Daniel Jones
@dcjones.bsky.social
Computational biologist at Fred Hutchinson Cancer Center (See my work here: https://dcjones.github.io/). I also post about baking, books, and Seattle politics.
Reposted by Daniel Jones
Seen our Transit Tracker project on social media? You can learn how to build your own here: transit-tracker.eastsideurbanism.org
Transit Tracker
Transit Tracker is a DIY customizable public transit arrivals board for your home.
transit-tracker.eastsideurbanism.org
November 16, 2025 at 5:46 AM
Seen our Transit Tracker project on social media? You can learn how to build your own here: transit-tracker.eastsideurbanism.org
Got my copy of the inaugural issue of Seattle-centric baking magazine Crumb. It's good! www.readcrumb.co
November 15, 2025 at 7:43 PM
Got my copy of the inaugural issue of Seattle-centric baking magazine Crumb. It's good! www.readcrumb.co
Reposted by Daniel Jones
The last five months with Claude Code have completely changed how we work.
matsen.group/agentic.html details:
• How agents work (& why it matters)
• Git Flow with agents
• Using agents for science
• The human-agent interface
Questions? What has your experience been?
matsen.group/agentic.html details:
• How agents work (& why it matters)
• Git Flow with agents
• Using agents for science
• The human-agent interface
Questions? What has your experience been?
Agentic Coding For Scientists
A four-part series on using coding agents like Claude Code for scientific programming, covering fundamentals, workflows, best practices, and the human side of AI-assisted development.
matsen.group
November 13, 2025 at 5:08 PM
The last five months with Claude Code have completely changed how we work.
matsen.group/agentic.html details:
• How agents work (& why it matters)
• Git Flow with agents
• Using agents for science
• The human-agent interface
Questions? What has your experience been?
matsen.group/agentic.html details:
• How agents work (& why it matters)
• Git Flow with agents
• Using agents for science
• The human-agent interface
Questions? What has your experience been?
Reposted by Daniel Jones
seattle's political geography is as wild as (and presumably at some level is reflective of) its physical geopraphy
November 13, 2025 at 12:37 AM
seattle's political geography is as wild as (and presumably at some level is reflective of) its physical geopraphy
Cosign this. I was frustrated on election night when no seemed to be able to say what exactly the range likely outcomes was.
Fortunately @elections.kingcounty.gov provides a lot of historical data. I had fun digging into it with @ronpdavis.bsky.social and learning it's actually fairly predictable!
Fortunately @elections.kingcounty.gov provides a lot of historical data. I had fun digging into it with @ronpdavis.bsky.social and learning it's actually fairly predictable!
WAY too many of our political pundits wrote as if history barely exists--acknowledging the "progressive shift" but saying little to nothing about how big it usually is, and acting as if Katie was super behind and maybe-just-barely had a chance.
Those narratives were almost all mirage.
Those narratives were almost all mirage.
November 12, 2025 at 3:50 AM
Cosign this. I was frustrated on election night when no seemed to be able to say what exactly the range likely outcomes was.
Fortunately @elections.kingcounty.gov provides a lot of historical data. I had fun digging into it with @ronpdavis.bsky.social and learning it's actually fairly predictable!
Fortunately @elections.kingcounty.gov provides a lot of historical data. I had fun digging into it with @ronpdavis.bsky.social and learning it's actually fairly predictable!
Reposted by Daniel Jones
Like many of us, I've been waiting with baited breath for the Mayoral results for a week.
Putting together the Wilson PAC & raising the majority of its funds made me even more invested & amped up the roller coaster.
Despite my emotional journey, the result was predictable, (though not certain).
Putting together the Wilson PAC & raising the majority of its funds made me even more invested & amped up the roller coaster.
Despite my emotional journey, the result was predictable, (though not certain).
November 12, 2025 at 3:11 AM
Like many of us, I've been waiting with baited breath for the Mayoral results for a week.
Putting together the Wilson PAC & raising the majority of its funds made me even more invested & amped up the roller coaster.
