Hello Bioinformatics lovers,

I am eager to send you my weekly newsletter because I can not wait to see you smile.

Of course, I can not see your smile,

but I can imagine...

I hope the little nuggets make you feel heard and learn something useful.

Today, we will talk about this dreadful situation we all face:

Can you make a figure for my talk tomorrow?” — A Day in the Life of a Bioinformatician

If you’ve ever worked with wet lab collaborators, this line will sound familiar:

“I have a presentation tomorrow.”​
And with that, your bioinformatician quietly begins to die inside.

Let’s clear something up:
Bioinformatics isn’t a push-button science.

There’s no “Run Analysis” button.
No “Export to Nature” shortcut.
What looks like a polished figure takes hours—sometimes days—of work.

Here’s what actually happens behind the scenes.

Step 1: “Where’s the data?”​
“Oh it’s in an S3 bucket.”
Great.
Now I need to install the AWS CLI, configure access keys, set the region…

Still haven’t downloaded a single file.

Step 2: Cluster drama​
“SSH into the HPC,” they say.
Or: “Use Google Cloud.”
Cool, now I’m generating SSH keys, requesting access, and spinning up virtual machines.

Step 3: The tool that time forgot​
“Use this GitHub repo—it’s amazing!”
Updated: 2019.
Dependencies: Python 2.7, ancient compilers, and hope.
Installation fails the first 3 times.

Step 4: The metadata mess​
Okay, the tool works now.
But wait—what’s this?
Sample sheet has merged Excel cells and inconsistent IDs:
​Sample_1, sample-1, S1, ctrl1 — all the same sample.

Step 5: QC chaos​
Matrix loads. Time to run PCA.
Looks weird.
Why?
Tumor and normal samples got swapped.
Again.
Plot → sanity check → panic → fix.

Step 6: The request​
You finally get to analysis.
You plot UMAPs, clusters, marker genes.

Then you hear:
​“Can you label everything and send it by 8AM?”​
It’s already 5PM.

Step 7: The figure sprint​
So you…
Write the script.
Adjust color palettes.
Resize Panel B.
Fix font size.
Export to PDF.

Laptop crashes.

This is the real bioinformatics.
It’s not just R or Python.
It’s data detective work.
It’s sanity checks.
It’s system admin.
It’s science.

What can we all do better?

✅ Don’t request miracles the night before a talk
✅ Respect that clean figures come from clean data
✅ Treat your bioinformatician as a co-author, not a plot machine
✅ Communicate early and often

To every bioinformatician out there…​
The one pulling all-nighters to make someone else’s data look publishable:
I see you.
You’re the invisible hand in half the figures at every conference.

You deserve credit.
And a long nap.

Other posts that you may find useful from last week

1. ​10 tools to make a better flowchart than in PPT 🧵 ​
2. The pitfalls of class prediction in omics 🧵
3. You won’t remember what you did. The importance of documentation for bioinformatics.
4. How to disown a process and re-parent it to a screen session​
5. Need to replace a pattern, but only in column 5? use this awk trick.
6. 🧵 Why the obsession with p < 0.05 is hurting science. A meme. A truth. A reality check. (if you can not state your null hypothesis, you do not understand p-value)
7. In high-dimensional bio data—transcriptomics, proteomics, metabolomics—you're almost guaranteed to find something “significant.” Even when there’s nothing there.
8. A good database to mine: Genomics of Drug Sensitivity in Cancer​
9. ​A trick to filter a VCF file and maintain the header
10. 🧵 You just got your hands on early clinical trial RNA-seq data. Excited? You should also be cautious. Here's why. 👇
11. ​12 websites to learn computation and many others! 🧵 Bookmark 👇
12. 🧵 Unix pipes are magic. But real power comes when you build them like LEGO. One piece at a time. 👇 ​

Reply "YES" if the newsletter is helpful for you :)

Also, I will be writing more technical tutorials on my blog. You will get notified when it is out!

Happy Learning!

Tommy aka crazyhottommy

PS:

If you want to learn Bioinformatics, there are other ways that I can help:

1. My free YouTube Chatomics channel, make sure you subscribe to it.
2. I have many resources collected on my github here.
3. I have been writing blog posts for over 10 years https://divingintogeneticsandgenomics.com/​

Stay awesome!