 10.1016/j.biomech.2019.04.019
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

Conference Papers

Ning W, Sharma K, Sourbron SP, Benemerito I, Marzo A. Distinguishing hypertensive renal injury from diabetic nephropathy using MR imaging and computational modelling of renal blood flow, VPH2022 September 2022, Porto, PO In proceedings
Benemerito I, Jordan B, Mustafa A, Marzo A. Quantification of the effects of ageing, hypertension and atherosclerosis on flow reversal during a mechanical thrombectomy procedure, BioMedEng21 September 2021, Sheffield, UK In proceedings
Benemerito I, Narata AP, Narracott A, Marzo A. Pulsatility indices can inform on distal perfusion following ischaemic stroke, CMMBE September 2021, Online event, In proceedings
Benemerito I, Narata AP, Narracott A, Marzo A. Identification of biomarkers for perfusion following an ischaemic event, CMBE September 2021, Online event, In proceedings
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

PhD theses

Mustafa A. An efficient computational approach to guide intervention in treatment of stroke. PhD Thesis, 2021
Melis A. Gaussian process emulators for 1D vascular models. PhD Thesis, 2017.

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}}

AWehenkel / openBF