An introduction to solving biological problems with Python

Today's Presenters

09:30-10:00: [0h30] Introduction
10:00-10:30: [0h30] Session 1.1 - Print and Variables
10:30-10:45: break
10:45-12:15: [1h30] Session 1.2 - Simple data types, Arithmetic and Saving code in files
12:15-13:30: lunch break
13:30-14:30: [1h00] Session 1.3 - Collections: Lists and String
14:30-14:45: break
14:45-15:45: [1h00] Session 1.4 - Collections: Sets and Dictionaries
15:45-16:00: break
16:00-17:00: [1h00] Wrap-up

There is a course webpage with links to the materials, example solutions to the exercises etc.:
- http://pycam.github.io
All course materiel is available on GitHub in our python-basic repo
We’d like you to follow along with the example code as we go through the material, and attempt the exercises to practice what you’ve learned
Questions are welcome at any point!
If you have specific projects/problems you like to use Python for we are happy to (try to) help during the exercises

Python is a dynamic, interpreted general purpose programming language initially created by Guido van Rossum in 1991
It is a powerful language that supports several popular programming paradigms:
- procedural
- object-oriented
- functional
Python is widely used in bioinformatics and scientific computing, as well as many other fields and in industry
Python is available on all popular operating systems
- Macs
- Windows
- Linux

Python is considered to come with "batteries included" and the standard library provides built-in support for lots of common tasks:
- numerical & mathematical functions
- interacting with files and the operating system
- ...

Python is an interpreted language, this means that your computer does not run Python code natively, but instead we run our code using the Python interpreter
There are three ways in which you can run Python code:
- Directly typing commands into the interpreter: Good for experimenting with the language, and for some interactive work
- Using a Jupyter notebook: Great for experimenting with the language, and for sharing and learning
- Typing code into a file and then telling the interpreter to run the code from this file: Good for larger programs, and when you want to run the same code repeatedly

How you start the interpreter will depend on which operating system you are using, but on a Mac or Linux machine you should start a terminal and then just type the command python3
This will print out some information about your installation of python and then leave you with a command prompt which looks like >>>
You can then type commands and press Enter when you're done. Python will run the code you typed, and might display some output on the line below, before leaving you with another prompt.
If you want to exit the interactive interpreter you can type the command quit() or type Ctrl-D

We will see later how to save code in a file and run it.

The Jupyter Notebook is a web application that allows you to create and share documents that contain live code, equations, visualizations and explanatory text.
Jupyter provides a rich architecture for interactive data science and scientific computing with:
- Over 40 programming languages such as Python, R, Julia and Scala.
- A browser-based notebook with support for code, rich text, math expressions, plots and other rich media.
- Support for interactive data visualization.
- Easy to use tools for parallel computing.

See Installing Jupyter Notebook
For new users, we recommend installing Anaconda. Anaconda conveniently installs Python, the Jupyter Notebook, and other commonly used packages for scientific computing and data science.
Start the notebook server from the command line:
```
jupyter notebook
```
You should see the notebook home page open in your web browser.