Robert Aboukhalil

Co-founder at of

[Robert Aboukhalil @RobAboukhalil]

Really excited to unveil https://t.co/3DKXXBuxFD, an interactive playground for learning bioinformatics command-line tools like bedtools, bowtie2, and samtools (and more to come!) 🧑‍💻 🧬

Thanks to @aaronquinlan, @BenLangmead, and @mike_schatz for feedback and tutorial ideas.

[Robert Aboukhalil @RobAboukhalil]

Link to full video: https://t.co/v3ctL8MBFE

[Robert Aboukhalil @RobAboukhalil]

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.

[Nishant Jha @parambulat0r]

while working on a soon-to-be opensourced project, I noticed @nvidia uses Nitro Bio's sequence viewer component!!

[Robert Aboukhalil @RobAboukhalil]

💻 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.

https://t.co/75fWAGQBug

[Samuel Lampa - Also: smllmp.bsky.social @smllmp]

Wow, https://t.co/ow3TbkdDp0 now provides a tutorial for viral phylogenetics that you can run right in your browser 🙌
https://t.co/xg1f6rBc7B
#microbinfie #bioinformatics #training
via @RobAboukhalil

[Robert Aboukhalil @RobAboukhalil]

@MostlyTechPod @aarondfrancis Great episode as usual! @aarondfrancis You mentioned wanting to spin up 100's of databases temporarily. You've probably seen this before but in case you haven't: https://t.co/gFkzJKxwxx lets you run postgres in the browser

[Robert Aboukhalil @RobAboukhalil]

@parambulat0r @pyodide It is!

[Robert Aboukhalil @RobAboukhalil]

📢 Excited to share new features on https://t.co/3DKXXBduDD:
- Python playground to quickly test code
- Customize how much RAM the command-line can use: 512MB, 1GB, 2GB (previously fixed at 1GB)
- Confetti animations when you finish a tutorial 🙃

[Robert Aboukhalil @RobAboukhalil]

🦠 New tutorial on https://t.co/3DKXXBduDD: Learn to build phylogenetic trees from viral sequences, going from multiple sequence alignment to tree generation and rooting 🧬 💻

https://t.co/aTsivHzFil

[Robert Aboukhalil @RobAboukhalil]

We always tell people to create a portfolio to showcase their work. Today, we're releasing a template to get you started: https://t.co/RDRAjRkQ6t

It's for scientists and engineers who want a living resume of projects, work timelines, and blog posts that demonstrate expertise.

[Robert Aboukhalil @RobAboukhalil]

In 2024, https://t.co/3DKXXBduDD 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: https://t.co/dCTARpAlOJ

[Robert Aboukhalil @RobAboukhalil]

@ShahedAlAsmi Sure thing! In the meeting, attendees submit questions to the Q&A panel in Google Meet and everyone upvotes their favorite questions. When your question is up next, we make you a collaborator so you can (optionally) unmute/turn on video to give context, and we have a discussion.

[Robert Aboukhalil @RobAboukhalil]

📢 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 when the next ones are: https://t.co/hzHTSl1Qpe (login with Google, then "Join Group")

[Robert Aboukhalil @RobAboukhalil]

@DCGenomics @marianattestad Of course, we’d love to have you there!

[Maria Nattestad @marianattestad]

We are hosting free bioinformatics office hours on Feb 19th at 10am-noon PST. Bring your bioinformatics career or technical questions, and @RobAboukhalil and I will try to answer them.
Sign up here: https://t.co/9OT1VER4Xd
Please share especially with early career scientists!

[Robert Aboukhalil @RobAboukhalil]

🌲 New tutorial on https://t.co/3DKXXBduDD: Learn to build phylogenetic trees from closely related genomes using ska2.

https://t.co/rnu5f99oxm

[Robert Aboukhalil @RobAboukhalil]

@vsbuffalo Agreed. Feel free to share those ideas though. I know that many bioinformatics engineers are looking for useful tools they can contribute to the field.

[Robert Aboukhalil @RobAboukhalil]

https://t.co/bqovTA2c9C

[Robert Aboukhalil @RobAboukhalil]

🎁 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.

Link in the next tweet because Twitter hates links.

[Maria Nattestad @marianattestad]

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: https://t.co/boPqs0Rsil