Collaborative? Collaborate with whom? How?
Perhaps there are those who seek out ancient tombs, break them open, and after comprehending what is inside, destroy the contents, so that their eyes may be the only ones to have seen such wonders. We'll define such pathological cases to be outside of science. Instead, science is inherently collaborative, with each individual practitioner generally working on a piece of a puzzle that can be seen more clearly when the pieces are put together. Each of you will be given your own piece to puzzle over, but research is much more enjoyable when you are in contact with your colleagues working on similar pieces as your own. Although We may at times pay visits to outside researchers also interested in the puzzle, your most immediate colloborators will be your colleagues in class who will be given related sequences and use related tools, particularly BioBIKE.

Puzzles... pieces...? What research are we going to to?
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 elements, those that cause tuberculosis or leprosy). The reason for this choice is that another VCU class (BNFO 251/252 Phage Discovery Lab) has spent considerable time isolating and purifying new mycobacteriophages. Our analytical efforts can complement theirs. They are most concerned this semester with making sure that the new DNA sequences are accurate and identifying genes within the sequences. We'll do some of that, but our main effort will be towards a larger scale analysis, identifying functional classes of genes and characteristics across a range of phages, both new and old. Our work will become integrated into the work of others, work by many researchers and undergraduate classes throughout the United States.

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

• 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.

BioBIKE? What's that?
BioBIKE (Biological Integrated Knowledge Environment) is designed to provide biologists with no computer programming experience the opportunity to access and manipulate mass data creatively. It is also the programming language we will use in this course as a teaching tool and as the primary tool in the collaborative research projects.

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.