Let's Experiment : Assessment Questions • iBiology

Module	ID	Question
Module 0: (Introduction)
Module 1: An Introduction to Experimental Design
	Q1	In 2-3 sentences, describe an experiment you plan to do (or are currently doing), and would like to use as the basis for the assessments in this course. If you aren’t at the point of doing an experiment, it could be one you’ve already done, one of the featured case studies, or one from your favorite publication.
	Q2	What’s the research question you’re trying to address?
	Q3	Do you have a hypothesis(es)? If so, what is it/are they?
	Q4	How does this experiment (from Q1) address your question/hypothesis? What are the expected outcomes?
	Q5	Why are you doing this experiment? Where does it fall on the “prioritization of experiments” flow chart?
	Q6	What’s the model system you plan to use and why? (e.g., Is the model system readily available in lab? Is it amenable to the technique you wish to apply and/or to the subject you wish to study? Is it appropriately generalizable to your subject of interest?) What are the strengths and weaknesses of the model system given your research question and experimental setup?
Module 2: Key Elements of Experimental Design
	Q7	List the variables in your experiment and identify which ones are independent, dependent, and controlled. a. Independent variables: b Dependent variables: c. Controlled variables:
	Q8	What could be confounding variables in your experiment, and how might you handle them (e.g., control them, randomize samples, etc.)?
	Q9	Describe the controls you plan to include in your experiment?
	Q10	How will the controls you listed above help you analyze and interpret your experiment? Are they addressing any confounding variables?
	Q11	Do you have any internal controls in your experiment? If so, please explain them. If not, justify why they are not practical or necessary for your experiment.
	Q12	List all of the sources of random variation (biological and technical) that you can think of that may interfere with your ability to observe the true effect you are trying to measure in your experiment.
	Q13	How are you going to use replicates to address/account for sources of random variation? – What are your biological replicates? – What are your technical replicates?
	Q14	What’s your plan for repeating the experiment? How many times will you repeat it, assuming it works consistently? Will you use the same or different reagents? Will you do it on a different day or week? What strategies will you employ to ensure you aren’t introducing confounding variables between repeat experiments?
	Q15	How will/did you estimate the sample size you will use (i.e., how many biological replicates?) and why? Will/Did you rely on literature, or perform pilot experiments? Whom will you consult for help?
Module 3: Account for Bias
	Q16	Describe in 3-5 sentences how rigor and transparency will be incorporated into the experimental design of your experiment.
	Q17	For your planned experiment(s), what hypothesis or experimental outcome are you particularly excited about and/or invested in?
	Q18	How do you see this as potentially biasing how you design and carry out your experiment?
	Q19	How is the experiment designed in a way that will “disprove” your hypothesis? What choices have you made in the design of the experiment to account for the possibility that other explanations or hypotheses are “true”?
	Q20	Regarding your own project or set of experiments, how can you ensure you are getting representative sampling and that you are treating your samples or groups equally?
	Q21	For the experiment, what measurement bias might exist? What will you do to remove the bias in how you take measurements? Will you try blinding?
	Q22	For your experiment, what type of measurements will you make?
	Q23	What type of data do you expect to have (e.g., categorical, continuous)?
	Q24	If your data type is qualitative, how will you analyze it?
	Q25	If your data type is quantitative, what type of statistical test are you considering to use and why?
	Q26	Identify a statistician or statistics expert whom you will consult for your experimental design and list their name here.
Module 4: Gear Up to Do the Experiment
	Q27	Provide a link to your experimental protocol (or otherwise identify it). After reviewing it, do you have any questions? Concerns?
	Q28	Have you plotted this experiment over the number hours, days, weeks? Approximately, how long will it take in total to complete?
	Q29	What reagents do you need to acquire or prepare before you start the experiment?
	Q30	Include a list of key reagents and materials.
	Q31	Identify which ones need to be validated or authenticated.
	Q32	How are they going to be validated or authenticated? What methods will you employ to test whether the reagents work and/or are what you think they are?
	Q33	Open up your lab notebook to a random day in the past (say 6 months, if it goes back that far). Read over what you have written. If you had to redo that day’s experiment using only what is written in your lab notebook, could you? Are there things you wish you had included? What would you change about your recordkeeping now that you have thought about it?
	Q34	Find out your institutional and lab guidelines for record keeping and record them here. Are you adhering to those guidelines?
	Q35	Take a recent experiment you have done and write up the experiment (in your notebook or elsewhere) using Neil’s notebook model. Is this how you normally do your notebook? What do you think about Neil’s process? Will you change how you keep your records after seeing this model?
Module 5: Getting the Experiment to Work
	Q36	Are you going to pilot this experiment? Why or why not? If so, how are you going to break this down into a smaller scale, more manageable experiment? What will the pilot look like?
	Q37	When someone says, “I got my experiment to work,” what does that mean to you? Please don’t jump ahead to the next section to get the answer. Just write out the first thing that comes to mind. This question is just to get you thinking ahead of the next unit.
	Q38	What do you anticipate will be the challenges in getting your experiment to work and how might you address them? (Or are you already troubleshooting? If so, how are you approaching your experimental difficulties?)
	Q39	In an experiment you are doing now, list all of the sources of variation that you can think of that may interfere with your ability to observe a true effect from factors of interest.
	Q40	For these sources of noise, what can you do (or what did you do) to minimize the noise?
	Q41	What conditions might you need to optimize and how might you optimize them?
	Q42	Let’s consider the possibility that your experiment works consistently as expected after several repeat experiments. What are you going to do next? What new experiments, new questions, or approaches are you going to do?