Daniel Sommer
@dsommer.bsky.social
Genomics and Computers
Roche Sequencing Software and Sequence Analysis
Learning LLMs
Roche Sequencing Software and Sequence Analysis
Learning LLMs
Reposted by Daniel Sommer
ish is a grep-like CLI tool that uses optimal alignment instead of exact matching.
It’s record-type aware, supporting line, FASTA, and FASTQ records.
Built in Mojo as a proof of concept for bioinformatics.
🧵1/5
It’s record-type aware, supporting line, FASTA, and FASTQ records.
Built in Mojo as a proof of concept for bioinformatics.
🧵1/5
Ish: SIMD and GPU Accelerated Local and Semi-Global Alignment as a CLI Filtering Tool https://www.biorxiv.org/content/10.1101/2025.06.04.657890v1
June 9, 2025 at 1:05 PM
ish is a grep-like CLI tool that uses optimal alignment instead of exact matching.
It’s record-type aware, supporting line, FASTA, and FASTQ records.
Built in Mojo as a proof of concept for bioinformatics.
🧵1/5
It’s record-type aware, supporting line, FASTA, and FASTQ records.
Built in Mojo as a proof of concept for bioinformatics.
🧵1/5
Reposted by Daniel Sommer
I was waiting two years to see this out!! The genomic location of bacterial genes is not random!!! Congratulation on the authors (Martin Lercher and Team!). www.science.org/doi/10.1126/...
Most bacterial gene families are biased toward specific chromosomal positions
The arrangement of genes along bacterial chromosomes influences their expression through growth rate–dependent gene copy number changes during DNA replication. Although translation- and transcription-...
www.science.org
April 10, 2025 at 7:43 PM
I was waiting two years to see this out!! The genomic location of bacterial genes is not random!!! Congratulation on the authors (Martin Lercher and Team!). www.science.org/doi/10.1126/...
Reposted by Daniel Sommer
“You are a traitor.”
An absurd and insulting thing to say to anyone who posts what Senator Kelly did.
And even more insulting since he served as a U.S. Navy captain and a NASA astronaut.
Kelly was a combat pilot and flew 39 combat missions during Operation Desert Storm in the Gulf War.
An absurd and insulting thing to say to anyone who posts what Senator Kelly did.
And even more insulting since he served as a U.S. Navy captain and a NASA astronaut.
Kelly was a combat pilot and flew 39 combat missions during Operation Desert Storm in the Gulf War.
March 10, 2025 at 3:37 PM
“You are a traitor.”
An absurd and insulting thing to say to anyone who posts what Senator Kelly did.
And even more insulting since he served as a U.S. Navy captain and a NASA astronaut.
Kelly was a combat pilot and flew 39 combat missions during Operation Desert Storm in the Gulf War.
An absurd and insulting thing to say to anyone who posts what Senator Kelly did.
And even more insulting since he served as a U.S. Navy captain and a NASA astronaut.
Kelly was a combat pilot and flew 39 combat missions during Operation Desert Storm in the Gulf War.
Reposted by Daniel Sommer
1/ We’re nonprofit. We’re independent. We only answer to readers like you.
Investigative journalism isn’t free to do, but thanks to 70K+ members, it’s free to read.
Investigative journalism isn’t free to do, but thanks to 70K+ members, it’s free to read.
March 10, 2025 at 4:01 PM
1/ We’re nonprofit. We’re independent. We only answer to readers like you.
Investigative journalism isn’t free to do, but thanks to 70K+ members, it’s free to read.
Investigative journalism isn’t free to do, but thanks to 70K+ members, it’s free to read.
Reposted by Daniel Sommer
While things are getting sorted over on the other app…
Smash that subscribe button on my NFL starter pack for free agency reactions 👇
go.bsky.app/8RH6KbH
Smash that subscribe button on my NFL starter pack for free agency reactions 👇
go.bsky.app/8RH6KbH
March 10, 2025 at 3:34 PM
While things are getting sorted over on the other app…
Smash that subscribe button on my NFL starter pack for free agency reactions 👇
go.bsky.app/8RH6KbH
Smash that subscribe button on my NFL starter pack for free agency reactions 👇
go.bsky.app/8RH6KbH
My favorite thing about San Francisco
February 25, 2025 at 5:29 AM
My favorite thing about San Francisco
Reposted by Daniel Sommer
This National Treasure sequel sucks
Now, with alt text, to ensure everyone fully understands exactly what we're dealing with with the 19-yo Canadian calling himself Big Balls who, along with a few other nerds, seem to have had exclusive control over the United States Treasury Department since Friday
February 2, 2025 at 9:10 PM
This National Treasure sequel sucks
Reposted by Daniel Sommer
The Air Force is stripping Tuskegee Airmen lessons from basic training curriculum because of our White supremacist government.
