Research project... What is it?
Research... Why do it?
Research... How to start?
Research project... How?!?!?

Research project... What is it?

By the end of the semester you will have conceived, planned, executed, written up, and presented a research project that you believe extends the world's knowledge of some aspect genome analysis in a significant way. Each project will be yours alone, however, there will be significant points of contact amongst the many projects of you and some of your colleagues. To gain benefit from that overlap, you will meet in small groups (~5 people) to share insights and tricks. The experiments and written report, however, will be your sole responsibility.

The knowledge you gain from your project and present to the world will come from computational experiments that you perform. You will not be able to find the answer to your question on the web for the simple reason that the question you ask has never been asked before (so far as we know).

You can learn more about the research project -- how it will be done, the time-line of events, and the range of topics -- by visiting the Research Project Unit Page.

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.

But no matter what direction your life will head, you will be well served by gaining facility in scientific thought, which ranks right up there with reading, writing, and arithmetic in its life-changing capacity. Just as there's no way to learn how to ride a bike unless you hop on the bike, neither is there a way to learn how to think scientifically, without thinking scientifically, which means doing research (in a broad sense).

Research... How to start?

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 251/252: 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 300: 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 genome analysis. There will be a great deal of room for creativity, both in the conception of the project and its execution.
   
• BNFO 492 and/or 497: Independent Research and/or Research and Thesis - A semester-long (and preferably longer) engagement with an established research group, mentored by a faculty member.
   
• BNFO 420: Applications in Bioinformatics - A focused group project addressing through research over a semester an unsolved problem in bioinformatics.

Research project... 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.