OBJECTIVES

1. Adopt a new mindset
2. Aborb computer programming
3. Add simple calculations to your toolbox
4. Gain comfort in reading research articles

1. Adopt a new mindset -- that of bioinformatics
"Introduction to Bioinformatics"... You've no doubt taken many courses called Introduction to X where you've learned the basic concepts of X, enabling you to move on to Advanced X. You have a pretty good idea what X is going into the course, perhaps through colleagues who are X majors or a high school X course or perhaps even a hard-hitting TV show with a dashing Xologist as the main character.

That's fine when X is a mature field with a well-defined body of knowledge.
X is not bioinformatics.

Some courses focus on how to use state-of-the-art (also known as soon-to-be-extinct) tools.
Not this one.

Some focus on the timeless precepts behind bioinformatic tools.
That's a different course.

We will focus instead on something you can take away and use now and twenty years from now: the viewpoint of bioinformatics. The only way I know to help you grasp that viewpoint is to put you in a situation where you're using that viewpoint through problem-solving and within an actual scientific project. So that's what we'll do.

Much of the first half of the course will be devoted to getting you to a position where you can work productively on the Project, which will occupy most of your time the second half of the course.

2. Absorb computer programming, bioinformatics' most basic tool
Without understanding how the psychologist's contraption works, a dog paws the lever (or maybe paws the air), hoping for a reward. Without understanding how computer programming works, biologists paw glitzy applications, hoping for results. Without the ability to program the computer to do what you want it to do (rather than allow it to program you), you're pretty much stuck on the sidelines to cheer.

Those of you who have become comfortable in programming a computer will find it as difficult to imagine not being able to do so as to imagine not being able to do long division. Those of you who have never programmed will be delighted to discover that learning long division is the more difficult task. You who do not know a programming language will know one (BioBIKE) by the end of the course.

The combination of a digital computer and a creative human can do amazing things that neither could do alone. In particular, it makes possible the exploration of massive amounts of information, which is at the heart of bioinformatics.

However, this is not a course in computer programming. To learn how to make a computer work reliably, efficiently, and beyond reach of the idiocies of foolish humans is the subject of long study, a study few want to undertake. But just as you all learned how to write (but not necessarily write great poetry), in this course you will all learn how to create for yourself basic but extremely useful shopping-list computer programs.

3. Add simple calculations to your toolbox
Nature sets traps for the unwary, and in bioinformatics, she sets BIG traps. Quantitative thinking is our best defence. I'm not talking about fancy math. I've probably had fewer classes and know less higher math than most of you in this class. I mean simple high school math, applied daily to the world around you. Probability (i.e., creative counting) will pop up time and again through our bioinformatic travels.

I don't count statistics as simple math, but they can be understood intuitively, and they can protect us from idiocy. Unfortunately, without an intuitive understanding of them, they often produce idiocy themselves. Periodically we'll examine common statistics to try to understand what they really mean, then we'll use them to our advantage.

4. Gain comfort in reading research articles
Research articles are difficult to read. It's much easier to have someone else read them and tell you what they said. Textbooks do this. So do web pages. Then why do you need to read research articles?