TeachingJupyterNotebooks

This repository contains resources for the Open Science workshop for teaching about jupyter notebooks.

Clone this repository to your working directory.

git clone https://github.com/BioinfoNet/TeachingJupyterNotebooks.git
Download Anaconda for your operating system for Python 3. Use this link
Follow the install instructions for your operating system. Here are the instructions.
Afterwards, navigate to the directory where the folder is using cd and ls. Then run this command in your terminal

conda env create -f environment.yml

This will create an environment called jupyter-notebook-tutorial. You can activate it like this

`source activate jupyter-notebook-tutorial`

In your terminal, in the directory where you cloned this repository. Run this command

jupyter notebook jupyter-notebook-slides.ipynb

Alternatively, let's get packages which will enable you to use the tools that are demonstrated.

Open your terminal. Type this command to get Nbextensions

pip install jupyter_contrib_nbextensions

jupyter-contrib nbextension install --sys-prefix
Now to get the interactive dataframe tool called qgrid

pip install qgrid
Then get bioconda. This avails tools commonly used for bioinformatics e.g samtools, bowtie and bwa. Follow the steps in this link
To get tools specifically for bioinformatics. Get scikit-bio pip install scikit-bio

The repository has a number of files that constitute elements of the jupyter notebook. They include:

README.md : Markdown text with an explanation of how the user can make use of these resources.
environment.yml: Has instructions to create the same environment the creator has in your own system.
jupyter-notebook-slides.ipynb: Contains the presentation that shows the reader how to use notebooks with bioinformatic examples mostly.
files: Has a variety of files from notebooks, fasta, fastq files among other files.
storeddf.ipynb: Contains created dataframes of counts of specific bases of several microbes 16S rRNA gene.

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