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

Outline

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

1. Source Control Management with Subversion - why need an SCM for science, SCM is not only for code (data, plots, writing papers, etc.), introduction to subversion (what is a repository, how to set one up, how to make basic commits, retrieving a past version, seeing diffs, collaboration using svn, 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