Python replication for the results from the eLife manuscript:
Gkanias, E., McCurdy, L. Y., Nitabach, M. N. & Webb, B. An incentive circuit for memory dynamics in the mushroom body of Drosophila melanogaster. Elife 11, e75611 (2022).
DOI: 10.7554/eLife.75611
The "incentive circuit" (IC) is a model of the mushroom body in the fruit fly brain that receives sensory input and reinforcements and modulates the motivation state of the animal. In this model, the motivation states are limited into: attraction and avoidance. This repository allows reconstructing the results presented in the original article. Below, you can find information of how to set up the environment and run the examples that generate the appropriate figures.
In order to be able to use this code, the required packages are listed below:
In order to install the package and reproduce the results of the manuscript you need to clone the code, navigate to the main directory of the project, install the dependencies and finally the package itself. Here is an example code that installs the package:
mkdir ~/projects
cd ~/projects
git clone https://github.com/InsectRobotics/IncentiveCircuit.git
cd IncentiveCircuit
pip install -r requirements.txt
pip install .
Note that the pip project is needed for the above installation.
The generate_manuscript is an iPython notebook that reproduces the results for the figures and associates them to the manuscript. If the notebook is not rendering, you can try this link. Alternatively, you can find the scripts that create the plots in the manuscript in the examples directory and run them using:
python any_file_you_want.py --flag --option value
It is necessary to add the src directory to the PATH variable or install the package.
You can reproduce the results by running:
python run_bennett_2021.py
python plot_data.py --stats --only-nids --verbose
python plot_model.py --only-nids --values --weights --verbose
python create_arena_paths.py --nb-flies 100 --nb-time-steps 100 -R 10 --dir "data" --verbose
python plot_arena_fishbone.py -R 10 -V "A and B" --dir "data" --verbose
python plot_arena_fishbone_weights.py -R 10 -V "A and B" --dir "data" --verbose
python plot_arena_paths.py -R 10 --dir "data" --verbose
python run_unpaired_a.py
python run_handler_2019.py
where --only-nids plots only the neurons associated to the incentive circuit;
--values and --weights enable plotting of the responses and KC-MBON synaptic weights of the model over time respectively;
--stats prints the logistics of flies in the data-set;
--nb-flies specifies how many flies to simulate;
--nb-time-steps the number of time-steps per repeat;
-R the number of repeats for each experiment;
--dir the directory where to store or load the data from;
-V specifies which subset of flies to plot, depending on the odours they have visited; and
--verbose allows printing in the console during the processing of the files.
If you have any issues installing or using the package, you can report it here.
The code is written by Evripidis Gkanias.
Copyright © 2022, Evripidis Gkanias; Institute of Perception, Action and Behaviour; School of Informatics; the University of Edinburgh.