Hey Bioinformatics lovers,

Tommy here.

Quick question: How many times have you stared at a blank terminal after a crash, wondering, “What the hell did I just type?”

If you’re like most bioinformaticians I talk to, the answer is too damn many.

Last week, I was knee-deep in a bulk RNA-seq analysis. Hours invested. curl to download the data, STAR to align the fastqs.

Then—bam. yeah, pun intended :) Something went wrong. Everything gone.

No history. No notes. Just me, rebuilding from scratch like a caveman rediscovering fire.

Sound familiar?

Here’s the brutal truth: Manual logging commands isn’t just annoying—it’s killing your productivity.

You’re typing samtools view, STAR align, every time, praying your bash history doesn’t betray you

Also, you may work on multiple projects, and those commands are all interwoven in the command history.

If you follow me, you know I am a big fan of reproducibility. (Read my blog post on this topic).

Without those command notes easily accessible:

Manuscripts stall. Collaborations fracture. And that grant deadline? It laughs in your face.

I get it. We’ve all romanticized the “hacker life.” But romance doesn’t pay the bills when you’re re-running pipelines for the third time.

Enter Liminal.

Not some bloated IDE. Not another Jupyter gimmick.

This thing runs in your shell like a ghost in the machine. Every command? Captured automatically.

Timestamps, context, searchability—all woven into a reproducible notebook you can export, share, or revive months later.

I tested it on my RNA-seq nightmare.

Setup: 2 minutes. Results: My entire session rebuilt in seconds. No more “What was that flag?” panic.

Now? My workflows are bulletproof. Reproducibility? Automatic. Time saved? At least 10 hours a week—time I now spend on actual science, not detective work.

But don’t take my word. Here’s what it does for you:

1. Eliminates the “Lost Work” Horror: Auto-logs everything. Crashes? Laughable.
2. Scales Your Brain: Fuzzy search pulls up that one grep from last quarter. Memory optional.
3. Zero Learning Curve: Point it at your terminal. Run. Done.

If you’re tired of the terminal tax on your sanity, head to Liminal, right now.

Install it. Run one session. If it doesn’t click, delete it—no harm.

But I bet it will. Because in bioinformatics, the real edge isn’t more compute. It’s not losing what you build.

Forward this to that postdoc drowning in commands. They’ll owe you a beer.

What’s your biggest terminal time-suck? Reply—I’ll feature the best in the next one.

Make it reproducible.

Other posts that you may find useful

1. A secure web-based, collaborative terminal​
2. ​Why are intronic reads in single-cell data?
3. ​Why are intronic reads in bulk-RNAseq?
4. ​How to debug installing tool errors?
5. Ever wondered why analyzing RNA-seq data feels like walking through a fog with 20,000 dimensions?
6. I was featured in The Data Wire by Pure Storage: Data challenge comes before the algorithm/AI challenge.
7. You can not do Bioinformatics with hard cutoffs and thresholds​
8. In a rapidly changing AI landscape, how do you stay relevant?
9. ​Benchmarking scRNA-seq copy number variation​
10. The LINCS L1000 project has collected gene expression profiles for thousands of perturbagens at a variety of time points, doses, and cell lines
11. ​Good tutorial: Removing tumour purity, library size and batch effects from the TCGA breast cancer RNA-seq data using RUV-III-PRPS
12. AI won't replace you. But a biologist using AI will.​

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/​

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Stay awesome!