Introduction to Bioinformatics: Objectives and Strategy of Course

BNFO 301

Introduction to Bioinformatics
Course at a Glance: Objectives...and Why?

Spring 2010

Make progress towards becoming an independent producer of new insights and solutions

Define problems rather than have them handed to you
Gain comfort in reading research articles
Take control over your own education

Understand how bioinformatics lets us see biology in a new light

Adopt a new mindset

Realize that the tools of bioinformatics are within your grasp

Quantitative thinking -- a powerful tool to understand the world
Creative computation -- extend your powers over more than can fit in your mind

Make progress along the long road towards becoming an independent producer of new insights and solutions

Arguably, the most important function of a college education isn't to get a degree, nor to get job next year, but rather to prepare yourself for the rest of your life. Just as learning to read and do arithmetic many years ago made you a more capable person in all aspects of your life, so can many higher order skills that few already possess upon entering college.

Define problems rather than have them handed to you
If ever find yourself working a job where all the decisions are made for you, then it's probably a short term job. Prepare for automation to eventually push you to the unemployment line. Machines beat humans in well-defined repetitive tasks, while humans beat machines in fuzzy problems, where insight is required to figure out what the problem actually is. Like any other skill, finding sense in ill-defined problems takes practice. You will have it.

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 most web pages. Then why do you need to read research articles? If you value your lives, you need to be able to feel comfortable reading the primary literature! Why? I could write for hours on this... In fact, I have.
Take control of your education
Leave school, and you'll find nary a syllabus, nary a multiple choice exam, nary even a grade except in the most basic sense. Whatever you learn will be your choice (learning nothing is also a choice). Can you build your own syllabus? Compose your own exams? Grade yourself? If not, it's time to learn how.

Understand how bioinformatics lets us see biology in a new light

"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.

Realize that the tools of bioinformatics are within your grasp

Quantitative thinking
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.

Creative computation
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. hose 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 can do alone. In particular, it makes possible the exploration of massive amounts of information, which is at the heart of bioinformatics and increasingly at the heart of biology.
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.