BISC195 - Essential Skills for Computational Biology

This course is designed to teach you practical skills for using code to answer biological questions.

We will largely be learning one programming language in particular - julia - but you will learn concepts and practices that should be relevant to any language (other common languages used in biology are python, R, and perl). No prior experience with writing code is required to do well in this course.

Using this course

This course is paired with lectures, but the written lessons and exercises should stand alone. And even if you are in the lectures, there is a lot of important information contained in the written lessons.

This section explains where to find lesson material, including lessons and assignments, how to read the written material on this website, and how to get the most out of taking this course.

To get the most out of this course, you should:

1. Thoroughly read all of the lesson content. I have done my best to keep lessons concise, with minimal diversions. This keeps things shorter, but it means that most of the content is important. If you skip or skim sections, you may miss important concepts and have trouble completing assignments.
2. Run the code in all "Practice," "Exercise," and "Example" blocks. This will be described in more detail later, but it is imperative that when their are code examples, you run them, and try to understand the output. Programming is more about practice than theory, and if you are only reading, you will not learn.
3. Make your own modifications to code in "Practice", "Exercise", and "Example" blocks. You will learn best by doing. See what happens when you change spelling, leave out parts of a command, or add additional text. Most of the time, this will produce errors, but professional programmers encounter errors all the time. Learning which mistakes lead to which errors is a critical skill in programming. I will warn you when going off the beaten path with code might be dangerous.
4. Run all the code in the examples and exercises from Think Julia A lot of information will be redundant between the book, lectures, and course content, but this is intentional. Have I mentioned before how important practice is?
5. Fail early and fail often. Embrace your error messages. If you never make a mistake, you are not learning how to program. If you are practicing enough, trying new things, most of the time you will fail. This is expected, and this is a good thing. When you do an experiment in the lab, you rarely get an error message when things go wrong. Error messages can be daunting at first, but they often contain useful information. Appreciate them!

Reading lesson content

All of the course materials can be found on this website. Lectures, written content and practice problems, readings, and assignments can all be found with the appropriate lesson. There are also indices for each type of lesson content.

• Lesson index
• Lecture index
• Readings index
• Assignment index

Call-out boxes

Each lesson is broken up into multiple pages, with one major concept or skill per page. It is a good idea to go through lessons in order, though each page should stand on its own (eg practice problems will not carry from one page to the next).

Throughout lessons, there will be colored boxes that contain different kinds of information:

Code formatting

Throughout the course, you will see examples of code. Sometimes, code will appear "inline" with other text, but will be formatted differently so that it's clearly code. For example, x = 2 and f(x) = 2x + 3.

Other times, code will appear in a block. The following is julia code:

function my_func(x, y)
    for i in 1:x
        println(i + y)
    end
end

As you can see, this block of code is formatted differently from normal text.

Sometimes, you will see "command prompts" such as $ for the shell or julia> for the julia REPL (don't worry if you don't know what the shell or a REPL are right now). In these cases, when copying the code, do not include the command prompt. I will remind you about this again when it comes up, but just as an example, the following is a shell command and its output:

$ ls -l ~/Desktop

  rw-r--r--   1  ksb  staff    30 KiB  Wed Apr  8 20:12:59 2020  C0005_3F_1A_1000k_1_profile.tsv
  rw-rw-r--   1  ksb  staff     4 GiB  Wed Mar 18 15:48:06 2020  ko_profiles.sqlite
  rw-rw-r--   1  ksb  staff     9 MiB  Mon Mar  9 16:41:35 2020  metadata.sqlite
  rw-r--r--   1  ksb  staff     0 B    Fri Mar 27 15:07:47 2020  test.txt

In this example, you would type just ls -l ~/Desktop and press enter. Notice that in the second block, there is no command prompt ($) a the beginning. That's because this is output, and is not intended to be run as code.