Finding a research topic

1. What is a suitable research topic?
2. How to find a topic?
3. Examples of good and bad topics

A. What is a suitable research topic?

1. It should permit discovery of something new
   This isn't a term report. By the end of the semester, you should have found something, through the activities of your own hands, that has never been found before. That's a major goal of this research project
    
2. It should be amenable to discovery through bioinformatics tools
   (Please see the name of the course at the top of this page)
    
3. It should be related to bacteriophage
   We want to maintain a focus as a class so that we share a common basis for discussion. That focus should intersect with the interests of the Phage Discovery lab so that they're in the game too. We will have a joint symposium with them at the end of the semester. So, topics should focus on bacteriophage, not on bacteria, animals, or plants.
    
4. It should be related in some way to your group topic
   You can learn from your group members and they can learn from you if there is some common core that connects your projects.
    
5. It should be small enough to allow significant progress in the time allowed
   You have only six weeks or so. You can do a lot in six weeks, but in that finite period, you can't reach a satisfying end point if you set the finish line too far away.
    
6. It should be large enough so that your research will be interesting to others
   It should not be focused on some obscure phage, unless that phage is uniquely interesting in a way that has broader implications. Better to broaden the topic to allow comparisons between phages, so that generalities can be drawn.
    
7. It should be focused enough so that you can absorb the entire field
   You will be constructing an exhaustive bibliography of your field, as you have defined it. For this to be possible, the topic must be so focused that your field encompasses a countable number of articles.
    
8. Can you find a research article that accomplishes part of what you propose to do?
   If someone else has done what you want to do, then you know it's do-able. Of course, you also know that your topic isn't new and so you should look elsewhere for a topic. However, if you find an article that describes how to do what you want to do with one phage (or sets of phages), you can draw on the tools presented to ask a similar question with a different phage (or sets of phages). It isn't necessary to find this magic research article, but your life is much easier if you do.
    

B. How to find a topic?

1. Extract ideas from review articles
   On the Research Project page, you'll find a link to your group (click Groups if you need a reminder as to what group is yours). On your group page, you'll find one or more review articles related in some way to the group topic. If you skim these articles, you can find areas of interest that the authors consider to be related to the group topic. One or more of these areas may spark your interest. You might also profit from finding better review articles yourself (here's how).
    
2. Extract research article references from review articles
   One of the primary benefits of a review article is that it provides you with pertinent references, particularly references to research articles. Review articles can save you hours of searching! Look particularly for research articles that sound like they may approach the problem from a bioinformatic angle (though it's often difficult to tell from just the title.
    
3. Search for pertinent research articles
   You'll find nothing more helpful to your project than a good research article (see A.8 above). You can find them using methods you already know. Browse many to search for one or more that use bioinformatics tools to address your area of interest.
    
4. Focus
   Undoubtedly, your first stabs at a topic will be too big. When you use it to search for articles, you'll get thousands. By browsing some of the articles you find, you can ask yourself what key words may more pointedly describe those that are truly of interest to you. Or, if you have no idea at first how to do this, browse the articles for those that sound interesting to you, and use them to focus your project. Experiment with different key words to cut down the size of the topic.
    

C. Examples of bad topics

• "Lysis proteins of bacteriophages"
  Way too big. You wouldn't finish this for years. Focusing on a particular lysis protein would be better, but even that might be too much. Focusing on a particular lysis protein in a particular class of phages might work.
   
• "How do phages replicate their DNA?"
  Way too diffuse. Sounds like the topic of a general term report. It's hard to see what you could hope to discover yourself within this huge umbrella.
   
• "The DNA ligase from the enterobacteriophage RB16"
  Too small. It would be more interesting to focus on the characteristics of DNA ligases from enterobacteriophages in general.
   
• "Restriction enzymes that destroy phage DNA"
  Despite the title, this has nothing to do with any phage protein. Rather, the focus is on bacterial proteins that affect phage. Big difference. You could turn this around and study some mechanism by which phages avoid destruction.
   
• "The big, the bad, and the beautiful"
  Poetic, perhaps, but this topic offers no clue what will actually be studied.