3.5 - Do : Learn about reproducible research and research ethics

As a technical and scientific expert, you offer the world something unique and important: the ability to use tools like software and statistics to discover and interpret facts about the world. 

As you develop greater expertise, you'll also build the ability to advise others on how to analyze and interpret data. Not only that, you'll be able to assess what other people say. You'll build the ability evaluate claims other people are making about data.

As you gain greater expertise, it's important for you to know about professional standards and ethics.

You especially need to know about professional standards and ethics before you start working full time in the field. This is because, unfortunately, from time to time, people in our field face situations where our coworkers or superiors are making incorrect statements, either on purpose or by mistake.

Being wrong is not an ethical lapse. In fact, the most productive and celebrated researchers are often wrong. Being wrong is part of doing research. However, many researchers fall prey to the temptation to insist that our interpretation or results are correct even when we know that they are not. This is possibly the worst thing a scientist can do, because the entire point of being a scientist is finding the truth.

So, before you go much further in your bioinformatics educational journey, we are going to take a little time for you to get familiar with tools and concepts you can use to avoid getting into hot water, ethically speaking. 

For this assignment, please read the following materials:

(1) On being a scientist: Responsible conduct of Research Links to an external site., focusing on chapters related to reporting data, research misconduct, sharing of research results, conflicts of interest (pp. 43 - 47), and the role of the researcher in society. 

(2) Then, please watch the lectures by Keith Baggerly, where he describes how he and his colleagues discovered a problem with a cancer research study involving bioinformatics. 

(3) Then, read the article about a medical student who also noticed problems with this work. His story gives you a real-world example of how someone without a lot of seniority coped with the realization that his research supervisor's research findings were incorrect.

(4) Last but not least, read the section on literate programming from: The five pillars of computational reproducibility: bioinformatics and beyond.

After reading the above, write your answers to the following questions:

(1) What prompted you to become a scientist and/or an engineer? 

(2) What are your professional goals -- what would you like to be doing professionally in the three or years after you finish your degree?

(3) Read the case studies from pp. 8 - 18 (Treatment of Data, Mistakes and Negligence, and Research Misconduct" from On being a scientist: Responsible conduct of Research. Links to an external site. Pick one case study where you feel like you have a strong sense of what to do in the situation. Write about what you think of the situation and how you would handle it if had happened to you.

(4) Describe how mastering literate programming (R markdown or Jupyter notebooks) can increase your credibility as a researcher and help you gain the trust and respect of your superiors and peers. Tip: Review the endings of Dr. Baggerly's talks.