What Instrument Protocol Did I Actually Use?

Puttering around with some ideas for future experiments on our autonomous lab, I realized a potential software engineering gap that in my very hot take is ubiquitous in the industry.  For complex instruments such as thermocyclers, plate readers, imagers and many others, a run involves triggering a specified protocol.  These protocols are often saved on the instrument under a name, enabling a protocol to be called by name.  But what are you actually running?  If I'm correct that my new worry is a valid one, it will be something every effort to standardize access to instruments - such as PyLabRobot and the proposed Model Hardware Standard - 

What About BOB-Seq?

An interesting new approach to short read RNA-Seq library preparation bobbed into view this week, using click chemistry to barcode samples before any enzymatic processing.  This bioorthogonal barcode sequencing approach - aka BOB-Seq -  offers great promise in the burgeoning space of perturbing cell lines with drugs or other agents and then profiling the RNA.   

Sequence That Moldy Lanternfly!

Googling on some keywords from a social media post led to an interesting PNAS article from 2019 on two fungi which can infect the spotted lanternfly.  Lanternflies are a species accidentally imported from Asia which have been striking fear into many plant lovers in the Northeastern US.  If they'd just stick to tree-of-heaven, an imported plant that grows well in the US but accrues little to any love, but instead they suck sap from a wide variety of trees and vines, with particular love for grapevines, many orchard trees. and maples - among others.   They have still been spreading alarmingly up the I-95 corridor - often hitching rides as egg masses on the undersides of cars.  Biological control methods are of great interest - birds and toads apparently will consume lanternflies but equilibrium hasn't been reached.  The PNAS paper, written by researchers from Cornell University, looked at two native fungi which can attack lanternflies.  What surprised me on further searching is that one of these fungal species has no genome assembly at NCBI!!!! 

Does Your Instrument Strand Its Data in an Proprietary Binary Format?

This week we hosted the first REAL (Readiness & Engagement For Automated Labs) Summit; today that was followed by Ginkgo Datapoints Summit.  Both were fascinating surveys of the leading edge of automated data generation and feeding that data into AI models.  That data generation relies on linking sample preparation instruments to data generation instruments.  Two of my recent pieces were around issues of interfacing with instruments: Anthropic's proposed but not disclosed Model Hardware Standard and some of my (perhaps painfully naive) stabs at evaluating instrument Application Programming Interfaces (APIs).  I had commented that some instruments lack APIs - but what if even worse the data is still locked into a proprietary format?

A Marvelous Demonstration of This Proposition Which This Context Window is Too Narrow To Contain

My friend and former colleague Ash Jogalekar tweeted out an interesting result recently, which is now expanded into a preprint. Using an intelligent agent, he had generated a mathematical proof and then applied it to an interesting problem in nucleic acid structure design.  Ash also freely confessed that he lacked the mathematical background to evaluate the proof himself, which means it is utterly hopeless for me to dream of comprehending the proof since he has far more mathematics understanding than I do.  That touched a very sore spot in current mathematical academic discourse: how to deal with AI-generated proofs

Notes On Instrument APIs Critiques I Delegated to Claude

In my previous post about the Model Hardware Standard from Anthropic, I mentioned some exploration I've been running on instrument APIs.  Given our Catalyst Agent skills, a model such as Claude can evaluate what gaps exist between a given API and what we would require to integrate into our RAC autonomous laboratory environment.  I've run only a few APIs through, and I'm not going to reference which ones, but I have seen some patterns.  The whole process has been very thought-provoking.

Model Hardware Standard: What Is It? Seriously, That's What I'm Asking.

Anthropic, the company behind Claude, announced a new initiative called the Model Hardware Standard (MHS).  It's a way to enable intelligent agents to talk to laboratory instrumentation - well, that's what it's billed as.  But as first surfaced in a tweet by Sina Booeshaghi, if they want to be a standard they're taking a counterproductive path to it, as the announcement was only that.  A blogpost extolling the goals of MHS is given accompanied by testimonials from two early access sites , but no open and substantive description of MHS itself that would allow evaluating what it can and cannot do.  

Recombination-Based Autonomous Protein Structure-Function Search

An interesting preprint showed up last week in the autonomous agent-driven experimentation space - an area I'm paid to be very interested in.  This didn't run on our hardware, but we certainly could reproduce the experiment on our autonomous laboratory installation Nebula if the preprint had all the critical details (I'll try not to kvetch constantly about that, but it is an annoying brake on my eagerness to reproduce some or all the results).  Anyone could run it on our Cloud Lab - I haven't priced it out but this should come in at a very reasonable number.  What I found particularly clever is the solution to the problem of keeping protein engineering by AI in a reasonable cost envelope - and this is accomplished by relying on chimeras which can be a generated from one round of DNA synthesis and then clever shuffling.

