Research... Why do it?
Research... How?
Research... What will it be?
Research... What specific topic?
Research... But I don't know how!

Research... Why do it?
There is a broad consensus that learning is deeper and more persistent when it is done with the whole mind engaged, through active inquiry. Here are reports from two panels that drew the conclusion that the research should be a part of the undergraduate experience:

Boyer Commission on Educating Undergraduates in the Research University (1998). Reinventing Undergraduate Education: A Blueprint for America's Research Universities. Stony Brook, NY.

American Association for the Advancement of Science (2011). Vision and Change in Undergraduate Biology Education: A Call to Action.

What do you say? Well, by your presence in this class and your chosen major (most if not all of you), you evidently think that some brand of science is interesting. And research lies at the heart of science, so you need to know what it's about. And there's no way to do that except by diving in.

Research... How?
Doing research is difficult, even for those with experience at it, and you probably have none. In fact, most of your time in school has been spent doing anti-research -- trusting what other people say. It is not easy to break people of the habit.

We (the sages in the Center for the Study of Biological Complexity) have tried to find a way to ease you into research over the course of your stay at VCU:

• BNFO 251: Phage Discovery Lab - Last year, many of you joined in on a research project to understand the variation in mycobacteriophage genomes. You were given the tools and had ample direction concerning their use. Still there was some room for creativity.
   
• BNFO 491: Molecular Biology Through Discovery - Last semester, many of you learned how to extract truth from research articles, find a question one step beyond what is already known, and develop a proposal for an experiment to address the question. But you didn't actually do the proposed experiment.
   
• BNFO301: Introduction to Bioinformatics - This semester you will conceive and perform a project concerning the comparative analysis of phage genomes. There will be a great deal of room for creativity, both in the conception of the project and its execution.
   
• BNFO392: Guided Research - A semester-long (and preferably longer) engagement with a research project within a group, mentored by a faculty mentor, and interacting with others at VCU and beyond working in the same field.
   
• BNFO420: Applications in Bioinformatics - A focused group project addressing through research over a semester an unsolved problem in bioinformatics.

Research... What will it be?
From centuries of research and a decade of genome sequencing projects, we know a great deal of the plants, animals, and bacteria that compose the biosphere. But lump all of those organisms together, and you still won't come close to the number of viruses on earth. And of this group, we know shockingly little. You and your collaborators will join a nationwide project to make some sense of the diversity of viruses on earth.

We will be focusing on mycobacteriophages, viruses that infect Mycobacteria, a large class of bacteria (you may have heard of some of the nastier sorts, those that cause tuberculosis or leprosy). The reason for this choice is that this group of phages is the focus of a national research effort, including the efforts of our own Phage Discovery Lab. Most of the effort has been devoted towards isolating and purifying new mycobacteriophages and identifying genes within the new phages. Our larger scale analysis adds a new dimension, identifying functional classes of genes and characteristics across the full range of mycobacteriophages and beyond.

Our class will be divided into smaller groups (~5 people), each devoted to some aspect of phage biology. Each member of the group will become an expert on some finer slice of the general area and do computational experiments within that slice to learn something new about phage genomes.

By the end of the semester you will have written and presented a description of your experiments and their results. You will also have posted your results to a website that can serve as a resource for others who study phages.

You can see a bit about the project from the following links:

• Why Study Bacteriophage? - A rationale as to why this is likely the most important thing you can do with your semester
• Mycobacteriophage DataBase - A site summarizing what is known concerning mycobacteriophages, particularly new phages analyzed by classes such as ours
• Hatfull GF (2010). Mycobacteriophages: Genes and genomes. Annu Rev Microbiol 64:331-356. A general review of what is known about mycobacteriophages and the kinds of topics you may address
• PhAnToMe - A loose group of those dedicated to the analysis of phage genomes.

Research... What specific topic?
The topic may be anything related to genome analysis that falls within the focus of your group. That focus will be decided later in the semester, chosen from a list of possibilities.

How to find a specific topic?

READ!!! It is surprisingly easy to reach the periphery of what is known, if you digest a few research articles. You'll be given both encouragement and direction of how to go about doing this.

Research... But I don't know how!
Completing a meaningful laboratory research project within the space of a few weeks would be virtually out of the question, but things move faster on the computer. Your project will be completely computational, so you have a chance.

But learning a programming language to give you that chance -- it seems beyond hope that you could learn enough in the weeks before you get started on the project, unless you are already a programming wizard.

In the best of all possible worlds there should be no difficulty. If you can formulate your questions in a logical way, an intelligent computer should be able to translate them into computer language. We don't yet live in that world, but we will use a knowledge environment, BioBIKE (Biological Integrated Knowledge Environment), that greatly reduces the time required for novice programmers to become productive in genome analysis.

Here's a reference that describes the goals and workings of BioBIKE:

Elhai J, Taton A, Massar JP, Myers JK, Travers M, Casey J, Slupesky M, Shrager J (2009). BioBIKE: A web-based, programmable, integrated biological knowledge base. Nucl Acids Res 37:W28-W32.

It will be a lot of fun.