In my undergraduate degree we spent a lot of time studying the history of science and development of the scientific method, and its important to convey some of this to students undertaking independent research projects even if they have not studied it so extensively. Following the scientific method gives the research a clear structure and makes the whole process much easier in the long run!

Here is a decent summary diagram of the whole thing from https://www.sciencebuddies.org/ which appears to be designed to help US students with science fair projects, but is nevertheless totally suitable for my purposes here:

The question might come from an observation, from a previously identified gap in the scientific literature, from your disagreeing with something you read in the literature, or it might even arrive while you are brushing your teeth (so I’m told).

One aspect of this procedure that seems to pose difficulties is constructing a testable hypothesis. There are of course some research questions for which it is easier or harder to devise a testable hypothesis but its important, prevents bias in your research, and makes the whole process cleaner and easier to actually execute. A hypothesis is a statement, not a question. Your hypothesis is not the scientific question in your project. The hypothesis is an educated, testable prediction about what will happen, and its important to establish the hypothesis before you start the experiments or data analysis tests as these should be designed to test the hypothesis.

So, the key is that before we set out to answer the research question by performing an experiment and observing what happens, we first clearly identify what we “think” will happen in response to a given set of circumstances.

• We make an “educated guess” about what we expect to happen
  
• We write a hypothesis from this
  
• We set out to disprove the hypothesis using specifically designed tests/experiments/analyses
  

Here are some examples of good, poor and bad hypothesis, also from Science Buddies

Here is a more in-depth blog from Bethan Davies about designing good academic research studies for students: http://www.antarcticglaciers.org/students-3/postgraduate-students/research-design/

And the accompanying seminar that Bethan gave as part of the Association of Polar Early Career Scientists (APECS) webinars (skip to minute 2 where it starts for real):

Bethan also has a useful blog post with more practical advise for completing a BSc or MSc dissertation or thesis: http://www.antarcticglaciers.org/students-3/writing-your-dissertation/