Learning protein function through autonomous experimental interaction

Coban Brooks,  View ORCID ProfilePascal Notin,  View ORCID ProfilePhilip A. Romero

https://www.biorxiv.org/content/10.64898/2026.08.14.744985v1

SIMB Notebook: The Frontiers of Protein Engineering

The Society for Industrial Microbiology (SIMB) annual meeting in Austin the first week of the month was great fun.  I caught up with two Warpers, saw some other contacts from that era and met a bunch of new friends.  Plus I showed the flag for autonomous laboratories with a talk in a session on applying AI to the field - and got a chance to talk to multiple users of our systems at customer sites. Murphy's law struck in that our PR on four academic placements of autonomous labs came out about 20 hours after my talk.   In addition to the  session I appeared in, I attended a keynote on protein engineering, a session on enzyme engineering, and a whole day of talks on natural product research - plus all the posters.  I have a few notes that are maddeningly incomplete & I apologize in advance for the quality of attributions.  But here are a few observations on the space on protein engineering, which I am trying to level up to "barely dilettante" grade.

HiFi's Not Very Pacific Waters

PacBio had a major shakeup early this month. First came a large round of layoffs, which caught several individuals who were very much the face of innovation on social media.  Next came the sudden retirement of CEO Christian Henry, who has appeared in this space multiple times, and the elevation of CFO Mark Van Oene to the top seat.  

When PCR Gives You Lemons...

I wish to highlight an interesting new preprint from a group at Danish Technical University which explores the schmutz in PCR reactions, demonstrates some surprising conclusions, shows how their results might be very relevant to a common use of amplicon sequencing, and demonstrate a specific utility running PCR on in cases where typical PCR absolutely can't succeed.  Put another way, how often do people patent what was previously considered uninteresting experimental artifacts?

Dad Had Manuals, I Have An Agent

My father was a very methodical person, and that particularly applied when he decided to purchase the second IBM PC clone to appear on the market.  A whole host of manuals appeared on his desk and when I started skimming them it was clear he had been there first.  Sentences highlighted, marginal notes and of course editing marks to suit his sense of grammar and style.  The hardware, operating system, and APL programming language by far represented the most complex technology in the house - easily more complicated than everything else put together.

Element's Curious Patentsieg

Last week news broke that Element Biosciences had won a patent lawsuit against Illumina, and that it affected MiSeq.  MiSeq???? How did a patent battle in 2026 affect a platform launched nearly a decade and a half ago?  And which had been launched about five years before Element incorporated.  Which is being put out to pasture, though the MiSeqDx version What witchcraft is this?  I've done limited digging - I really dislike trying to dig through patents - and it is a strange case.

Fiber-Seq: Plasmids Model Chromosomes Well

A recent publication in Molecular Cell involving Fiber-Seq caught my attention, though I've since discovered this preprinted over a year ago.  One of the challenges in exploring the effects of genetic variations is the cost & effort to generate collections of variation which can be profiled by available methods.  This paper explores using Fiber-Seq on transfected plasmids and finds that, with important caveats, transfected plasmids evoke the same patterns of chromatin protection as the corresponding nuclear DNA.  This opens up the possibility of exploring large sets of variants for their effect on chromatin structure and either feeding that data into models or using it to understand clinical non-coding variation.  Or why not both?

The Simulator That Isn't There

Okay, this is one of those cases where I kvetch about other people not having built the tools I want to use - perhaps a bit of a insufferably egotistical position.  I mean, what gives me the chutzpah to do that?  My title, according to me, is "Automation Visioneer", so that gives me the right - though again, self-given title, self-given right.  But I hope you'll bear with me, because I think (there again, me! me! me!) it is an interesting observation on a curious gap in the software world - one that could make a very interesting project for someone so inclined. Oh, and this is one of the "a bit of promoting the product" entries - which means I get to blog on company time.

Countable Labs Raises Funds, Heads to Clinic

I caught up by teleconference recently with Countable Labs CEO Giovanna Prout, fresh off Countable Labs' $26M equity fundraising - a round which was oversubscribed.  Top on my agenda: what is Prout's vision to turn that money into products.  And how will Countable balance building molecular tools vs. applying those tools to clinical problems?

Alex Hastie Returns to BioNano, Takes CSO Reins

An interesting news item this week is that BioNano Genomics has appointed Alex Hastie as Chief Scientific Officer.  Hastie is an obvious choice for CSO, as for many years he was very much the public scientific face of BioNano's development.  .  But in February 2025 he left BioNano and headed to Arima Genomics.  But after a bit over a year at Arima and then a short stint at Inocras, Hastie has returned to the fold.

E.coli Doesn't Like Diets Either, At Least Genomic Ones

Another interesting preprint that fits several recent themes - genome minimization, discontinuation of products - comes from a Japanese group that reports on significantly reducing the genome of E.coli.  They tried for 1.7Mb but ended up settling - for now - with a 2.3Mb genome.  That's only about half the size of the strain they started with, but not at all a small genome.  

Shredding Genomes: Establishing Plausible Deletability

There's an interesting new preprint from Jay Shendure's lab which introduces the technique of Shred-Seq, which is a Cas3-driven approach to generating large deletions across a large eukaryotic genome.  By creating diverse collections of deletions, Shred-Seq enables identifying hidden non-coding sequences of functional importance.

The Commercial End for Fluidigm Technology?

Last week brought news that Standard Biotools, which is what Fluidigm morphed into, is being acquired by Treeline Biosciences, a drug developer.  The deal values Standard at about its cash position - and Treeline made it immediately clear this is a reverse merger to grab the cash and in effect go public by also grabbing Standard's stock listing.  What Treeline has made very clear is that they have absolutely no interest in is Standard's existing tools portfolio.