https://github.com/KendrickOrg/kendrick

Domain-Specific Modeling for Epidemiology
https://github.com/KendrickOrg/kendrick

dsl epidemiology infectious-diseases mathematical-modelling model-driven-engineering pharo pharo-smalltalk smalltalk

Last synced: about 2 months ago
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Domain-Specific Modeling for Epidemiology

• Host: GitHub
• URL: https://github.com/KendrickOrg/kendrick
• Owner: KendrickOrg
• License: mit
• Created: 2012-03-29T15:37:36.000Z (over 12 years ago)
• Default Branch: master
• Last Pushed: 2022-11-18T10:13:31.000Z (over 1 year ago)
• Last Synced: 2024-05-08T17:31:06.983Z (about 2 months ago)
• Topics: dsl, epidemiology, infectious-diseases, mathematical-modelling, model-driven-engineering, pharo, pharo-smalltalk, smalltalk
• Language: Smalltalk
• Homepage:
• Size: 13.9 MB
• Stars: 47
• Watchers: 12
• Forks: 14
• Open Issues: 76
• Metadata Files:
  • Readme: README.md
  • Contributing: CONTRIBUTING.md
  • License: LICENSE
  • Code of conduct: CODE_OF_CONDUCT.md

Lists

• awesome-pharo - Kendrick - Domain-Specific Modeling for Epidemiology. (Scientific libraries)

README

        


Kendrick

  


    DSL and Simulation Plarform for Epidemiology Modeling

    


    Explore the docs »

    


    


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[![Pharo version](https://img.shields.io/badge/Pharo-10-%23aac9ff.svg)](https://pharo.org/download)

![CI](https://github.com/KendrickOrg/kendrick/workflows/CI/badge.svg)

[![Coverage Status](https://coveralls.io/repos/github/KendrickOrg/kendrick/badge.svg?branch=master)](https://coveralls.io/github/KendrickOrg/kendrick?branch=master)

[![License](https://img.shields.io/badge/license-MIT-blue.svg)](https://raw.githubusercontent.com/KendrickOrg/kendrick/master/LICENSE)

Kendrick provides an embedded Domain-Specific Language and a Simulation Plaform for mathematical epidemiology modeling. It helps epidemiologists craft custom analyses cheaply. It's based on [Pharo](http://www.pharo.org/) and it's open source under MIT licence. Classes of epidemic model include deterministic compartmental models, stochastic individual contact models, and individual-based network models.

Kendrick is based extensively on several Pharo ecosystem tools including [PetitParser](http://www.moosetechnology.org/tools/petitparser) and [Roassal](http://agilevisualization.com/) visualization engine.

[![Screenshot](images/screenshot.png)](https://raw.githubusercontent.com/KendrickOrg/kendrick/master/images/screenshot.png)

## Citation

If you are using Kendrick for research, please cite our work as:

> Mai Anh BUI T., Nick Papoulias, Serge Stinckwich, Mikal Ziane & Benjamin Roche (2019), *The Kendrick modelling platform: language abstractions and tools for epidemiology*, BMC Bioinformatics volume 20, Article number: 312 URL:

https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-019-2843-0

## Documentation

You will find documentation about Kendrick meta-model and DSL here: https://github.com/KendrickOrg/kendrick/blob/master/documentation/meta-model/meta-modelv3.org

A previous version of Kendrick is also described in a chapter of the [Agile Visualization book](http://agilevisualization.com/).

## How to install the development version of Kendrick from github

* Download Pharo 10.0 VM depending of your platform: http://pharo.org/download

* Load Kendrick: Open Pharo 10.0 image then right-click anywhere to open the main menu. Choose Playground to execute script. Paste the script below in Playground, select all then right-click and choose Do it to execute this.

* You need first to update the Iceberg version in your image. See CONTRIBUTING.md for more details.

```Smalltalk

Metacello new

        repository: 'github://KendrickOrg/kendrick';

        baseline: 'Kendrick';

        onWarningLog ;

        load

```