Despite my emotional journey, the result was predictable, (though not certain).
Putting together the Wilson PAC & raising the majority of its funds made me even more invested & amped up the roller coaster.
Despite my emotional journey, the result was predictable, (though not certain).
Really wasn't a sure thing a few drops ago (it could have followed one of these shallower historical trajectories and missed the mark), but it's certainly nearly a sure thing now.
November 12, 2025 at 12:32 AM
Really wasn't a sure thing a few drops ago (it could have followed one of these shallower historical trajectories and missed the mark), but it's certainly nearly a sure thing now.
Reposted by Daniel Jones
Katie Wilson leads by 1346 votes!
November 12, 2025 at 12:05 AM
Katie Wilson leads by 1346 votes!
Updating my plot on Katie Wilson's latest numbers compared to previous races. Progressive vote share sometimes drops a little in the last few percent, but it's extremely unlikely that it's enough to reverse her lead at this point.
November 11, 2025 at 12:56 AM
Updating my plot on Katie Wilson's latest numbers compared to previous races. Progressive vote share sometimes drops a little in the last few percent, but it's extremely unlikely that it's enough to reverse her lead at this point.
They're calling him the Nate Silver of Seattle.
(Except I learned stats and epistemology from books, not internet poker, and I haven't cooked my brain with twitter addiction.)
(Except I learned stats and epistemology from books, not internet poker, and I haven't cooked my brain with twitter addiction.)
Last big drop of ballots hits this afternoon, so we'll see if I'm right, but I think Katie Wilson is going to win (by a narrow margin).
As shown here, she needs to as well or better in the last 17% of the ballots as she did on Friday's drop. The good news is that this is pretty likely.
As shown here, she needs to as well or better in the last 17% of the ballots as she did on Friday's drop. The good news is that this is pretty likely.
here's my attempt, with the red line showing where wilson would end up if she wins the same portion of remaining ballots that she won in the latest batch — it ends up being just a 0.2% margin
November 11, 2025 at 12:03 AM
They're calling him the Nate Silver of Seattle.
(Except I learned stats and epistemology from books, not internet poker, and I haven't cooked my brain with twitter addiction.)
(Except I learned stats and epistemology from books, not internet poker, and I haven't cooked my brain with twitter addiction.)
Reposted by Daniel Jones
Incredible. Progressive challenger Katie Wilson now has a 91-vote lead in Seattle’s race for mayor. She had been steadily gaining on incumbent Bruce Harrell.
There are about 8,000 ballots left to count.
There are about 8,000 ballots left to count.
November 10, 2025 at 11:57 PM
Incredible. Progressive challenger Katie Wilson now has a 91-vote lead in Seattle’s race for mayor. She had been steadily gaining on incumbent Bruce Harrell.
There are about 8,000 ballots left to count.
There are about 8,000 ballots left to count.
Reposted by Daniel Jones
Last big drop of ballots hits this afternoon, so we'll see if I'm right, but I think Katie Wilson is going to win (by a narrow margin).
As shown here, she needs to as well or better in the last 17% of the ballots as she did on Friday's drop. The good news is that this is pretty likely.
As shown here, she needs to as well or better in the last 17% of the ballots as she did on Friday's drop. The good news is that this is pretty likely.
here's my attempt, with the red line showing where wilson would end up if she wins the same portion of remaining ballots that she won in the latest batch — it ends up being just a 0.2% margin
November 10, 2025 at 5:05 PM
Last big drop of ballots hits this afternoon, so we'll see if I'm right, but I think Katie Wilson is going to win (by a narrow margin).
As shown here, she needs to as well or better in the last 17% of the ballots as she did on Friday's drop. The good news is that this is pretty likely.
As shown here, she needs to as well or better in the last 17% of the ballots as she did on Friday's drop. The good news is that this is pretty likely.
Turns out the ongoing debate about the dangers of increased surveillance in the city was not entirely hypothetical.
