| 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? | |
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