Collaborative? Collaborate with whom?
Each of you will be paired off with a member of the international community of cyanobacteriologists for the purpose of a research project to be accomplished this semester. The cyanobacteriologists, though expert in their fields, know little of bioinformatics and nearly nothing of BioBIKE. They will provide the biological expertise and insights into the problem. You will provide the bioinformatic insights and knowledge of BioBIKE.

BioBIKE? What's that?
BioBIKE is an integrated knowledge and programming environment 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.

Research? How will that work?
First of all, you need to make yourself indispensible. You'll do this by learning something about bioinformatics and about BioLingua. Then, later in the semester, you'll make contact with your collaborator to define the problem brought by the collaborator in terms that can be addressed computationally. Initially this can be done through e-mail or phone.

The execution of the project is best done collaboratively in real-time. BioBIKE allows multiple people to sign on to the same space at the same time, so both you and your collaborator can watch the same results as one person or the other tries something out. You will probably be the person who suggests different techniques to get to the desired insight, while your collaborator will probably be the person who will be able to see the big picture more clearly and recognize which results are interesting and which might have trivial explanations.

It may arise during your collaboration that you see what you want to do but don't know technically how to do it within BioBIKE. You may think, if there were some magical way of extracting X from a sequence, then I would be able to get the answer I want. If you don't know that magic, the time has come to consult with me, or with TA Ryan, or the BioBIKE Help Desk, whose job it is to build magical tools that enable biologists to do simple things in simple ways.

The research project is so important that midway through the semester I will cancel half the classes and use that time for individual consulations with you about your projects.

What is the ultimate result?
Ultimate,... I don't know, but over the course of the collaboration, you will learn the background of the problem (the big picture your collaborator can provide) while at the same time your collaborator will learn how to use BioBIKE (the technical know-how you can provide). During the last week of the semester you will present your findings in the form of a web-page, as part of the 2nd Annual VCU Bioinformatics Symposium. More on that later.

Why cyanobacteria?

• I happen to know a good bit about cyanobacteria
• I have a lot of friends who also know a good bit about cyanobacteria
• BioBIKE is set up for cyanobacteria, thus arguably cyanobacteria, more than any other group of organisms, has the most user friendly environment for creative analysis by nonprogramming biologists
• It really doesn't matter what organism you learn on. The principles are the same.