@darachm@therealworld

@bwhite5290 @kenbwork "Trained on massive amounts of high-quality data"

We have reached a tipping point. Societal and technological pressures are sparking a shift from animal testing to AI. Animal testing is currently a pillar of biomedical research. While animal testing has been responsible for tremendous advancements in human health and life-saving discoveries, questions arise on whether we can do better. Societal and technological pressures are converging to shift the world from animal testing to AI. This shift to AI will enable a completely new class of experimentation that brings the best aspects of basic early-stage experiments and premium late-stage animal tests and avoids the problems associated with each of them. Trained on massive amounts of high-quality data, AI could give us the cost efficiency and speed of early-stage experiments, the human and physiological relevance of late-stage experiments, and new, deeper insights into the mechanism of action to better contextualize the "why" that drives the results. Read more about this future here: aibiodesign.com/p/how-ai-will-…

Questions or comments? Please try the discussion options on the preprint so everyone can see it, and/or email me Email on preep, also ppiseq AT-THE-DOMAIN-OF rhesis SEPARATED-BY-DOT com

What do we find? Expressed in yeast, Nsp4 seems to stick to KDELR* - that could be part of mechanism for replication foci formation via retrograde, ORF7B seems to stick to taste-receptors 🤔, and many more. Not complete screen, but methods ready for non-specialist applications!

Here's methods for pooled gen of PPI-screening split-tag yeast assay libraries tldr; is gateway&gibson, then longread+Nextflow(w/ itermae), then select and shortread seq, fitness with FitSeq (fork) - a lotta PPI quants Also: ~4x your yeast transforms with this one simple trick

"As our Arab and Muslim neighbors are beaten and silenced, we fear the atmosphere in Germany has become more dangerous—for Jews and Muslims alike—than at any time in the nation’s recent history. We condemn these acts committed in our names."

@mbeisen Overlay journal in your future? ngl I am planning to submit something to PLoS One soon!

I still believe deeply in the need for a radical restructuring of science publishing to create an open and fair system that works well for science, for all scientists everywhere, and the public that supports us, and am proud of the steps we have taken to begin to get us there.

@gitlab @nextflow @SingularityApp And yall up and cancelled @mbeisen ? Wow. There's never a non-monetizable moment here on The Platform....

Check it if you want a pipeline on @gitlab for doing de novo plasmid assembly of long-read data separated out by barcode. Yeah random-fragmentation works and you don't need to know the barcodes ahead of time (but that probably helps) @nextflow + @SingularityApp

Arrayed in vivo barcoding for multiplexed sequence verification of plasmid DNA and demultiplexing of pooled libraries ift.tt/sIBVFiK #biorxiv_synbio

@iskander @myphysicsvoyage @bluesky take meee

@myphysicsvoyage I was about to say that I'm out of codes but then the sky gods heard my cries of anguish. Thanks @bluesky!

Got ~20 more invites, let me know if you need one. My heuristic for who I send them to is I scroll through each person's feed and look for any sign of participation in or engagement with scholarly research of any kind.

@mossomest @markowenmartin Thanks for mention. I'd be down to help folks (students etc) work on standardizing a design, just for kicks. It's really cheap, basically a ministat (TM) with the IR LED & sensor setup Probably start with a batch reactor, do the perturbations manually to show nutrient shifts

@markowenmartin Lots of good suggestions here but if you're interested in doing things super cheaply, I want to plug this amazing coffee can turbidostat that @darachm built a while ago! rhesis.com/posts/turbidos…

For many years now, I have been trying to find a way to measure growth of bacterial liquid cultures in an automated way. I have tried one commercial device which did not work. So I am still looking for a "recording turbidostat" that I can afford out of pocket (no grant). 1/2

@skryazhi @_miloj @s_venkataram Also, I hope the community around the @varianteffects can engage with it. I think there's obviously a lot of methods/skills transfer, and they may have more niche applications to develop on top of and around the work

@skryazhi @_miloj @s_venkataram It looks really good. I haven't had a chance to go through it in detail, but y'all hit on pretty much everything, and I am looking forward to getting into it with a journal club next week. This is going to help a lotta people - good work!

Nice to see this out! link.springer.com/article/10.100… This was such an enjoyable collaboration with @_miloj and @s_venkataram. I learned so much in the process. Thank you guys! Also thanks to @darachm for giving us valuable feedback on the preprint!

@kevinfolta @MIT @kesvelt And it's polio virus not polio

@kevinfolta @MIT @kesvelt 589 cases are vax derived. Esvelt point stands that virus genomes mutates a lot (to simplify), but this is not a sign of someone who is experienced or deeply familiar in what they are talking about.

Talking Biotech 379 - In the modern noise of lab leaks and man-made viruses, how likely is it that biotech could be weaponized? Dr. Kevin Esvelt joins the podcast to discuss a dark side of molecular biology. @MIT @kesvelt share.transistor.fm/s/c27ff950

@kevinfolta @MIT @kesvelt "perhaps the first biotechnology that will really spread on its own" has he heard of myxoma virus

@kevinfolta @MIT @kesvelt Anyone who refers to recovering infectious virus as "the booting up process" is worth a bit of skepticism

@kevinfolta @MIT @kesvelt But hey good to interview some voices from outside of biotech

@kevinfolta @MIT @kesvelt So identifying and studying viruses is valuable because zoonotic spillover is the source of new viral threats, and yes a ranked order list is important for prioritizing limited research bucks, and yes you can get useful research done without it circulating in a pandemic