PlantBreedGame is a software implementing a serious game to teach selective breeding via the example of a fictitious annual plant species to students at the master level.
It takes the form of a Shiny application, benefiting from the R programming language and software environment for statistical computing.
This software is available under a free software license, the GNU Affero General Public License (version 3 and later); see the COPYING file. The copyright is owned by the Institut National de la Recherche Agronomique (INRA) and Montpellier SupAgro.
It is versioned using the git software, the central repository being hosted here on GitHub, and the institutional repository being hosted there on SourceSup.
README file is available at https://sourcesup.renater.fr/plantbreedgame/.
You can discover an example online here. But if you want to install the game on your own computer or server, read on!
Before using this game, you need to install R as well as various packages, listed in the file
Then it should work on Unix-like operating systems (GNU/Linux, Mac OS) as well as on Microsoft Windows.
Locally on your computer
- Retrieve the Shiny application, by downloading it as a ZIP archive (then unzip it and rename the directory).
Here is how to do it in a terminal for Unix-like operating systems:
wget https://github.com/timflutre/PlantBreedGame/archive/master.zip unzip master.zip mv PlantBreedGame-master PlantBreedGame
The package can also be installed after cloning the git repository:
git clone firstname.lastname@example.org:timflutre/PlantBreedGame.git
Then, enter into the
PlantBreedGamedirectory; inside, run the script
plantbreedgame_setup.Rmdusing Rmarkdown to simulate the initial data set. It also creates all the necessary files and database for the game to function, and initiate the game with two players, "test" (no password) and "admin" (password
Finally, open a R session, and execute the following commands:
library(shiny) setwd("path/to/PlantBreedGame") runApp()
A web page should automatically open in your default web browser, and you should be able to start playing. See the explanations below in the section "Usage".
To set up your own server
It is highly recommended to start by installing the application on your computer (see the previous section).
First, you need to have a Shiny server installed and running, say, in
We only tested with the open source version, but it should also work with the pro version.
For all this, have a look at the official documentation.
Second, you need to add an application to the server. Start by downloading, for instance in your home, our Shiny application as a ZIP archive or clone the git repository (see explanations in the previous section):
cd ~ wget https://github.com/timflutre/PlantBreedGame/archive/master.zip unzip master.zip mv PlantBreedGame-master PlantBreedGame
Then, create a new directory for the application (let's call it
and copy inside the content of our Shiny application you just downloaded:
cp -r ~/PlantBreedGame-master/* /srv/shiny-server/breeding-game
By default, the Shiny server runs as a unix user named
You hence need to create a unix group, named for instance
breeding, to which the
shiny user can be added (the Shiny server may need to be restarted for this to be taken into account).
Everything inside the
breeding-game directory should be readable and writable for users who are part of the
This is particularly the case for the data set (
data directory, generated by running
plantbreedgame_setup.Rmd, see the previous section).
chgrp -R breeding /srv/shiny-server/breeding-game chmod -R ug+rw,o-rwx /srv/shiny-server/breeding-game
Now go to the URL of the
breeding-game application made available by your Shiny server.
If you encounter an error, look at the log, for instance:
Errors may be due to missing packages, otherwise report an issue (see below). Once all requested packages are installed, you should be able to start playing. See the explanations below in the section "Usage".
Once the application is installed and working, please read the game rules (tab
How to play?) and start by downloading the initial data set as well as example files showing how requests should be formatted (all files listed at the bottom of the tab
How to play?).
Before making any request, such as phenotyping, you need to log in (tab
To get a sense of how the interface works, you can use the "test" breeder with the "tester" status which doesn't require any password and isn't subject to time restriction.
All your files, whether they are inputs for a request or outputs of a request, are available for download in the tab
Identification (once logged in).
But remember that regular players (not testers nor the game master) have time restrictions.
This means that, even if a plant material request is successful, you will have to wait before using your new genotypes in other crosses or before requesting data on it.
Similarly, even if a phenotyping/genotyping request is successfull, you will have to wait before downloading the output file.
For your selection to work, you need to analyze the initial data carefully.
Theory tab can be helpful.
Evaluation tab can be used to compare new genotypes (from different players) with the initial lines.
If you want to organize a real playing session, you need to create as many breeders as there are players or player teams.
For this, you need to log in as the "admin" breeder with the "game-master" status.
Initially, its password is set to
1234, but this can (and should!) be changed via the tab
This tab also allows a game master to create new breeders and sessions, among other things.
You can modify some key parameters of the game, e.g., effective population size, heritabilities, genetic correlation.
For this, you need to edit the setup file
plantbreedgame_setup.Rmd, notably by changing the parameters' values in the sections
Simulate haplotypes and genotypes and
Simulate phenotypes (e.g., subsection
Simulation procedure for trait 1).
As the authors invested time and effort in creating this game, please cite the following letter to the editor of Crop Science:
Flutre, T., Diot, J., and David, J. (2019). PlantBreedGame: A Serious Game that Puts Students in the Breeder’s Seat. Crop Science. DOI 10.2135/cropsci2019.03.0183le
Thanks to Philippe Brabant (AgroParisTech) and Jean-Luc Jannink (Cornell) for their feedbacks.
When encountering a problem with the package, you can report issues on GitHub directly (here).
You can contribute in various ways:
report an issue (online, see the above section);
suggest improvements (in the same way as issues);
propose a pull request (after creating a new branch).