Put that in a headline.
www.expressnews.com/news/article...
Put that in a headline.
www.expressnews.com/news/article...
January 25, 2025 at 11:16 AM
The Air Force is stripping Tuskegee Airmen lessons from basic training curriculum because of our White supremacist government.
Put that in a headline.
www.expressnews.com/news/article...
Put that in a headline.
www.expressnews.com/news/article...
Reposted by Daniel Sommer
In which we propose (by analogy with variational autoencoders) that the genome instantiates a compressed representation of the form of the organism in a space of latent variables
January 17, 2025 at 4:34 PM
In which we propose (by analogy with variational autoencoders) that the genome instantiates a compressed representation of the form of the organism in a space of latent variables
Reposted by Daniel Sommer
Really coming down now in Gaithersburg/North Potomac . Streets are getting covered too. Be safe out there
January 19, 2025 at 8:48 PM
Really coming down now in Gaithersburg/North Potomac . Streets are getting covered too. Be safe out there
Reposted by Daniel Sommer
Hackathon! Register by 2/15: guides.library.cmu.edu/hackathon
"Machine learning and AI approaches to multimodal problems in computational biology."
March 3-5. Hosted by CMU Libraries, @dnanexus.bsky.social + @dcgenomics.bsky.social at @carnegiemellon.bsky.social in PGH (virtual option available)
"Machine learning and AI approaches to multimodal problems in computational biology."
March 3-5. Hosted by CMU Libraries, @dnanexus.bsky.social + @dcgenomics.bsky.social at @carnegiemellon.bsky.social in PGH (virtual option available)
January 16, 2025 at 6:23 PM
Hackathon! Register by 2/15: guides.library.cmu.edu/hackathon
"Machine learning and AI approaches to multimodal problems in computational biology."
March 3-5. Hosted by CMU Libraries, @dnanexus.bsky.social + @dcgenomics.bsky.social at @carnegiemellon.bsky.social in PGH (virtual option available)
"Machine learning and AI approaches to multimodal problems in computational biology."
March 3-5. Hosted by CMU Libraries, @dnanexus.bsky.social + @dcgenomics.bsky.social at @carnegiemellon.bsky.social in PGH (virtual option available)
Reposted by Daniel Sommer
Tom Brady clearly read the big book of football cliches from cover to cover and memorized it
January 12, 2025 at 10:39 PM
Tom Brady clearly read the big book of football cliches from cover to cover and memorized it
Reposted by Daniel Sommer
The reality is that Salesmanship is the differentiation between the two parties.
The Dems couldn't sell dollar bills for 50c
Trump has found his audience and can sell them dollar bills for $5
When everything is a story the algorithm flashes at you as you scroll, you better be selling fast
The Dems couldn't sell dollar bills for 50c
Trump has found his audience and can sell them dollar bills for $5
When everything is a story the algorithm flashes at you as you scroll, you better be selling fast
It is truly about who tells a better story — or really a story people want to hear and makes them see what they believe rather than believe what they see.
More jobs have been created under Biden than during the full terms of Trump, Obama, or Bush 43. @danprimack.bsky.social www.axios.com/2025/01/10/i...
January 12, 2025 at 12:52 AM
The reality is that Salesmanship is the differentiation between the two parties.
The Dems couldn't sell dollar bills for 50c
Trump has found his audience and can sell them dollar bills for $5
When everything is a story the algorithm flashes at you as you scroll, you better be selling fast
The Dems couldn't sell dollar bills for 50c
Trump has found his audience and can sell them dollar bills for $5
When everything is a story the algorithm flashes at you as you scroll, you better be selling fast
Reposted by Daniel Sommer
x
X has ~18m daily USA users. @bsky.app, ~1.5m.
Is it worth 20 MINS a day to proactively recruit and bring your friends, neighbors,relatives, businesses, anyone who is or could be a user, to @bsky.app?
If Bluesky ends up with more users than the others, you destabilize musk, zuck, trump.
X has ~18m daily USA users. @bsky.app, ~1.5m.
Is it worth 20 MINS a day to proactively recruit and bring your friends, neighbors,relatives, businesses, anyone who is or could be a user, to @bsky.app?
