iiinova — where your digital self keeps evolving

Haha yea that’s exactly what I did. See the whole thread :)

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I also integrated Dot, my interactive dot plot tool, into Assemblytics, since they both work from the same input .delta file of assembly-to-reference alignments.

Interactive dot plot tool named Dot running inside Assemblytics.

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And I spent like a day just polishing things and another day getting it up on PyPI and Bioconda. But I would have never had the energy to start (let alone finish) this project without a modern AI agent to do the heavy lifting.

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Now it doesn't need a server anymore! I used AI to rewrite all the R scripts and that one Perl script into Python, now you can `pip install assemblytics`! And then I told the AI to use Pyodide to turn it into a web app, and it just did it. It worked right away, but of course I did a lot of testing.

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Maria Nattestad 🧬💻 @omgenomics.com · 12/02/2026

Okay I'm sorry if you're all getting tired of it, but here's yet another I-built-this-with-AI post. It is my first time really vibe-coding something, but it's for a good cause: updating my old academic software Assemblytics that I had nearly shut down multiple times due to server issues.

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We visited Plasmidsaurus and had tons of interesting takeaways, so we went back to record a whole podcast episode with them and film a lab tour for our YouTube channel. Here are both:

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Reposted by Maria Nattestad 🧬💻

Robert Aboukhalil @robert.bio · 09/10/2025

Just published an interactive article about a magical algorithm known as the Burrows-Wheeler Transform, which powers sequence alignment tools like bowtie and bwa: sandbox.bio/concepts/bwt It's also notoriously unintuitive so I'm hoping this article helps you build that intuition.

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Reposted by Maria Nattestad 🧬💻

Robert Aboukhalil @robert.bio · 13/08/2025

There's now a race to apply AI to every imaginable field of biology. The problem is: unless you understand the biology really well, it's easy to think you've solved the problem when you haven't even come close. youtu.be/o097zC7CM5I

AI in biology: distinguishing hype from reality

Robert Aboukhalil @robert.bio · 15/04/2025

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Reposted by Maria Nattestad 🧬💻

We always tell people to create a portfolio to showcase their work, so today we're releasing a template to get you started: github.com/omgenomics/p... It's made for scientists & engineers who want a living resume that showcases projects, work timeline, and blog posts that demonstrate your expertise

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Maria Nattestad 🧬💻 @omgenomics.com · 18/02/2025

We sent out a calendar invite to everyone who signed up, so check your spam filters!

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Maria Nattestad 🧬💻 @omgenomics.com · 12/02/2025

We just released a new video on how to get more out of those “let’s chat” conversations when job hunting, based partly on my past experiences being on the receiving end of requests for advice and job referrals: youtu.be/bpQaIvqqkKw

You might be networking wrong

Maria Nattestad 🧬💻 @omgenomics.com · 10/02/2025

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🧬🖥️ We are hosting free bioinformatics office hours on Feb 19th at 10am-noon PST. Bring your bioinformatics career or technical questions, and @robert.bio and I will try to answer them. Sign up here: tally.so/r/mOb6dM Please share especially with students and early career scientists!

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Reposted by Maria Nattestad 🧬💻

Mike Schatz @mikeschatz.bsky.social · 07/02/2025

Friends are looking for jobs. Collaborators are dropping off papers. Funds are being pulled away. But let’s just pretend everything is normal.

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Reposted by Maria Nattestad 🧬💻

Robert Aboukhalil @robert.bio · 17/12/2024

🎁 New RNA-Seq tutorial! Learn to run differential expression analysis with DESeq2, and create your own bioinformatics projects using public data and the Expression Atlas 🧬 🖥️ youtu.be/NGbZmlGLG5w

RNA-seq tutorial with DESeq2: Differential gene expression project

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I almost missed the part where it's not just text size but also the pixel circumference of the track that determines how much space the text needs. This is before and after adding a fix to take circumference into account.

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And here's that spirograph case again now that I added some guardrails, namely restricting max total space <= 2π. There is a beauty to radial geometry that gets me every time 😍

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I got the heuristics just right so the pins slide over just enough as text gets bigger.

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Ooh fun, it's making an interesting pattern when there are too many data points. I think it's because the little pins wrap around so far that they connect to the other side of the circle. It's pretty. Reminds me of the spirograph toy from when I was a kid.

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Thanks to the Circa user who requested this for giving me a good excuse to code today :)

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Robert Aboukhalil @robert.bio · 27/11/2024

I'm working on a little feature for Circa. It's been over a month since I really coded with all the other startup things like marketing and "strategic thinking" taking up my brain space, so it's really nice just to sit down and code a little algorithm and some SVG paths for overlap-avoiding text.

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Reposted by Maria Nattestad 🧬💻

I made a little swiss army knife tool for quickly inspecting FASTA/FASTQ sequences, including GC content, codon analysis, reverse complement, and file format conversions: 🖥️ 🧬 42basepairs.com/tools/sequen...

42basepairs.com

Sequence Analysis - 42basepairs

Bioinformatics sequence analysis on FASTA and FASTQ files, including reverse complement, GC content calculations, codon usage analysis, and converting your files to FASTA, FASTQ, or SAM format

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Maria Nattestad 🧬💻 @omgenomics.com · 22/11/2024

🧬 🖥️ This was a fun one to make: We reviewed 10 CVs sent in by our audience, and here are the 7 common mistakes we kept seeing: youtu.be/qXPJpnrfX_4

We reviewed 10 of our subscribers' CVs!