BNFO 301 
Introduction to Bioinformatics
Course at a Glance (Strategies): Summaries
Spring 2014 

One or two times over this semester you will be asked to write a summary of one experiment from one research article. At first, this will not be an easy task -- far from it!

Then why do it?

Research articles are the source of scientific truth, but they are exhausting to read,... if you're intent is to understand everything they contain. On the other hand, the task becomes easier if you learn how to extract just what you need from an article to answer your specific question. What you need is a result that addresses your question and an understanding of how that result was obtained. Without the result, you have just a claim with no basis. Without the method, you have no limit on the reach of the result. Without any of that you have no measure of truth, except the reputation of the author. That may be how the world often works, but it's sure not science!

Writing summaries trains you to read articles in this way, to focus on what you need. Each summary you write makes the next one easier, until you are able to write summaries in your head as you read the article. In short, learning how to write a focused summary is learning how to read a research article.

Which article? Which experiment?

  • You are seeking a research article (not news, not review), one of interest to you, possibly related to your proposal.
  • A research article can be recognized by its presentation of actual experimental results (not merely conclusions) and a description of the methods used to obtain them, sufficient to enable someone else to replicate the experiment. If you can't identify both, you haven't found a research article.
  • Find one or more using previously described search strategies.
  • Your life will be easier if you choose an experiment that is relatively self-contained, one that can be described without needing to slog through other experiments in the article.

What if I don't understand half of the experiment?

Don't panic! Focus on the other half, and ask what, if anything is missing from the story you are trying to tell. If you are stumped by a technique used in the article (and this may be a common experience), first ask yourself if you need to understand this technique in order to tell your story. If not, then forget about it. But if you judge the technique to be essential for your understanding (and your reader's understanding) of the experiment you've chosen, then do whatever is necessary to gain the insight you need. Hit the web. Read another article. Talk with your colleagues. Talk with me. Whatever it takes.

How do I write a summary of a research article?

Your summary should be written aimed at an audience of your peers, students like yourself except without the benefit of having experienced this course. Have a specific face in mind as you write. The summary should perform a service for that person.

The summary should consist of a few well organized short paragraphs that address the following:

  • Introduction of problem
    What is the big picture surrounding the experiment? How is that area of general interest logically connected to the question addressed by experiment? What hole existed in our knowledge before the experiment was performed?
     
  • Description of experiment
    Describe how one experiment was performed in sufficient detail that the reader will thoroughly understand the principle. There is no value, however, in providing detail that is useful only in replicating the experiment (e.g. the composition of a buffer, etc). Avoid terms that will be unfamiliar to the reader, or if they're useful, then define them.
     
  • Result of experiment
    Describe what was observed, not the authors' conclusion based on that observation. A figure from the article may be helpful. If you use one, don't be afraid to relabel it to be more easily understood by the reader.
     
  • Observations and connections
    What insight can be drawn from the experimental result? Does it answer the question? Does it have higher implications? It may or may not be useful to briefly relate other results from the paper, but do this only to the extent they illuminate the experiment you've chosen to present.

What NOT to do?

  • Don't ignore your audience. Your audience is people like yourself. I am not your audience. Always ask yourself whether you would have understood last year what you are writing. Write unto others as you would have others write unto you.
     
  • Don't quote. This isn't a literary analysis. Quotations are almost never used in scientific writing, because it is generally the content, not the phrasing, that's important. People are not authorities in science. Nature, as seen through experimental evidence, is the only authority. Cite the work of others -- their experimental evidence -- not their words.
     
  • Don't paraphrase. You might think that paraphrasing is a reasonable strategy. "After all," you might say, "the authors know what they are talking about and I don't." That may be true at the moment, but confusion is a temporary condition and only you can tell your story to your audience. The authors have a much larger story to tell to a much different audience. It's just as likely that you can piece together a coherent and pertinent story from theirs as you could piece together a hummingbird from an F16.

    How to avoid paraphrasing? Easy. Look outside of yourself. Put the paper down and imagine explaining the experiment to a specific person, some colleague. Focus on the needs of that colleague. If you can't meet your colleague's needs, identify why you can't -- what, specifically, are you unsure of? Go back to the article and other resources and fill the hole in your knowledge, then walk away and try again. Finally, write down what you said, including drawings or other visual aids your colleague needed.
     
  • Don't pass your ignorance on to your reader. If you don't understand what the authors are saying, neither will we. Find a way to avoid a topic you're confused by, or if there's no way around it, do whatever is necessary to gain insight.
     
  • Don't merely recite conclusions. Interpretation is fine, but only after you've given us the facts of the matter, the results. What was the actual data?

Examples

  • Here is an example of a good summary.
  • Here is an example of a bad summary.
  • And here's one in between (though not just right).