Open writing projects/Scientific Programming with Python and Subversion/Outline

Outline

• sections marked with '(modular)' can be re-written using a different technology (i.e. git instead of svn)

Introductory remarks

• Why this book
  • motivation - lots of training in what science to do with computers, but little training in how to do it
  • for beginners - assumes no prior knowledge, introduces tools as they are needed in a typical scientific investigation using computers
  • for experienced scientists - introducing new tools to do some of these tasks
  • goal - to make managing projects easier, but more importantly to promote good scientific practice through these methods
• Introduce scientific themes throughout the book
  • Some bioinformatics theme - maybe use an example from one of the NCBI coffee breaks

Source Control Management with Subversion

• What is source control?
  • like Word 'track changes' or wiki 'history' but for all the files in a project.
  • A way to keep a history of every step in a process.
  • Not only for computer code, but for data, plots, paper manuscripts, etc.
• Introduction to subversion (modular)
  • What is a repository
  • How to create a repository
  • How to make bosic commits
  • Seeing differences between versions
  • Retrieving past versions
  • Collaboration using subversion
• Advanced Topics
  • Branching and Merging

2. An Introduction to Python - the basics here

3. Making scientific plots with python - introduction to graphics

4. Crunching numbers with python - numpy, maybe bio examples

5. Unit testing for scientists - introduction to unit testing, why do it, how structure the tests, how can do it with nose

6. Complete case study - wrapping it all together

7. Advanced topic - using SWIG and psyco to speed up python code