Welcome, Fellow Windows Wally!
Ever felt intimidated by those bioinformaticians typing mysterious commands in their black screens? Wished you could analyse protein or DNA sequences without clicking through endless web interfaces? Want to impress your colleagues by casually mentioning you "just BLASTed some sequences in the terminal"?
You've come to the right place. Join me, a proud Windows Wally that dabbles in the Windows Subsystem for Linux, as we journey from the comfortable world of GUIs to the powerful realm of command-line bioinformatics.
What Does Bioinformatics actually mean?
Life is defined by billions of letters (called bases) in our DNA. Their precise order codes sequences of different letters (amino acids) that make up proteins. Depending on how these amino acids organize themselves, proteins can perform almost magical tasks: building bones, transporting oxygen, creating more proteins, or even breaking down plastic. All this biological magic is encoded in simple letter sequences—something computers are really good at reading. So, understanding these letters is (sort of, not really) understanding life itself. And that's exactly what bioinformatics does!
Bioinformatics is the science of using computers to understand biological data. One could consider it to encompasses everything from analysing sequences and assembling genomes to solving protein structures and even designing completely new proteins.
Why the Command Line?
SpeedAnalyse thousands of sequences while you would have been still clicking on NCBI. AutomationScripts do repetitive tasks while you grab coffee. ControlAccess parameters and options that the web interfaces hide from you. ReproducibilityShare exact commands with friends instead of "click here, then there..." Cool-Factor Typing commands in a dark terminal? That's worth it alone.
Who's a Windows Wally?
Windows You know, that operating system everybody uses. For UNIX users: this is hyperbole.Wally The person who spends ten minutes looking for their glasses while wearing them. We've all been there. Windows Wally Someone that is afraid of the command line and likes the comfort of clicking icons.
Terminal User Smugness Syndrome (TUSS)
Medical Alert Learning even the very basics of command line bioinformatics may cause TUSS. Symptoms include Visible smugness after using simple commands. Leaving the terminal open all the time, for no reason. Explaining why vim is superior at parties, and involuntary scoffing at Excel users. Treatment Regular exposure to GUIs and remembering that often, clicking an icon twice is faster than writing a script.
Available Tutorials
1. Protein Bioinformatics Basics
Learn to harness the Linux command line, BLAST through protein databases, cluster sequences with CD-HIT, align them with ClustalO/MUSCLE, and build beautiful phylogenetic trees. Warning: May cause acute terminal user smugness syndrome.
2. Large-Scale Sequence Analysis
Coming Soon! When your dataset grows from "cute" to "oh no". Handle millions of sequences without your computer catching fire (99.9% of the time). Features FAMSA, CD-HIT, FastTree and other tools that sound like spells Harry Potter would have used if he was a biologist.
3. Genome Assembly for Beginners
Coming Soon! Learn to piece together genomes like a puzzle, except the pieces are millions of short DNA reads and the picture on the box is blurry. We'll use Cutadapt, FastQC, assemble with Newbler or SOAPdenovo then predict genes and pretend we know what N50 means.
Why This Blog Exists
For Windows Users
Written by a Windows user, for Windows users. No judgment, limited Linux elitism, and practical step-by-step guidance. Mac should work too, I guess.
For Biologists
I'm a Biochemistry student, not a computer scientist. These tutorials are written for biologists that want to expand their in silico skills, like me.
Engaging
Bioinformatics doesn't have to be dry — these tutorials aim to make commands fun. As if they weren't already.
About the Author
Hi! I'm Max Stetina, a MSc Biochemistry student at UCT Prague, and a proud Windows Wally. After wondering why "real" bioinformaticians looked so smug with their terminals, I decided to join them and discovered the joys of the command line myself, although I am still fond of my WW title.
"If I can learn it, so can you. Probably faster."