pasna-acr-currbio2021

Original data and analysis code for Carreira-Rosario et al. "Mechanosensory input during circuit formation shapes Drosophila motor behavior through Patterned Spontaneous Network Activity", Current Biology 2021. (https://doi.org/10.1016/j.cub.2021.08.022)

Prerequisites

The analysis code pasna2021 only supports Python3, so in the commands below, the pip and python commands should refer to a Python3 install. You can either install Python3 directly or through a package manager like Conda.

Data

1. Open a terminal, and note the current directory, in which the command below will clone the code from GitHub.
2. Clone pasna-acr-currbio2021:

> git clone https://github.com/ClandininLab/pasna-acr-currbio2021.git
> cd pasna-acr-currbio2021
> cd data

3. Inside the data directory, there are four folders corresponding to data from four main experiment groups. Each group except wt contains a control (ctl) folder and an experimental (exp) folder. Within each folder, there is a .xlsx file containing summary information for each embryo. The fluorescence time course of each embryo is in a separate .csv file.

Analysis Code Installation

1. Go back to the top pasna-acr-currbio2021 directory.
2. Install pasna2021:

> pip install -e .

If you get a permissions error when running the pip command, you can try adding the --user flag. This will cause pip to install packages in your user directory rather than to a system-wide location.

Running the Example Analysis Code

1. If you do not have an installation of Jupyter, install Jupyter Lab or Notebook.

> pip install jupyterlab

2. In a terminal tab, navigate to the examples directory and open one of the Jupyter notebooks. The notebooks contain all the analysis performed for the paper.

> cd examples
> jupyter notebook analyze_wt.ipynb