You can't really understand an experiment until you do it yourself. And without an understanding of the experiment, you can't really understand the limitations of the results: What are the likely sources and magnitude of error? How dependent is the experiment on the experimental system? And so, you can't really understand the implications of the results. Unfortunately, you can seldom run to the lab and perform the experiment you just read about, even if you have a lab well equiped with the tools of molecular biology.

But bioinformatics is different. Experiments that rely on computation and digital data (a greatly increasing number of biological experiments) can often be replicated by anyone with a computer and the will to do so. I can't tell you how many times I've stared dimly at an article until I powered up the computer and did the experiment myself. Then the lights flashed.

We're focusing on molecular biology this semester, not bioinformatics. Nonetheless, I will make every attempt to give you the opportunity to perform (in some sense) the experiments you read about. Sometimes the experiment can be simulated on the computer. Other times it is possible to at least analyze the data. Expect, one way or another, to do what you read, as much as possible.

Some simulations will be done within an integrated molecular biology/programming environment called BioBIKE. There's no need for you to learn how to program -- this semester (but wait until next...). I'll be doing almost all the programming myself necessary to make the simulations work.

If you want to read more about what BioBIKE is all about and how it works, here are some links:

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. Nucleic Acids Research (2009) 37:W28-W32

Elhai J (2011). Humans, Computers, and the Route to Biological Insights: Regaining Our Capacity for Surprise. J Comp Biol 18:867-878.