wahura / teachingjupyternotebooks

Training materials for the Open Science Workshop held in Nariobi

TeachingJupyterNotebooks

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

---

Setting Up

• 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

---

Project Structure

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.