iiinova — where your digital self keeps evolving

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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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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Robert Aboukhalil @robert.bio · 24/06/2026

New on sandbox.bio: a FastQC playground you can use for teaching QC analysis of sequencing data. It runs entirely in the browser, GUI and all (thanks to CheerpJ and WebAssembly!) ➡️ sandbox.bio/playgrounds/...

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Robert Aboukhalil @robert.bio · 22/12/2025

One last bioinformatics puzzle before the holidays: Can you figure out the file formats of unlabeled sequence data? 🎅 sandbox.bio/puzzles/form...

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

"The reference genome is essentially folded using the BWT, which allows the search for read alignments to take on a bow-tie shape in the index" Hmmm... @benlangmead.bsky.social

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Robert Aboukhalil @robert.bio · 01/07/2025

📢 Excited to share these new features on sandbox.bio: - Python playground to quickly test code - Customize how much memory the command-line can use! Choose between 512MB, 1GB, 2GB (previously fixed at 1GB) - Confetti animations when you finish tutorials 🙃 (obviously the most important improvement)

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Robert Aboukhalil @robert.bio · 10/06/2025

Excited to announce our first interactive article on sandbox.bio, about genomic ranges: sandbox.bio/concepts/gen... Move & resize the ranges to see how that affects bedtools operations like merge and intersect in real time!

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Robert Aboukhalil @robert.bio · 26/05/2025

Nice work! Just a nitpick regarding the sentence below: we've been compiling sequence aligners to WebAssembly for a while now at biowasm.com :)

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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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Robert Aboukhalil @robert.bio · 05/03/2025

In 2024, sandbox.bio had >170,000 tutorial page views! 🥳 The most popular tutorials were: 1. Terminal basics 2. Genomic intervals with bedtools 3. Terminal exercises 4. Data exploration with awk 5. DNA sequencing QC Check them out here: sandbox.bio/tutorials

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Robert Aboukhalil @robert.bio · 24/02/2025

📢 Our first bioinformatics office hours were a lot of fun, so we will be hosting more of them this year! We will also invite special guests to co-host 👀 Join this Google Group to be notified of future office hours: groups.google.com/a/omgenomics... (log in with Google, then "Join Group")

Screenshot of the office hours with Maria and Robert answering a participant's question.

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Robert Aboukhalil @robert.bio · 17/01/2025

🌲 New sandbox.bio tutorial: Learn to build phylogenetic trees from closely related genomes using ska (the tool, not the music) 🖥️ 🧬 sandbox.bio/tutorials/sk...

Command-line interface: running "ska" and creating a phylogenetic tree

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Robert Aboukhalil @robert.bio · 15/12/2024

Agreed. Another benefit of having docs within the app is that you can give personalized help, eg if the user doesn’t have enough permissions to perform an action. That’s harder to do if docs are hosted separately.

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Robert Aboukhalil @robert.bio · 10/12/2024

I found 80 terabytes of uncompressed genomics files in public S3 buckets on 42basepairs 😯 That's thousands of dollars a month in additional storage and egress costs 💸

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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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Robert Aboukhalil @robert.bio · 22/10/2024

This paper gets it. 🧬 🖥️

"One of the core issues of Bioinformatics is dealing with a profusion of (often poorly defined or ambiguous) file formats"

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Robert Aboukhalil @robert.bio · 15/09/2023

Sneak peek of sandbox.bio v2 👀 Some of the new tools we will support: Freebayes, SeqKit, Lumpy, Kraken2, Jellyfish, Mummer, Kallisto, ViralMSA, Sniffles. What other tools and tutorials would you like to see?

Write Bash scripts in vim/nano and run them

Support for a lot more bioinformatics tools

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