Robert Aboukhalil
@robert.bio
Co-founder at https://omgenomics.com. Creator of https://42basepairs.com, https://sandbox.bio, https://biowasm.com, https://levelupwasm.com. Bioinformatics, genomics.
About me: https://robert.bio
About me: https://robert.bio
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.
It's also notoriously unintuitive so I'm hoping this article helps you build that intuition.
October 9, 2025 at 5:05 PM
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.
It's also notoriously unintuitive so I'm hoping this article helps you build that intuition.
"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
Hmmm... @benlangmead.bsky.social
September 9, 2025 at 2:26 PM
"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
Hmmm... @benlangmead.bsky.social
📢 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)
- 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)
July 1, 2025 at 4:26 PM
📢 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)
- 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)
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!
Move & resize the ranges to see how that affects bedtools operations like merge and intersect in real time!
June 10, 2025 at 4:27 PM
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!
Move & resize the ranges to see how that affects bedtools operations like merge and intersect in real time!
Nice work! Just a nitpick regarding the sentence below: we've been compiling sequence aligners to WebAssembly for a while now at biowasm.com :)
May 26, 2025 at 9:53 PM
Nice work! Just a nitpick regarding the sentence below: we've been compiling sequence aligners to WebAssembly for a while now at biowasm.com :)
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
It's made for scientists & engineers who want a living resume that showcases projects, work timeline, and blog posts that demonstrate your expertise
April 15, 2025 at 5:03 PM
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
It's made for scientists & engineers who want a living resume that showcases projects, work timeline, and blog posts that demonstrate your 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
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
March 5, 2025 at 12:37 AM
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
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 of future office hours: groups.google.com/a/omgenomics... (log in with Google, then "Join Group")
Join this Google Group to be notified of future office hours: groups.google.com/a/omgenomics... (log in with Google, then "Join Group")
February 24, 2025 at 10:49 PM
📢 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")
Join this Google Group to be notified of future office hours: groups.google.com/a/omgenomics... (log in with Google, then "Join Group")
🌲 New sandbox.bio tutorial: Learn to build phylogenetic trees from closely related genomes using ska (the tool, not the music) 🖥️ 🧬
sandbox.bio/tutorials/sk...
sandbox.bio/tutorials/sk...
January 17, 2025 at 11:28 PM
🌲 New sandbox.bio tutorial: Learn to build phylogenetic trees from closely related genomes using ska (the tool, not the music) 🖥️ 🧬
sandbox.bio/tutorials/sk...
sandbox.bio/tutorials/sk...
Agreed. Another benefit of having docs within the app is that you can give personalized help, eg if the user doesn’t have enough permissions to perform an action. That’s harder to do if docs are hosted separately.
December 15, 2024 at 3:49 PM
Agreed. Another benefit of having docs within the app is that you can give personalized help, eg if the user doesn’t have enough permissions to perform an action. That’s harder to do if docs are hosted separately.
I found 80 terabytes of uncompressed genomics files in public S3 buckets on 42basepairs 😯
That's thousands of dollars a month in additional storage and egress costs 💸
That's thousands of dollars a month in additional storage and egress costs 💸
December 10, 2024 at 6:38 PM
I found 80 terabytes of uncompressed genomics files in public S3 buckets on 42basepairs 😯
That's thousands of dollars a month in additional storage and egress costs 💸
That's thousands of dollars a month in additional storage and egress costs 💸
If you think bioinformatics is hard today, you should have seen it in 1985 😬 🧬 🖥️
November 11, 2024 at 5:28 PM
If you think bioinformatics is hard today, you should have seen it in 1985 😬 🧬 🖥️
This paper gets it. 🧬 🖥️
October 22, 2024 at 5:48 PM
This paper gets it. 🧬 🖥️
Sneak peek of sandbox.bio v2 👀
Some of the new tools we will support: Freebayes, SeqKit, Lumpy, Kraken2, Jellyfish, Mummer, Kallisto, ViralMSA, Sniffles.
What other tools and tutorials would you like to see?
Some of the new tools we will support: Freebayes, SeqKit, Lumpy, Kraken2, Jellyfish, Mummer, Kallisto, ViralMSA, Sniffles.
What other tools and tutorials would you like to see?
September 15, 2023 at 6:25 PM
Sneak peek of sandbox.bio v2 👀
Some of the new tools we will support: Freebayes, SeqKit, Lumpy, Kraken2, Jellyfish, Mummer, Kallisto, ViralMSA, Sniffles.
What other tools and tutorials would you like to see?
Some of the new tools we will support: Freebayes, SeqKit, Lumpy, Kraken2, Jellyfish, Mummer, Kallisto, ViralMSA, Sniffles.
What other tools and tutorials would you like to see?