Links to related projects and references
Project structure and reproducibility is talked about more in the R research community. Here are some projects and blog posts if you're working in R that may help you out.
- Project Template - An R data analysis template
- "Designing projects" on Nice R Code
- "My research workflow" on Carlboettiger.info
- "A Quick Guide to Organizing Computational Biology Projects" in PLOS Computational Biology
Finally, a huge thanks to the Cookiecutter project (github), which is helping us all spend less time thinking about and writing boilerplate and more time getting things done.