Put code and data in separate subdirectories.
Plan to separate raw data from processed data.
Always apply the the 5 Cs: be Clear, Concise, Consistent, Correct, and Conformant.
Pick a scheme for organizing data
Tools that capture the experimental environment, such as Docker, ReproZIP, and CDE.
Tools that capture the sequence of the computations such as Jupyter Notebook.
Backup your data files every while.
Use GNU Make to automate the research process.
For writing your manuscript use latex and Bibtex.
Use version control system such as Git
Deposit your data in a repository for long-term preservation.