https://github.com/insigneo/openbf-db

openBF population generator
https://github.com/insigneo/openbf-db

Last synced: 5 months ago
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openBF population generator

• Host: GitHub
• URL: https://github.com/insigneo/openbf-db
• Owner: INSIGNEO
• License: other
• Created: 2017-10-09T09:34:06.000Z (over 8 years ago)
• Default Branch: master
• Last Pushed: 2022-12-21T08:56:27.000Z (about 3 years ago)
• Last Synced: 2025-09-07T00:32:27.316Z (5 months ago)
• Language: Jupyter Notebook
• Homepage:
• Size: 6.66 MB
• Stars: 5
• Watchers: 1
• Forks: 2
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

          
# __openBF__-db

[![TUoS](https://img.shields.io/badge/-The%20University%20of%20Sheffield-blue.svg?colorA=ffffff&colorB=009fe3&logo=data%3Aimage%2Fpng%3Bbase64%2CiVBORw0KGgoAAAANSUhEUgAAAA4AAAAOCAMAAAAolt3jAAABsFBMVEUAAABmZplVVYBLPHheUYZJPXlSR3pCOnNgWIdoYI9FPnVMQXc0JGM0KmhEOXI0MW8xMW2Ph6yYkrOWj6%2BOiayinLqWkbIcWJkdWJezrsW2sciclrWmoL0cWpkbXJuCfqQVba4Vba2tqsKBgKWXkbGgm7ioo7%2Bln7umobyppcClob0RdrgSd7ikoLuXkbEeeKwieqmYkrKkn7sAneAAn%2BMBnN8Dn%2BIEj9IEkNQEoOMFi88GicwHnuAInuAVaqkVgrEWa6sWiskYj84ek88mk8wmqOInqOIqhrA4qd45qd87kaA8q988q%2BA9qN0%2Fk51Aqd1CqdxCqd1JnqtNnc9OnKVPnItSmsZUmqZVlsFVnYZVns1bst9ds99ftN9isNtitN9joa1msdtnveZqoaRqrNZqvuZsrdZvk2lylWR0nKZ2oJx%2BfKOBf6WEn5eGr3iIr3eduNWfmbifmrifudWim6mjnKmloLymrz2psTuuqb6uqsOwq8C0taG2tqS4tqy4tra6uTC6ui6%2FsCK%2FsCPBvdHDv9LFwtfGwtjOy9rPzdvUlaHmkpb%2B%2FPz%2B%2Fv7%2F%2FPz%2F%2F%2F9OZpcfAAAAM3RSTlMABQYRExUZHyAgJS8xMTFTVFleZmiJkpOTmp2oqba9wsTFxcfO0dPX3OLj5%2Bf19v39%2Fv4kncL4AAAAvElEQVR4AWNgYBIQV9Q20NdRkOBnZGBg4DExTQ9taIzMMDbhA3PdzMqbmyosXaHc4kCvvHy%2FgAIINzElvL%2B%2FvzcoLQ7E5bX1TOhq624P8bDhBnLZTEwye%2Fr7%2BpNNTFgYgMApJreuprY%2BK94RyOGSlEv19XZx9vFPkpViZ1BRZ7WKdq%2Bsto%2B1ZtZQYhAp1FS2iCopDTaX1yoSZmDgkNHrsAuLcOjUleZkAAGxqtbsnJYyUQYoEFIzMlQVBLEA%2FZgsl9iPrB4AAAAASUVORK5CYII%3D)](https://www.sheffield.ac.uk)

[![INSIGNEO](https://img.shields.io/badge/-INSIGNEO-red.svg?colorA=ffffff&colorB=cf2020&logo=data%3Aimage%2Fpng%3Bbase64%2CiVBORw0KGgoAAAANSUhEUgAAAA4AAAAOCAMAAAAolt3jAAABC1BMVEUAAAD%2FAAC%2FAADMGhrRFxfSHh7VHBzJGxvTISHKICDMHx%2FOHR3RJCTTIyPOISHPICDMHR3NIyPNICDRISHQHx%2FQHx%2FOHx%2FQISHOICDQICDQHx%2FOHx%2FPISHQISHQICDOICDQISHOICDQICDPISHPICDQISHPICDPICDOHx%2FPISHPISHQISHPICDPISHPISHQICDOICDOICDPHx%2FPICDPICDOICDPICDPICDPICDPHx%2FPICDPICDQICDPICDPHx%2FQISHOICDPICDPICDPICDPICDPHx%2FMISHOICDPICDQICDPICDPISHPHx%2FPICDPICDPICDPICDPICDPICDOICDPHx%2FPICDPICDPICDPICDi8V76AAAAWHRSTlMAAgQKCxESExcYGRocHR8gIyRITVFSU1ZYYWJjZGZnaWxucXV5fH%2BAg4SFjI%2BUlZeYqKuusbK2ubrDxcbHycvMzdHU2Nrb4uLl5%2Bnq6%2Bzt7u%2F09vf7%2FP3%2B%2FHERCQAAAKVJREFUeAEdx%2BVCg2AAhtHHAANDMQRD7ECwO7DDjViM7b3%2FK9n4zr9Dxdk6jjc4s02si46kK7tMLGDuW%2Fq%2FvdxZlt5shh7VWhsGTqWvTVYll0q4PjMyy7VuYHQ7nIL98oVMAey183sI9EtNPpzXfz7BV8aHIpi%2Fe3ch1iuHysYxnFxHTDf1bD7xpMKBxa6Kk6WVKFXPY8BLZTQWMMYOHvK%2FZHcS6AOapR0V%2FpSSVQAAAABJRU5ErkJggg%3D%3D)](https://insigneo.org/)

