Philosophy of course
At whom is the course aimed?
Weekly events

Plausibly Asked Questions (PAQs):

What about me? I don't know anything about computer programming!

What about me? I don't know anything about molecular biology!

What about ME? I DO know {molecular biology|computer programming}.
Am I going to be bored out of my mind?

What is bioinformatics anyway?

A survey of basic tools through solving specific scientific problems

"Introduction to Bioinformatics"... sounds like you're going to get a panoramic view of the bioinformatic arts and a guide to the most important concepts that need to be mastered. No doubt, concepts are important and panoramas are exciting - and I'll try my best to keep them coming - but to my point of view, they are largely beside the point. To me, the course will have been successful not if you have mastered a body of knowledge by the end of the course, but if in twenty years time you have the tools to master a new body of knowledge, one that we can scarcely imagine.

For this reason we will not focus on how to use state-of-the-art (also known as soon-to-be-extinct) programs. We will focus instead on the basic tools of bioinformatics that will never go out of season, addressing them in the same way you might in twenty years: as a way to solve a new problem. From the start, you will solve actual scientific problems using the tools of bioinformatics. The background necessary to understand the problem and the solution will be provided as needed. (click here for more on the critical role of problem sets in this course).

By the end of the semester, you will have experienced from the inside a dozen or so examples of how bioinformatics can be useful in helping us understand the world and will have learned many of the most important concepts of bioinformatics, not as abstract ideas but built up by the needs of the challenge at hand, with the visible power to solve critical problems in biology.

Computer programming, the most basic tool

Of all the tools of bioinformatics, computer programming for one's own use is the most powerful. Fortunately, it is also very easy to learn, much easier than, say, high school mathematics. Learning this fundemental tool of bioinformatics allows you to see how the other tools really work and to manipulate them for your own uses. You who do not know a programming language will know one (Perl) by the end of the course. You'll learn it by modifying premade, workable programs, at first little parts and later major chunks. Developing the skill of reading programs and writing parts of them will enable you to make use of the large library of code available from many sources, often useful but usually doing not quite what you want.

At whom is the course aimed?

Those who are proficient in an area overlapped by bioinformatics:

• Molecular biology
• Computer science
• Biostatistics
• (others)

 
• Those who wish to use this proficiency as an entry point into bioinformatics

• Focus on a specific scientific problem taken from the literature or from experience
• Introduction of a commonly used bioinformatics tool that can solve the problem
• Explanation of molecular biology concepts necessary to understand the problem
• Explanation of computer programming concepts necessary to construct, modify, and thereby understand the tool
• Problem sets designed to introduce new concepts, integrate them within a real life context, and to solve the problem at hand

First of all, programming is a lot easier than you think, so long as you don't have to worry about complicated user interfaces. Second, a little knowledge can go a long way. There's quite a lot you can do through simple programs or modifying programs written by others. We will focus on learning how to understand what the critical part of the program is trying to do to the extent that you can change it to do what you want it to do. The course will isolate portions of a program for you to play with, reducing the flow of concepts to a manageable rate.

What about me? I don't know anything about molecular biology!

Fortunately, molecular biology is basically simple, because biological molecules tend to behave the way the world of our daily acquaintance behaves. While there is an incredible amount of molecular biology you COULD learn, you need to know very little of it to understand what's behind a specific biological problem. We'll feed you that little bit each week, and by the end of the semester you'll see that there are core concepts you run across time and again, and there are specific facts that you can readily learn as needed and forget when the time has passed.

What about ME? I DO know {molecular biology | computer programming}.
Am I going to be bored out of my mind?

I doubt it. You who know molecular biology will serve as course TA's to help those who don't. Likewise, you who know computer programming will serve as course TA's for those new to that art. It is doubtful that ANYone will know all of the molecular biology concepts required to understand all the scientific problems, and many of the algorithms we'll cover will be new even to the computer adept. So, as is often the case, those acting as TA's will be ahead of the students by reason of general background rather than a specific knowledge of the problems at hand, and through the act of teaching, the TA's may learn more than the students.

In addition, there will be problems that require joint expertise, requiring the meeting of minds geared towards biology and minds geared towards computers. Problem solving with others of diverse backgrounds may be useful in achieving one objective of the course: to encourage all students to speak and understand the various languages of bioinformatics.

What is bioinformatics anyway?
One plausible definition:

The application of information technology to the study of biological problems