Do I need to progam?

Learning to program can be a scary proposition. It is possible to use lots of bioinformatics tools without programming, such as the web-based analysis platform Galaxy. However, it isn’t necessary to learn a lot of programming for it to become a very powerful skill.

Here’s a few examples of commands that can be used through the Command Prompt/Line, along with a description of what they can do, to give you an idea about how a small number of short commands can make a big impact on a workflow:

• cat file – view contents of file (where ‘file’ is the name of the file)
• grep NA file – retrieves lines in file matching NA
• grep –v NA file – removes lines in file matching NA
• shuf –n 100 file – prints 100 random lines from file

It’s also possible to use scripting commands, such as awk, on the Command Line:

awk ‘$1>10{print $0}’ file – Prints whole lines ($0) where first column ($1) is greater than 10

awk ‘$1>10 && $3<0.1{print $1,$3}’ file – Prints columns 1 and 3 where column 1 is more than 10 and column 3 is less than 0.1

So you can see how using these kinds of short commands can allow you to investigate a large file without having to spend a lot of time opening it in a spreadsheet program to view the whole thing. This could save a lot of time with just a couple of very simple commands.

If you are keen to learn a language, Python and R are currently the most popular for bioinformatics. Which one you learn may depend on what you are interested in doing, for example if you want to create reproducible visualisations of your data, R is a great choice. If you are hoping to use machine learning, Python would be best to start with.

As a biologist, you have a big advantage over bioinformaticians you may work with – you know your data! So learning a little programming could help you increase that advantage even more.

The best way to get started? Find a problem and try to solve it, learning as you go. One problem could be to create a graph of some data you have. Or try out some different types of graphs and see how they compare. Using R would be good for this. There are examples of different types of plots and how you can create them in this R graph gallery.

There are many online courses and books that will help you get started and when you get stuck, search your problem online – someone else will have had the same problem before!

Take a few minutes to think about a problem you could do to help you start learning to program. You could get started on it now or wait until you have finished this collection.