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Reposted by Robert Aboukhalil

Samuel Lampa @smllmp.bsky.social · 2d

"Pro tip": If you are in a restricted environment & need quick access to a linux terminal running locally in the browser for some #bioinformatics messing around - check the sandbox.bio terminal playground. Made a bitly link for for convenience: bit.ly/bioterminal

Screenshot of the sandbox.bio playground for running a linux environment in the browser

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Robert Aboukhalil @robert.bio · 21d

Interesting! Have you written about this somewhere?

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Robert Aboukhalil @robert.bio · 21d

I still need to get around to reading the binseq paper, but I imagine a sandbox.bio tutorial might help spread the word? @noamteyssier.bsky.social let me know if you’d be interested

sandbox.bio - Interactive bioinformatics tutorials

sandbox.bio

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Robert Aboukhalil @robert.bio · 21d

I’m in the `seqkit seq` camp, easier to remember :)

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Robert Aboukhalil @robert.bio · 22d

a woman is making a funny face while looking at the camera .

ALT: a woman is making a funny face while looking at the camera .

media.tenor.com

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Robert Aboukhalil @robert.bio · 22d

Here is my deep dive into the FASTQ file format, and why you should not write Bash one-liners to parse FASTQ files: youtu.be/vFZtPTS9USE

Bioinformatics Basics: The FASTQ format and its pitfalls

YouTube video by OMGenomics

youtu.be

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Reposted by Robert Aboukhalil

Bede Constantinides @bedec.bsky.social · 26d

Blogged about how zstd --long fills the gap between fast and slow-but-high-ratio genome compression methods log.bede.im/2025/09/12/z...

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Robert Aboukhalil @robert.bio · 29d

It gets worse...

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Robert Aboukhalil @robert.bio · 29d

"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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Reposted by Robert Aboukhalil

Atul Gawande @agawande.bsky.social · Sep 1

9 CDC Directors going back to 1977 speak out. What RFK Jr has done to our nation’s public health system "should alarm every American."

It "is unlike anything we have ever seen at the agency, and unlike anything our country has ever experienced." www.nytimes.com/2025/09/01/o...

Opinion | We Ran the C.D.C.: Kennedy Is Endangering Every American’s Health

www.nytimes.com

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Reposted by Robert Aboukhalil

BF Francis Ouellette @bffo.bsky.social · Aug 26

From @jxtxfoundation.bsky.social | JXTX + CSHL 2025 Genome Informatics Scholarships | Up to $750 for domestic or $1,250 for international travel | Application deadline is September 15, 2025 | #OpenScience 🧬 🖥️ 🧪
⬇️
jxtxfoundation.org/news/2025-6-...

JXTX + CSHL 2025 Genome Informatics Scholarship

JXTX + CSHL 2025 Genome Informatics Scholarships

jxtxfoundation.org

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Robert Aboukhalil @robert.bio · Aug 13

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

YouTube video by OMGenomics

youtu.be

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Reposted by Robert Aboukhalil

Hank Green @hankgreen.bsky.social · Jul 28

I doubt that there is a single family in America that hasn’t benefitted directly from the NIH.

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Robert Aboukhalil @robert.bio · Jul 19

Oh interesting, good to know! I’d love to hear more about the kinds of issues he encountered if he’s ever inspired to write a post about it :)

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Reposted by Robert Aboukhalil

Niema Moshiri @niema.net · Jul 18

Shout-out to amazing @ucsandiego.bsky.social Bioinformatics new-grads Maddie Ritter and Kyra Fetter for writing this tutorial!

Samuel Lampa @smllmp.bsky.social · Jul 18

Wow, sandbox.bio now provides a tutorial for viral phylogenetics that you can run right in your browser 🙌
sandbox.bio/tutorials/vi...
#microbinfie #bioinformatics #training
via @robert.bio

sandbox.bio - Interactive bioinformatics tutorials

sandbox.bio

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Robert Aboukhalil @robert.bio · Jul 18

Thanks so much Samuel!

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Robert Aboukhalil @robert.bio · Jul 18

Hey @robp.bsky.social! 64-bit WebAssembly was only released in Chrome/Firefox a few months ago, and Safari doesn't support it yet, so it might be a while before I can switch over :)

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Robert Aboukhalil @robert.bio · Jul 18

💻 Just released a new tutorial: How to write a Bash script, featuring an IDE and a command-line running directly in your browser. No setup required.

sandbox.bio/tutorials/ba...

How to write a Bash script

Interactive Bash tutorial: learn to write your own Bash scripts and process user inputs using a command-line interface in your browser.

sandbox.bio

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Reposted by Robert Aboukhalil

Nils Homer @nilshomer.com · Jul 12

What's the equivalent in #bioinformatics?

xkcd.com/3113/

Fix This Sign

xkcd.com

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Robert Aboukhalil @robert.bio · Jul 1

📢 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 · Jun 26

🦠 New tutorial on sandbox.bio: Learn to build phylogenetic trees from viral sequences, going from multiple sequence alignment to tree generation and rooting 🧬 💻

sandbox.bio/tutorials/vi...

Viral Phylogenetics

Interactive viral phylogenetics tutorial: learn to run multiple sequence alignment, phylogenetic inference, and tree rooting using a command-line interface in your browser.

sandbox.bio

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Reposted by Robert Aboukhalil

Claus Wilke @clauswilke.com · Jun 10

I also reject the notion that "most biomedical literature is unreliable/untrue." This is simply not the case. The vast majority of biomedical research is so reliable we don't even think about it. And yes, some studies and even subfields have issues, but let's acknowledge all the things that work. 🧵

Richard Sever @richardsever.bsky.social · Jun 9

"Create a journal for replication work". 🙄

This comes up time again as if there aren't existing places to put replications. PLOSOne will taken them, plenty of other journals will, and bioRxiv has had an article type called "Confirmatory Results" since we launched in 2013!

Mallory Harris, PhD @malar0ne.bsky.social · Jun 9

JB plans for NIH: give grants for replication work. Create journal for replication work. Evaluate on metrics including efforts to facilitate replication, not just influence.

AH raises: funding this will take money from somewhere else. JB kind of shrugs this off but...FY2026 budget is a 40% cut.

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Robert Aboukhalil @robert.bio · Jun 10

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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Reposted by Robert Aboukhalil

Jason Williams @jasonwilliamsny.bsky.social · Jun 3

Here's why I think there is reason to be bullish on U.S. STEM education.

doi.org/10.1093/gene...

#STEM #STEMEducation

There’s never been a better time to be a STEM educator

Abstract. From its current vantage point, the future of US STEM education may appear bleak. Yet STEM education's strength and importance have never been gr

doi.org

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Reposted by Robert Aboukhalil

Ben Langmead @benlangmead.bsky.social · May 29

Industry friends, now is the time for MUCH more speaking out on behalf of academic colleagues under duress. Here are core open source methods that many of your products doubtlessly depend on either directly or indirectly (see en.wikipedia.org/wiki/HMMER) being abruptly defunded. Make noise.

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