Co-founder at https://xitter.cf/t.co/lzi12QAwN8 Creator of https://xitter.cf/t.co/aT0F84k2c1, https://xitter.cf/t.co/nb8XvXQt5O, https://xitter.cf/t.co/jxzLuIr45j
Joined April 2012
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Really excited to unveil sandbox.bio, 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.
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.
Robert Aboukhalil retweeted
while working on a soon-to-be opensourced project, I noticed @nvidia uses Nitro Bio's sequence viewer component!!
💻 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/bash-s…
Robert Aboukhalil retweeted
Wow, sandbox.bio now provides a tutorial for viral phylogenetics that you can run right in your browser 🙌
sandbox.bio/tutorials/viral-…
#microbinfie #bioinformatics #training
via @RobAboukhalil
📢 Excited to share new features on sandbox.bio:
- 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 🙃
🦠 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/viral-…
We always tell people to create a portfolio to showcase their work. Today, we're releasing a template to get you started: github.com/omgenomics/portfo…
It's for scientists and engineers who want a living resume of projects, work timelines, and blog posts that demonstrate expertise.
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
ALT Screenshot of sandbox.bio website
📢 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: groups.google.com/a/omgenomi… (login with Google, then "Join Group")
Robert Aboukhalil retweeted
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: tally.so/r/mOb6dM
Please share especially with early career scientists!
🌲 New tutorial on sandbox.bio: Learn to build phylogenetic trees from closely related genomes using ska2.
sandbox.bio/tutorials/ska2-i…
🎁 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.
Robert Aboukhalil retweeted
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
Just released 8 new data wrangling tutorials for biologists, thanks to @franciscomcouto!
➡️ sandbox.bio/community/data-p…
#bioinformatics
I'm bringing back email-based bioinformatics! Send an email to "[email protected]" with a chromosome name in the subject (e.g. chr1) and you'll receive simulated sequencing reads in your inbox 🙃
Did you know that BLAST searches used to be done by email?! I went down quite the rabbit hole for this video: youtu.be/imXQDiIsyjA
Did you know that BLAST searches used to be done by email?! I went down quite the rabbit hole for this video: youtu.be/imXQDiIsyjA
Robert Aboukhalil retweeted
Wow! Congrats PacBio! My PhD project with PacBio sequencing of a cancer cell line started only 10 years ago, and I've seen truly impressive improvements ever since: Longer reads, way lower costs, higher accuracy, and now it's not even the size of a fridge anymore!
✨It's here! Introducing Vega - the first benchtop long-read #sequencing system from #PacBio. With #Vega, industry-leading HiFi tech is now within reach.
We could go on about why it's so remarkable, but Vega's impact speaks for itself. Learn more here: pacb.com/Vega
#ASHG24
Don't tell @MariaNattestad but I borrowed her desk to film this video about the backstory behind the FASTA format:
youtu.be/7LA0IKsVloU