There was no sign ICE accessed Redmond's Flock system before Monday's arrests, but city officials said residents remained concerned about the technology.
Redmond turns off Flock Safety cameras after ICE arrests
www.seattletimes.com
November 10, 2025 at 7:38 PM
Turns out the ongoing debate about the dangers of increased surveillance in the city was not entirely hypothetical.
Last big drop of ballots hits this afternoon, so we'll see if I'm right, but I think Katie Wilson is going to win (by a narrow margin).
As shown here, she needs to as well or better in the last 17% of the ballots as she did on Friday's drop. The good news is that this is pretty likely.
As shown here, she needs to as well or better in the last 17% of the ballots as she did on Friday's drop. The good news is that this is pretty likely.
here's my attempt, with the red line showing where wilson would end up if she wins the same portion of remaining ballots that she won in the latest batch — it ends up being just a 0.2% margin
November 10, 2025 at 5:05 PM
Last big drop of ballots hits this afternoon, so we'll see if I'm right, but I think Katie Wilson is going to win (by a narrow margin).
As shown here, she needs to as well or better in the last 17% of the ballots as she did on Friday's drop. The good news is that this is pretty likely.
As shown here, she needs to as well or better in the last 17% of the ballots as she did on Friday's drop. The good news is that this is pretty likely.
Continuing to look at the late leftward swing in Seattle elections. Here's Katie Wilson's trajectory compared to every off-year election since 2017 (where there was a clear left candidate). Historically the swing usually surpasses what she needs to win (black line).
November 7, 2025 at 11:52 PM
Continuing to look at the late leftward swing in Seattle elections. Here's Katie Wilson's trajectory compared to every off-year election since 2017 (where there was a clear left candidate). Historically the swing usually surpasses what she needs to win (black line).
Reposted by Daniel Jones
Thanks to @dcjones.bsky.social, I have key info!
The progressive percentage of the Friday vote count is typically much higher on Friday than Thursday.
Moon's was 9% higher on Friday than Thursday.
Gonzales' was 5%
Wilson primary was 14%.
Thursday to Monday they were 12%, 4.5%, and 12%.
The progressive percentage of the Friday vote count is typically much higher on Friday than Thursday.
Moon's was 9% higher on Friday than Thursday.
Gonzales' was 5%
Wilson primary was 14%.
Thursday to Monday they were 12%, 4.5%, and 12%.
November 7, 2025 at 2:38 AM
Thanks to @dcjones.bsky.social, I have key info!
The progressive percentage of the Friday vote count is typically much higher on Friday than Thursday.
Moon's was 9% higher on Friday than Thursday.
Gonzales' was 5%
Wilson primary was 14%.
Thursday to Monday they were 12%, 4.5%, and 12%.
The progressive percentage of the Friday vote count is typically much higher on Friday than Thursday.
Moon's was 9% higher on Friday than Thursday.
Gonzales' was 5%
Wilson primary was 14%.
Thursday to Monday they were 12%, 4.5%, and 12%.
Updating my plot of historical counting trends in Seattle mayor elections. We are back to pretty a pretty standard trajectory (which is promising for Katie Wilson).
November 6, 2025 at 11:51 PM
Updating my plot of historical counting trends in Seattle mayor elections. We are back to pretty a pretty standard trajectory (which is promising for Katie Wilson).
Reposted by Daniel Jones
My take? @wilsonforseattle.bsky.social is still the favorite.
Until we have Thursday drop data (assuming it is election day dropbox data), we have no good reason to think otherwise, even if we do have reason to FEEL nervous.
rondezvouswa.com/p/katie-wils...
Until we have Thursday drop data (assuming it is election day dropbox data), we have no good reason to think otherwise, even if we do have reason to FEEL nervous.
rondezvouswa.com/p/katie-wils...
November 6, 2025 at 5:25 AM
My take? @wilsonforseattle.bsky.social is still the favorite.
