Nice quality of life improvement - Parabricks migrated their docs system to Fern so that it can better serve agents with a built-in MCP server. Check out the site and get a few ways to register it in your harness:
Angel Pizarro
@angelp.bsky.social
Product Architect in the NVIDIA Digital Bio team, once again a bioinformatics guy. Also a fussy coffee guy.
I was having a conversation the other day about car insurance. In short they were using one of those trackers to lower their insurance rate… I am vehemently opposed to it. Insurance is for catastrophes and you do NOT want to be dealing with corp lawyers during the aftermath. Full tort is the way.
A little-known feature of Nextflow is that it can support iterative processes - feeding process outputs back as inputs until a threshold is met. This is especially useful for ML training, molecular dynamics simulations, and other looped workflows. 📚 Find out more: hubs.la/Q04prlGh0
Running Until: Iterative Loops in Nextflow | Seqera
Nextflow can express iterative loops with a topic channel and an until check. Here's how to make a process feed on its own output, no recursion needed.
hubs.la
In DC for the ISMB conference this week. Have't been here is a while and it's nice to be back walking around familiar spaces.
For a conference of technical people, the ISMB website is .... really something
I think DJT is right that the average voter doesn’t care about the housing bill. It’s abstract and they wouldn’t see results until years from now (if ever). Fox is not covering it so they may not even know it exists. They only cover DJT “pressuring congress” to pass the SAVE act.
Great editorial use of AI as an assistive technology. Doesn’t outsource your voice/science/skills
Stephen Turner@stephenturner.us · last mo.I getting a pre-submission peer review on a manuscript is a great use for AI. You don't need a third-party tool. GPT-5.x and Opus 4.x are good, and open/community development of these skills/harnesses is the way. I wrote a Claude skill wrapping the Consensus MCP to do this. doi.org/10.59350/b35...
10 tips for getting better R code from your AI coding agent www.infoworld.com/article/4184... #Rstats
10 tips for getting better R code from your AI coding agent
With the proper setup and guidance, you can have Claude Code, Codex, Posit Assistant, and other coding agents writing R code like a pro. Here’s how.
infoworld.com
Stroke rate a good indicator he won’t last the full term. What happens after that is anybody’s guess.
I am of the opinion that a Rust rewrite should NOT have to have “Rust” or “rs” in the name, just bump the major version number. Glad to see Rob did so with salmon.
Rob Patro@robp.bsky.social · 2mo agosalmon 2.0 (the rust re-write) is now live! It's also the version you get if you install via bioconda. This is a from-scratch rewrite in rust, and the base for future development. I'll post a more detailed thread tomorrow, but you can read the docs here combine-lab.github.io/salmon/
salmon 2.0 (the rust re-write) is now live! It's also the version you get if you install via bioconda. This is a from-scratch rewrite in rust, and the base for future development. I'll post a more detailed thread tomorrow, but you can read the docs here combine-lab.github.io/salmon/
salmon
Fast, accurate transcript quantification from RNA-seq reads.
combine-lab.github.io
After looking at a Maeving for 4 years I decided it’s now or never. Took delivery of this awesome piece of kit a couple of days ago.
1/ What if you put all the ways that Jared Kushner is selling out America while lining his pockets into one place? In our new cover story, @cjcmichel.bsky.social did just that www.motherjones.com/politics/202...
Off to BioIT in Boston this week. Mainly to catch up with as many biotech folks as I can so we can figure out a way through this AI transformation together.
Thought of the day - striving to be the better person (taking the high road, turn the other cheek, etc) is hard sometimes. Sometimes you want to be petty but you know it’s not good for you in the long term so you hold back. Honestly I don’t know what is better but that’s how I operate
Wrote a quick blog on LinkedIn about some thoughts I've been having. www.linkedin.com/pulse/some-t...
Some thoughts on bioinformatics and AI Agents
Over the years, the bioinformatics community has adopted software engineering best practices to bring order to the chaos of self-taught programming. We embraced concepts like DRY (Don’t Repeat Yoursel...
linkedin.com
2 years ago I went to bed feeling great, woke up next morning with a painful ear and hearing loss (which became permanent). Because of a shingles infection in my auditory nerve. Get the vaccine if you're eligible www.wired.com/story/shingl...
You Should Be More Freaked Out by Shingles
The viral infection leaves millions with chronic pain, increased stroke risk, and lifelong nerve damage—yet vaccination rates remain dangerously low.
wired.com
I decided that this year I will be going back to my bioinformatics roots and working on ML in life sciences. I’ve been one step removed from the fray for a little over 5 years so it’ll be interesting to dive back in and see what’s what.
Nice thread summing up what everyone is going through right now.
Dare Obasanjo@carnage4life.bsky.social · 4mo agoAs we dig deeper into AI productivity gains, it helps to separately consider the impact at individual, team, and organizational levels. For individuals, AI can boost output but also create fake progress, side quests, and in some cases make people worse by turning passable work into AI slop.
Testing out Gemini for coding up a native macOS app for tracking espresso profiles, beans, etc. Should be interesting. Need a name for it though. Current front runners are “Grounds Control” and “Brew Base”. Suggestions welcome.
Project Hail Mary was a really great movie adaptation from the book. I agreed with a lot of what they needed to edit out for time, but it did lose some of the deeper character development as a result.
