Leave a note for the person returning to the project
That person might be you, two weeks from now. You open a folder and find three versions of the same figure, several prepared structures and a file called final_new. Which one belongs in the report? Start a plain-text README before the project grows. Write down the question, where the inputs came from, and the order of the steps. Sandve and colleagues recommend preserving the information needed to trace and repeat a computational analysis. You do not need an elaborate system to begin following that advice. [1]
Separate inputs, methods and outputs
Try keeping source structures, prepared files, run settings, raw outputs and report figures in separate folders. This is a working suggestion, not a rule about how every laboratory should operate. The important part is that an original download cannot be mistaken for a structure you have edited. Give each run a short identifier and use it in the output folder and your notes. When you compare two runs, write one sentence explaining what changed. The folder names should help you find that sentence again.
Save the software settings
A screenshot of a settings window is better than relying on memory, but a saved configuration or command is easier to reuse. Record the software version and the settings relevant to the calculation, including any random seed. If you adjust a file by hand, leave a note about what you changed and why. Sandve and colleagues specifically discuss random seeds and undocumented manual edits as reproducibility concerns. Make a habit of saving these details when you run the analysis, while they are still easy to retrieve. [1]
Check that someone else can repeat the steps
Before handing over the project, pick one figure and work backwards. Can you find the output behind it, the settings that produced that output, and the original input? Ask a classmate to try using only your README. Anywhere they have to ask you for directions is a useful place to add a note. This exercise checks whether the work can be followed; it does not prove that the scientific conclusion is correct. It does make the next review, correction or follow-up much easier.
A useful research handover explains not only what you found, but how another person can examine the path you took.
Sources & further reading
Educational reading. Illustrations and example data are not Chemizen Labs research results or clinical guidance.