IBIO-Banyuls2023-Python

Working with Google Colab

Opening Colab

Got to Colab's website, and in the popup window click on Github, then in the seach bar paste the following :

https://github.com/EmeEmu/IBIO-Banyuls2023-Python

You can then select the notebook you want to open, for example day1_discovering_the_data.ipynb.

Downloding the Helper files

In this repo, you will find a buch of helper functions in the sub-directory Helper_Functions. To load them into Colab run the following code in a cell :

!mkdir /content/Helper_Functions/
!wget -P /content/Helper_Functions/ https://raw.githubusercontent.com/EmeEmu/IBIO-Banyuls2023-Python/main/Helper_Functions/accessing_data.py
!wget -P /content/Helper_Functions/ https://raw.githubusercontent.com/EmeEmu/IBIO-Banyuls2023-Python/main/Helper_Functions/hmm_plotters.py
!wget -P /content/Helper_Functions/ https://raw.githubusercontent.com/EmeEmu/IBIO-Banyuls2023-Python/main/Helper_Functions/OrthoViewer.py

Downloading Data

All the data for this Python workshop is located in the following Google Drive. To work on this data from Colab, it needs to be downloaded to Colab's cloud storage.

Within Colab, you can download the entire folder by running the folling code :

!gdown --folder 1k21VhLoonOnoxxXyswrmE45VIB4FF00n

this will download all the files from the Google Drive to /content/banyuls_data/.

You can also download indivual files by providing the unique identifier in the url of the file in the following code. For example, for the file https://drive.google.com/file/d/1jIQw8EEIoS516plFFXtRIwS-0oey7kFt/view?usp=sharing, the identifier is 1jIQw8EEIoS516plFFXtRIwS-0oey7kFt :

!gdown 1jIQw8EEIoS516plFFXtRIwS-0oey7kFt

and the file will be downloaded as /content/fish1_different_directions.hdf5

Setting up Matplotlib for interactive plots

Working with interactive plots in Colab requires a little bit of preparation. You should run the following code :

!pip install ipympl
from google.colab import output
output.enable_custom_widget_manager()
%matplotlib widget

Working locally

Setting up the environnement

conda create --file ibio_env.txt --name ibio