Until we have Thursday drop data (assuming it is election day dropbox data), we have no good reason to think otherwise, even if we do have reason to FEEL nervous.
rondezvouswa.com/p/katie-wils...
Until we have Thursday drop data (assuming it is election day dropbox data), we have no good reason to think otherwise, even if we do have reason to FEEL nervous.
rondezvouswa.com/p/katie-wils...
Day 1 of over-analyzing Seattle mayor election: here's how the margin has changed in this and previous elections. (Grey line is what Wilson has to hit to win)
November 5, 2025 at 11:50 PM
Day 1 of over-analyzing Seattle mayor election: here's how the margin has changed in this and previous elections. (Grey line is what Wilson has to hit to win)
Reposted by Daniel Jones
holy shit i flew over it as it happened!
October 11, 2025 at 5:11 AM
holy shit i flew over it as it happened!
Reposted by Daniel Jones
The three AI outcomes
- we all become one with the machine god and shuffle off our mortal coils to live as a hive mind of cyborg superbeings
- we all die horribly and painfully in an alien world that has no use for human emotion, creativity, or intellect
- 1.5% TFP growth for seven years
- we all become one with the machine god and shuffle off our mortal coils to live as a hive mind of cyborg superbeings
- we all die horribly and painfully in an alien world that has no use for human emotion, creativity, or intellect
- 1.5% TFP growth for seven years
October 10, 2025 at 11:30 PM
The three AI outcomes
- we all become one with the machine god and shuffle off our mortal coils to live as a hive mind of cyborg superbeings
- we all die horribly and painfully in an alien world that has no use for human emotion, creativity, or intellect
- 1.5% TFP growth for seven years
- we all become one with the machine god and shuffle off our mortal coils to live as a hive mind of cyborg superbeings
- we all die horribly and painfully in an alien world that has no use for human emotion, creativity, or intellect
- 1.5% TFP growth for seven years
Reposted by Daniel Jones
Now that I'm settled in at @umasschan.bsky.social, I'm hiring at all levels: grad students, post-docs, and software engineers/bioinformaticians!
The goal of my lab is to understand the regulatory role of every nucleotide in our genomes and how this changes across every cell in our bodies.
The goal of my lab is to understand the regulatory role of every nucleotide in our genomes and how this changes across every cell in our bodies.
October 7, 2025 at 3:24 PM
Now that I'm settled in at @umasschan.bsky.social, I'm hiring at all levels: grad students, post-docs, and software engineers/bioinformaticians!
The goal of my lab is to understand the regulatory role of every nucleotide in our genomes and how this changes across every cell in our bodies.
The goal of my lab is to understand the regulatory role of every nucleotide in our genomes and how this changes across every cell in our bodies.
Excellent photo choice from Reuters
October 7, 2025 at 3:52 PM
Excellent photo choice from Reuters
Reposted by Daniel Jones
Congrats to Mary Brunkow of #seattle for #immunology discoveries leading to shared #Nobel ...
Congrats to Institute for Systems Biology.
#research #science
www.nytimes.com/2025/10/06/h...
Congrats to Institute for Systems Biology.
#research #science
www.nytimes.com/2025/10/06/h...
Nobel Prize in Physiology or Medicine Is Awarded for Work on Immune Systems
www.nytimes.com
October 6, 2025 at 1:24 PM
Congrats to Mary Brunkow of #seattle for #immunology discoveries leading to shared #Nobel ...
Congrats to Institute for Systems Biology.
#research #science
www.nytimes.com/2025/10/06/h...
Congrats to Institute for Systems Biology.
#research #science
www.nytimes.com/2025/10/06/h...
Reposted by Daniel Jones
ai2 is pretty consistently the most serious about open sourcing things that are useful for research imho
Introducing Asta DataVoyager—our new AI capability in Asta that turns structured data into transparent, reproducible insights. Built for scientists, grounded in open, inspectable workflows. 🧵
October 1, 2025 at 3:07 PM
ai2 is pretty consistently the most serious about open sourcing things that are useful for research imho