Key point – choose a system that recapitulates the aspects of the biological system that you want to investigate (you may not need to model every aspect of biology to answer the question)
Key point – consider research ethics in your model system choice. Is the added benefit you get from using animal/human subjects worth the cost to the subjects?
The decision of model system might be obvious and predetermined but you want to do the best experiment you can in the most appropriate way possible. Don’t fall into the trap of doing things in the same system that you always do without first considering if it really is the best for this specific question!
Model system choice is a decision between
Biological accuracy and complexity
Simplicity and tractability
(tractability = ability to be manipulated)
What do you actually want to know?
For some hypotheses you will only be able to test the questions in the context of the full organism or tissue. However, for other hypotheses, those complex environments will not allow you to unambiguously test your prediction.
Be aware that adding complexity might not only make your experiment longer/more expensive/harder but might also make it harder to interpret.
Next: Choosing between a Correlative or a Manipulative Study.