[![CompBioMed](https://img.shields.io/badge/-CompBioMed-yellow.svg?colorA=00&colorB=f4b540&logo=data%3Aimage%2Fpng%3Bbase64%2CiVBORw0KGgoAAAANSUhEUgAAAAoAAAAQCAMAAAAYoR5yAAAA81BMVEUAAAD%2F%2F%2F%2Bqqqr%2F%2F8z%2FzLP%2FyKT%2F1ar%2F4KP%2F9dj%2F5L%2Fm1bP%2F3bv%2Fx4Dw4eHbzJn%2F26%2F52Zn%2FzobQypT%2F6LveyLH%2FyID63d3%2F05P%2Fx3nt19fZzbT%2Fv2Dx0sHk0NDPtX7%2Fxln207D53abEr3f8vFjx1Jz%2FxWP%2FvmL%2FwWT%2Fw0f8vk7t0aj12aLBsnzz0qbTvZritmTAq3vWtF6%2FrIHHr4rJsor6vGPYu3vCsIft17rewJLCq3nw267KtYn%2Fv1vKtJL%2FvFPzz5v547H536P9uE%2FLrG7LsnHGsHbyvmXexIzWq130qkP3y3%2F8tUr3yYD6s0T8sz78tETsoiaWAAAAUXRSTlMAAgMFCg4YGRocHh4gIiMjKCorLS4uNDQ3OT1ISkxPUFFTVldYXV5eYWJkZWdnaGlqamttbW9wcXN1dnh5e35%2Bf3%2BAgYSFio6Sl5ydn6GkqK2fR9KlAAAAd0lEQVQI1zXGRQKCABRAwWdhY3d3t9iJ3d7%2FNC74zmo4H%2FH4AGBxoWIzetKUnDFu321c2vtUrdLx0y5j8oj9u3sPzFL9Ps9K86%2FmSho5FK77sgmglGKamLUA6gH6rkzHDzTcBDfe6BJYO6A4DKdDFmpOQG2PuskfKZ4MqTH%2F64gAAAAASUVORK5CYII%3D)](http://www.compbiomed.eu/)

[![License](https://img.shields.io/badge/License-Apache%202.0-blue.svg)](https://opensource.org/licenses/Apache-2.0)

The code in this repository can be used to generate physiological virtual population of vascular networks. The pulse wave propagation can be simulated with [openBF](https://github.com/INSIGNEO/openBF) solver. The network is based on [ADAN56 model](https://github.com/alemelis/openBF-hub/tree/master/models/boilleau2015benchmark/adan56).

__Requirements__:

- Python + [SALib](https://github.com/SALib/SALib) + NumPy

- Julia + [![openBF](https://img.shields.io/badge/-openBF-red.svg?colorA=ffffff&colorB=008080&logo=data%3Aimage%2Fpng%3Bbase64%2CiVBORw0KGgoAAAANSUhEUgAAABQAAAAOCAQAAACFzfR7AAAA10lEQVQoz4XQIUvDARCG8R%2BCaUEEqwwMwyKCYbImLCp%2BAoPJpMWyYFnfN1BBP4IGk0FkYBkyDYJgkBXTUOcYbFM8g0M3t%2F98rhz3Pnfh6GfKg7bQ8exG1hh2xE%2B9SCeLuT4xlC39RkeKUr1%2B1uWAGMKF%2Be9wW7gzgzX1IS2EhhVIaQnnSj6HlEerCsKrObgeeSeEPfvy7oUzqCaKVzLy3oUnpnWFsi3txIUP6%2BwKdQvIuh2pvdmAUwcyvfdM2PwjNx0mvz3tRAgVOZPGciw0LfqXmprlwdEX%2F8%2BRhjBYrRoAAAAASUVORK5CYII%3D)](https://github.com/INSIGNEO/openBF)

**Explore the virtual population [here](https://obfdb.herokuapp.com/obfdb)**

### How to

- First, the lower and upper bounds for each parameter should be defined. Fill `parameters/*.txt` with parameter ranges (min/max).

- Create SALib input files as

```bash

$ cd parameters

$ python write_ranges.py

$ cd ..

```

- SALib is used to sample input points via the Latin Hypercube method

```bash

$ python setup_simulations.py 

```

This will generate a folder with as many input sub-folder as `N`.

- Simulations can be run as

```bash

$ julia run_simulations.jl 1  

```

Alternatively, on SGE systems, use the batch script

```bash

$ qsub run_array.sh

```

- :clock1: Wait...