Protein Engineering in Middle & High Schools?

New tools in the protein design space seem to drop nearly daily now, and many of these are free to all, open source, or at least free for non-commercial use.  Since I'm in the cloud lab business, and we have workflows built or all but built that can support many protein engineers, I'm very curious about to whom I might market such services.  Given the ease of running these tools, will we see students at levels much below college start taking on protein engineering as part of the curriculum or as special projects?

The Cache

If the lunar prospecting startups hadn't been scanning the moon at ever greater resolution, perhaps it would have never been found on the far side, but nothing that shiny was going to go undetected. Multiple companies found it around the same time, and while they tried to stay quiet the news soon leaked out. A hastily assembled robotic mission succeeded in capturing high resolution images, which made it clear this was no natural meteor.  The lack of an impact crater would have been astonishing, but here was a metallic object that had clearly been crafted. 

Two Decades!

Today marks two decades since I started writing here.  It is not a coincidence that it is also twenty years since I was officially notified by Millennium Pharmaceuticals that my services would soon be no longer needed.  Millennium had a strict no social media policy. When rumors of major layoffs swirled, and especially when I was tipped off a few days early that I and nearly my entire department were getting the axe, I primed myself.  Of course, that meant twenty years ago I committed a severe breach of that social media policy, but I thought at the time I had only two weeks at risk.  Sure, they could have clipped my exit package, which was relatively generous, but I think management wasn't too worried as long as I didn't go causing trouble, as they were busy radically restructuring the company.

ASHG Notebook: Chatting with Alex Hoischen

I caught up with the eminently quotable Alexander Hoischen at ASHG.  After we spoke for about 15 minutes, I realized I should have been taking notes - and Hoischen was generous enough to go back through some key points with my pen scribbling.  He can also be counted on for some gastronomy - in this case some pastries he had purchased at a French bakery elsewhere in Montreal.

ASHG Notebook: seqWell's ONT Library Prep

seqWell CSO Joe Mellor gave me a quick tour of their new transposase library prep product for Oxford Nanopore sequencers. Since the early days of ONT, users have had two basic choices for genome library prep: rapid method relying on transposase or the ligation kits.  Rapid is so stupid simple even I can do it (just don't ask for my yields!); ligation requires more molecular biology skill due to multiple enzyme steps as well as bead cleanups.  Ligation had higher yields than rapid - so simple but lower yield rapid or much more complicated but higher yield ligation?  seqWell's approach is only slightly more complex than the rapid kit, offers a large number of barcodes, and has flowcell yields on par with ligation.

ASHG Notebook: Bruker PaintScape Illustrates Chromosome Architecture

I spent last week at ASHG in beautiful Montreal.  I've scribbled many notes in my notebook, and am planning to emit a series of pieces each focused on a single topic.  Some of these may be brief, but I hope still interesting.  Far too many of these cover topics I had similar notes on from AGBT that never made it into pieces - such as the following on Bruker's PaintScape instrument.

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.