The Oxford University Clinical Research Unit (OUCRU) in Hanoi is a small research group split across two sites – The National Hospital for Tropical Diseases (NHTD), and the National Institute for Hygiene and Epidemiology (NIHE). The group is involved with a range of research activities, mainly related to infectious diseases, with a particular focus on antibiotic resistance, vaccine-preventable diseases and influenza. It is also largely involved in translating research results into actionable policies, together with the Ministry of Health.
Our group is involved in a lot of population-based research around antibiotic use and antibiotic resistance. Levels of antibiotic use in Vietnam are very high, leading to the emergence and spread of bacterial strains that are resistant to antibiotic therapy.
Streptococcus pneumoniae is a bacteria that is commonly found inside the nose and throat, and usually does no harm. When this bacteria gets into the wrong places it can cause a clinical infection, such as pneumonia. If the strain of bacteria responsible for this infection is resistant to antibiotic therapy, the infection can become very difficult to treat.
We would like to develop an agent-based model to explore the emergence and transmission of resistant strains of S. pneumoniae in the community, and how this is related to current patterns of antibiotic use. Further, we would like to explore the potential effect of introducing public health interventions that may target the emergence of resistant strains (e.g. behavior-change interventions targeting unnecessary antibiotic use), or the transmission of resistant strains (e.g. vaccination, hand hygiene).
To do so, we will use the GAMA Platform. GAMA (GIS Agent-based Modeling Architecture) is an open-source software which has been developed with a very general approach, and can be used for many applications domains. GAML is the language used in GAMA, coded in Java. It is an agent-based language, that provides you the possibility to build your model with several paradigms of modeling. It is developed by several teams under the umbrella of the IRD/UPMC international research unit UMMISCO.
- A working GAMA Platform version above GAMA 1.8 RC 2 installed
- A clone of this repository unziped on your computer
You should start GAMA and set the root of the project (/path/to/OUCRU-Gama) as the workspace :
And start GAMA normaly with this.
In the main view, open the main.gaml file from the explorer on the left panel and press the green button main on top of the text editor
This will change the view from the editor view to the simulation view :
And from this view, you just have to press the green play button (
- GAMA Platform 1.8.0 - GAMA is a modeling and simulation development environment for building spatially explicit agent-based simulations.
- GAMA Language (GAML) - Custom high level language to create models with GAMA.
- OpenJDK 8 or Oracle JDK 8 - The Java Development Kit is an implementation of either one of the Java Platform released by Oracle Corporation in the form of a binary product.
Please post issues about that project here:
https://github.com/RoiArthurB/OUCRU-Gama/issues
Pull requests are welcome. For major changes, please open an issue first to discuss what you would like to change.
Please make sure to update tests as appropriate.
- Arthur Brugiere - Initial work - RoiArthurB
See also the list of contributors who participated in this project.
This project is licensed under the GPL3 License - see the LICENSE.md file for details