Scientific computing with Python

Other resources

Example scripts

Some short, annotated pieces of code in Python which will give you a flavour of the range of problems that you can tackle by programming with Python

• Analysis of human mtDNA genome. Demonstrates how to open text file hosted online and manipulate text. Download script
• Counting microbial colonies on an agar plate. Demonstrates displaying images and capturing mouse movement and clicks. Requires PyGame. Download script. Example images: (1,2)
• Automatically resizing images in a directory. Demonstrates automated image editing. Requires pillow (Python imaging library) . Download script. Example images: (1,2)
• Rearranging photographs of yeast cultures. Demonstrates automatic creation of directories, copying of files and pasting images together. Requires the pillow (Python imaging library) which you should install first. Also requires some example files which you should store in a folder on your H:\. Download script, although .zip file already contains script. Script should be in the same directory as images before beginning.
• A window with changing colours. Demonstrates creating windows and drawing text and objects on them using Python. Download script.
• Text to speech. Computer speech for MS Windows via Python. Requires the package pyWin32 which you should install first (for the appropriate version of Python and Windows). It also requires that your computer has the ability to generate sounds (e.g. play music). For this it needs to have a sound card, speakers (and volume turned up!). Download script
• Wordsearch. Text manipulation, creating and shuffling of lists and building arrays with Python. Requires the NumPy package. Download script

Other tutorials

Other online tutorials which are worth looking at if you would like to get a more complete picture of Python's capabilities.

• Code academy Excellent articles and exercises.
• Google code university Python class. Includes several video lectures.
• Python tricks - Learn more advanced Python quickly
• Project Euler - Many simple mathematical problems which can be solved by writing short, elegant pieces of code. Other people's solutions become available after you've solved a problem. This site is not dedicated to any specific programming language but Python is popular and so Python solutions are usually available. Since maths problems are easy to state precisely, this is a good way to practise programming.

Interesting packages

• pillow (Python Imaging Library) - for programmatic manipulation of photographs (e.g. microscopy images)
• NumPy (Numerical Python) - for efficient handling of large arrays
• SciPy (Scientific Python) - a collection of algorithms and mathematical tools for scientific analysis in Python.
• pandas - data analysis tools for Python. Includes useful data objects that are similar to dataframes in R.
• matplotlib - Create scientific plots directly in Python.
• PyGame - good for interactive software, capturing mouse motion etc. Difficult to install under OSX.

Google's pythonxy and Continuum Analytics Anaconda are good ways to install Python together with many useful packages for scientific computing.

Overview ∴ Installation ∴ First Script ∴ Execution ∴ Libraries ∴ Structure ∴ Other Resources

Last updated: April 2016