I saw a Youtube video by @omgenomics.com profiling the work that @plasmidsaurus.bsky.social has been doing in streamlining sample preparation for their Plasmid sequencing and RNA-seq products. Interesting to see @OpenTrons instruments *everywhere*, and how they turn operations "pipette triggers".

We just released a video from our visit to @plasmidsaurus.bsky.social, where we spoke with Mark Budde and team: www.youtube.com/watch?v=nS2o... Highlights include: ✅ 3D printed magnetic bead contraptions ✅ When sequencing more is easier than sequencing less ✅ Bread machine analogies

Playing with sandbox.bio. This was remarkably cathartic.

That tech oligarchs are noisy and incensed about the remote possibility of a wealth tax and utterly silent about the murder of a man who was only using the phone they invented to chronicle the thuggish government goon squads should tell you everything about these desiccated souls.

🚀 Our new paper on Alignoth just published in Bioinformatics! Alignoth generates self-contained interactive HTML read alignment plots from BAM files – Rust-based, portable, and ideal for headless workflows. 📄 doi.org/10.1093/bioi... #bioinformatics #genomics #rust @johanneskoester.bsky.social

Blogpost: I took an oral probiotic for a month and did microbiome sequencing at @Plasmidsaurus. blog.booleanbiotech.com/oral-microbi...

Releasing alignism, a small tool that I have found useful for doing multiple sequence alignment in browser. hgbrian.github.io/alignism/ - The hard work was done by the awesome biowasm team! - Does tree building too - V fast compared to e.g., muscle on EBI - Not tested that much!

I've been thinking about the "virtual cell" concept and wanted to write up a few thoughts. Specifically on how I think the prior experience in GWAS informs the most likely way these models will be useful. andrewcarroll.github.io/2025/12/23/t...

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

These are fun educational puzzles to improve debugging skills of students! thanks to @robert.bio for creating these sandbox.bio/puzzles

We are thrilled to announce the first official release (v0.1.8) of #𝗯𝗲𝗱𝗱𝗲𝗿, the successor to one of our flagship tool, #𝗯𝗲𝗱𝘁𝗼𝗼𝗹𝘀! Based on ideas we conceived of long ago (!), this was achieved thanks to the dedication of Brent Pedersen. 1/n

Workshop landing page with demos here -> wasmodic.github.io

@wytamma.bsky.social : so, it took a little bit of extra time (not the flight back from the CZI meeting), but I decided to just f#&$ing do it, and the basic code to build and parse with the auxiliary fastq index is working (github.com/COMBINE-lab/...). 1/2

Excited to announce a new bqtools tutorial on sandbox.bio by @noamteyssier.bsky.social! Learn about the BINSEQ file format, and how it can replace FASTQ files for better data compression and faster parallel processing: sandbox.bio/tutorials/bq...

BINSEQ is a high-performance format for sequencing data and bqtools is a CLI tool that lets you create and manipulate these files in the style of samtools. Excited to release a tutorial with @robert.bio showcasing how to use it to encode, decode, and grep sequences in the browser on sandbox.bio!

Interested in learning materials to prepare undergraduate students for working with pathogens and pathogen data? I’m hosting a small curriculum development sprint/workshop. Industry/clinical and educators needed. Please share. Apply by November 28, 2025 dnalc.cshl.edu/pdn-2026-wor...

Students often ask me how to get bioinformatics experience, and I say "projects, projects, projects!". And inevitably they say "okay but how do I find a project to do?". So I made this video with 15 project ideas: www.youtube.com/watch?v=dfJK...

New tool "bwt-svg" for making illustrations of the BWT and the many auxiliary arrays and other structures related to it. Pyodide-based no-installation-necessary interface here: benlangmead.github.io/bwt-svg/. (H/t to @robert.bio for pointing me to pyodide!) Full repo: github.com/benlangmead/....

This is wonderful to play with, highly recommended for anyone who wants to understand the BWT

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.

"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

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

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...

"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

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...

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-...

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

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

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

💻 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...

What's the equivalent in #bioinformatics? xkcd.com/3113/

📢 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)

🦠 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...

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. 🧵

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!

Here's why I think there is reason to be bullish on U.S. STEM education. doi.org/10.1093/gene... #STEM #STEMEducation

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.

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

Thrilled to announce the first release of the "Nanopore for Educators eBook" — nanopore4edu.org/latest/ #genomics #DNA #OxfordNanopore

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

We are experiencing an assault on science unparalleled by anything I’ve seen in my life. It’s not one issue or another anymore, the entire institution is under attack by the most powerful individuals in the country. This Friday, where will you be? standupforscience2025.org

📢 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")

"I've spent over five decades as a scientist in academia and the federal government," Harold Varmus, the former director of the N.I.H., writes in a guest essay. "Never before have I seen my profession so politicized as it is now under the Trump administration."

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

🧬🖥️ 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!

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

We now have a tutorial for SKA2 available to run interactively on sandbox.bio, going from genomes to trees: sandbox.bio/tutorials/sk...

Illumina and NVIDIA Team Up to Remake How to Train Your DRAGEN 🧬🖥️ omicsomics.blogspot.com/2025/01/illu...

Built a small sequence generator tool 🧬 You can: - constrain to specific bases, specific length - copy as fasta - free to use, all stored locally!

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