A Quick Guide to Organizing Computational Biology Projects
http://www.ploscollections.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000424
The purpose of this article is to describe one good strategy for carrying out computational experiments. It will focus on relatively mundane issues such as organizing files and directories and documenting progress. These issues are important because poor organizational choices can lead to significantly slower research progress.
The book Practical Computing for Biologists by Steven Haddock and Casey Dunn is a very informative book, find at
Practical Computing for Biologists http://practicalcomputing.org/
This NCBI handbook is useful and very informative https://www.ncbi.nlm.nih.gov/books/NBK21101/