iiinova — where your digital self keeps evolving

Reposted by Maria Nattestad 🧬💻

Robert Aboukhalil @robert.bio · 10/08/2026

You can now turn your GitHub repos into sandbox.bio tutorials! You get a shareable URL, where code blocks are runnable, and files are preloaded in the terminal. For example, @benlangmead.bsky.social used this in a recent kraken2 workshop. You can see it in action here: sandbox.bio/training/git...

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Reposted by Maria Nattestad 🧬💻

Robert Aboukhalil @robert.bio · 06/08/2026

I can't believe it's already been 5 years since I first released sandbox.bio! 🥳 To celebrate, next week we'll release one new feature every day of the week. Follow along at sandbox.bio/anniversary, or here on BlueSky.

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Reposted by Maria Nattestad 🧬💻

Robert Aboukhalil @robert.bio · 02/07/2026

Check out our new Makefile tutorial if you want to finally understand what those "make install" commands actually do when you paste them in your terminal, and how to use them in your work: sandbox.bio/tutorials/ma... Thanks to Stephen J Bush for contributing this tutorial!

sandbox.bio

Intro to Makefiles

Interactive make tutorial: learn to use and create your own Makefile using a command-line interface in your browser.

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Maria Nattestad 🧬💻 @omgenomics.com · 23/06/2026

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

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

youtu.be

AI in biology: distinguishing hype from reality

YouTube video by OMGenomics

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Reposted by Maria Nattestad 🧬💻

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

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 · 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

youtu.be

You might be networking wrong

YouTube video by OMGenomics

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

🧬🖥️ 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

youtu.be

RNA-seq tutorial with DESeq2: Differential gene expression project

YouTube video by OMGenomics

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Maria Nattestad 🧬💻 @omgenomics.com · 10/12/2024

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 🧬💻

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

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

youtu.be

We reviewed 10 of our subscribers' CVs!

YouTube video by OMGenomics

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Reposted by Maria Nattestad 🧬💻

Robert Aboukhalil @robert.bio · 15/11/2024

We just released 8 new data wrangling tutorials for biologists! sandbox.bio/community/da... 💻 🧬

sandbox.bio

Data and Text Processing

Command-line tutorials on data and text processing, by Francisco M. Couto.

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Reposted by Maria Nattestad 🧬💻

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

If you think bioinformatics is hard today, you should have seen it in 1985 😬 🧬 🖥️

From a paper about the Genbank database: "the database is available to any user in several forms: it is distributed on magnetic tape, on floppy diskettes and on-line" :)

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Maria Nattestad 🧬💻 @omgenomics.com · 07/11/2024

Investigating structural variants? I just released a tutorial video showing how I do this quickly and intuitively using my tools Ribbon and SplitThreader: youtu.be/TP-H9epbsTM #bioinformatics