If Bluesky ends up with more users than the others, you destabilize musk, zuck, trump.
January 6, 2025 at 10:31 PM
Reposted by Daniel Sommer
Describing a 10 min walk this way is the most American thing I've ever read
December 31, 2024 at 7:14 PM
Describing a 10 min walk this way is the most American thing I've ever read
Reposted by Daniel Sommer
It isn't a website but I find github.com/mufeedvh/cod... to be much better with token counting and other features.
GitHub - mufeedvh/code2prompt: A CLI tool to convert your codebase into a single LLM prompt with source tree, prompt templating, and token counting.
A CLI tool to convert your codebase into a single LLM prompt with source tree, prompt templating, and token counting. - mufeedvh/code2prompt
github.com
December 9, 2024 at 12:21 PM
It isn't a website but I find github.com/mufeedvh/cod... to be much better with token counting and other features.
Reposted by Daniel Sommer
How does Texas fall for a fake punt when Georgia’s punter is hurt?
December 8, 2024 at 12:02 AM
How does Texas fall for a fake punt when Georgia’s punter is hurt?
Reposted by Daniel Sommer
I made a little swiss army knife tool for quickly inspecting FASTA/FASTQ sequences, including GC content, codon analysis, reverse complement, and file format conversions: 🖥️ 🧬
42basepairs.com/tools/sequen...
42basepairs.com/tools/sequen...
Sequence Analysis - 42basepairs
Bioinformatics sequence analysis on FASTA and FASTQ files, including reverse complement, GC content calculations, codon usage analysis, and converting your files to FASTA, FASTQ, or SAM format
42basepairs.com
November 27, 2024 at 7:35 PM
I made a little swiss army knife tool for quickly inspecting FASTA/FASTQ sequences, including GC content, codon analysis, reverse complement, and file format conversions: 🖥️ 🧬
42basepairs.com/tools/sequen...
42basepairs.com/tools/sequen...
Reposted by Daniel Sommer
I feel like not enough people know about Quarto for creating documents.
How it works: Write in markdown and use Quarto to convert it to html, pdf, epub, ...
I produce my books with Quarto (web + ebook + print version). But you can also use it for websites, reports, dashboards, ...
quarto.org
How it works: Write in markdown and use Quarto to convert it to html, pdf, epub, ...
I produce my books with Quarto (web + ebook + print version). But you can also use it for websites, reports, dashboards, ...
quarto.org
Quarto
An open source technical publishing system for creating beautiful articles, websites, blogs, books, slides, and more. Supports Python, R, Julia, and JavaScript.
quarto.org
November 24, 2024 at 10:24 AM
I feel like not enough people know about Quarto for creating documents.
How it works: Write in markdown and use Quarto to convert it to html, pdf, epub, ...
I produce my books with Quarto (web + ebook + print version). But you can also use it for websites, reports, dashboards, ...
quarto.org
How it works: Write in markdown and use Quarto to convert it to html, pdf, epub, ...
I produce my books with Quarto (web + ebook + print version). But you can also use it for websites, reports, dashboards, ...
quarto.org
Reposted by Daniel Sommer
For all you Pythonistas out there, if you haven't tried `uv` yet, give it a go. It will blow you mind 🤯 it is essentially `cargo` (from the Rust world) for Python! Amazing it took so long for the ecosystem to get here, but we did. Astral.sh are doing some incredible things, with incredible devs
November 20, 2024 at 10:31 PM
For all you Pythonistas out there, if you haven't tried `uv` yet, give it a go. It will blow you mind 🤯 it is essentially `cargo` (from the Rust world) for Python! Amazing it took so long for the ecosystem to get here, but we did. Astral.sh are doing some incredible things, with incredible devs
Reposted by Daniel Sommer
OK...that option is now on the form.
November 17, 2024 at 12:46 AM
OK...that option is now on the form.
Reposted by Daniel Sommer
I made a starter pack for algorithmic genomics. It's certainly incomplete, but already has a ton of awesome peeps. Let me know if you know people I should add (with a focus on algorithms and data structures in genomics)
go.bsky.app/TRWCnZs
go.bsky.app/TRWCnZs
November 12, 2024 at 2:03 PM
I made a starter pack for algorithmic genomics. It's certainly incomplete, but already has a ton of awesome peeps. Let me know if you know people I should add (with a focus on algorithms and data structures in genomics)
go.bsky.app/TRWCnZs
go.bsky.app/TRWCnZs