Hello Bioinformatics lovers,

Happy New Year! Tommy here.

Two rounds of sickness in the last 2 weeks in the whole family. It was pretty tiring taking care of the kids and then

I had the symptoms. Wish everyone a healthy 2026!

Despite the sickness, I had the opportunity to finish three side projects with the help of AI coding tools:

1. I vibe-coded this website with base44 for you to learn R and Python on the web browser for free. No need for installation, you can even edit the code and run it in the browser. Thanks to the power of WebAssembly.

2. I updated ROSE with Claude Code, which is a tool to identify super-Enhancers in ChIP-seq or Cut&RUN/TAG data.

Now you can install it via pip and a great improvement in performance.

3. I updated my ChIP-seq snakemake pipeline with Claude Code. It was written almost 10 years ago and many things

were broken. Now it is working with Conda integrated, and it should work for you too. Try it out!

I am amazed at how much I have accomplished in a relatively short time.

I wanted to build the first R/python website last year and I tried a different tool called replit and it struggled.

I am so happy that one year later, the AI software engineering tool has improved so much.

For ROSE optimization and updating of my own Snakemake pipeline, I used Claude code. It is very powerful.

Even though it is very powerful, it still took me hours back and forth to make the final product work.

YOU STILL NEED TO KNOW THE BASICS.

I have over 10 years of experience in writing code, and it helped me spot the wrong things the AI tool does.

In one step, ROSE assigns the nearest genes to the superEnhancers, and it used 200Mb upstream and downstream window which is too big and Claude wanted to change it to 50KB. I instantly know it is not correct, some enhancers can be located MB away (check the SHH enhancer).

Nevertheless, embracing those AI tools can 10x your efficiency if you have a solid foundation.

If you are still learning, use those AI tools to help you learn. literally ask it to give you a learning plan.

Make sure you give the chatbot a detailed background of yourself and your objectives.

Happy Learning!

Tommy aka crazyhottommy

PS:

Forward this email to your friend if you find it helpful.

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!