Resources

These are online resources of interest for people attending the course.

Programming

Software Carpentry

• Project aiming at improving software skills of scientists for better research

General Python material

• The official documentation
• A list of courses

Testing

• Continuous integration testing with Travis.

Debugging

• A good resource

Writing documentation

• Automatic documentation on the web with Read the Docs

Python module packaging

• Submitting packages to the Python Package Index

Programmer skills

• A programmer skill matrix
• Another view on programmer skills evolution

Version control

Git documentation

• Git website
• The Pro Git book by Scott Chacon
• The reference manual
• Git graphical user interfaces

Workflows

• Using Git with Dropbox
• Using Dropbox as a private GitHub
• What you should not do

Papers about scientific computing

• Noble's "A quick guide to organizing computational biology projects"
• Wilson's "Best Practices for scientific computing"

Website preparation

Software Carpentry has a GitHub repository which explains how to generate a website and host it on GitHub. Jekyll, which is the static site generator of choice for GitHub, is written in Ruby, but Pelican is a good alternative written in Python for that. It uses Pygments for code syntax highlighting. A detailed explanation about how to publish on GitHub with Pelican is available here.

Bioinformatic course existing at Utu

There is a Master's program at UTU on Bioinformatics.

Please note that we do not intend this course to be a bioinformatic course: our objective is only to expose researchers who have to use computer tools for their research but do not have a formal IT education to some key concepts for a better use of their tools.