Robert Aboukhalil
@RobAboukhalil
Co-founder at https://OMGenomics.com Creator of https://sandbox.bio, https://42basepairs.com, https://biowasm.com
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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.
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…
Wow, sandbox.bio now provides a tutorial for viral phylogenetics that you can run right in your browser 🙌 sandbox.bio/tutorials/vira… #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/vira…
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/por… 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
📢 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/omgenomics.c… (login with Google, then "Join Group")
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…
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
youtube.com
YouTube
We reviewed 10 of our subscribers' CVs!
Just released 8 new data wrangling tutorials for biologists, thanks to @franciscomcouto! ➡️ sandbox.bio/community/data… #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
youtube.com
YouTube
Bioinformaticians used to run BLAST by email???
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
youtube.com
YouTube
Bioinformaticians used to run BLAST by email???
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…
Don't tell @MariaNattestad but I borrowed her desk to film this video about the backstory behind the FASTA format: youtu.be/7LA0IKsVloU
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