Introduction to Bioinformatics

This repository contains the material created or adapted from other (referred) sources for a first introduction to Bioinformatics using Python, R and jupyter notebooks for the 2nd course in the Degree on Biomedical Sciencesat the Universitat Internacional de Catalunya.

Getting Started

These instructions will lead you to the details needed to run the different tools ion your computer.

Prerequisites

In order to follow the course you are encouraged to install, in this order:

• miniconda

Then, from the terminal (in Mac OS and linux) or from the Anaconda prompt (in windows):

• jupyter notebooks:

  conda install jupyter
  

• required initial Python packages:

  conda install biopython
  

• if you want to clone this repository in your computer (not needed, as you can download individual files and open them in jupyter notebook), you can install GitHub Desktop to make it the easy way.

Tips

Typically, jupyter notebooksare run from the terminal (or the anaconda prompt in windows). If you use Mac you can create an automatorapplication with this simple code:

variable="'$1'"
the_script='tell application "terminal" to do script "nbopen '
osascript -e "${the_script}${variable}\""

ensuring you use bash as the interpreter and you mark the "pass as arguments" option.

Contents of this course

Navigate through the different notebooks in this repository for a thorough (and constantly updated) collection of tips and hints to get into Bioinformatics with Python in a simple manner.

• First General Introduction to Python for neophytes

Authors

• Jordi Villà-Freixa - Initial work - JordiVillaFreixa, 2020

See also the list of contributors who participated in this project.

License

This project is licensed under the MIT License - see the LICENSE.md file for details

Acknowledgments

• Thanks to my former PhD student Michael A. Johnston for providing a compelling collection of initial examples I have used here.