Howard Salis

Professor of synthetic biology & chemical engineering. De Novo DNA founder. Engineering microbes with predictive models & algorithms.

[Howard Salis @hsalis]

NEW PAPER led by @grace_vezeau! We rationally engineered synthetic riboswitches to carry out sense & respond for human biomarker proteins [mCRP and IL32-gamma] that indicate disease or infection. 16-fold activation without trial-and-error!
https://t.co/v2QHTikdmk

[Howard Salis @hsalis]

@ATinyGreenCell @Moon_Synth_Bio @jrkelly So much irony here that the CCP exploits labor with 9/9/6 conditions, few protective laws, fewer clinical regs, effectively competing with capitalistic countries that protects workers & patients with a 40-hr work week, OSHA, EHS, FDA, etc.

Karl Max would 🤯 looking at the CCP

[Sebastian S. Cocioba🪄🌷 @ATinyGreenCell]

SPLICECRAFT v1.0 IS LIVE!!!!!!!!!!!!

Open your terminal and type in "pipx install splicecraft" if you want to try it out, then spam "splicecraft update" often as I push updates frequently. A labor of love for the community I adore. Enjoy! 💚

[Howard Salis @hsalis]

@SynBio1 and 3) developing countermeasures (vaccines, treatments) so fast that any threat is mitigated before it becomes a national security issue. That removes state-sponsored attacks as existential threats. Bioterror is no longer terror-inducing.

[Howard Salis @hsalis]

@The__Taybor As a long time nanopore user, is it possible to extract the DNA that has passed through pores, using adaptive sampling to selectively pass or flick based on sequence correctness?

Would be a *great way* of combining DNA assembly & sequencing in one integrated workflow...

[Howard Salis @hsalis]

@SynBio1 Specifically: https://t.co/lpHx3pl7he
I wrestle with this question.

[Howard Salis @hsalis]

@SynBio1 What are your thoughts on a lab open-sourcing another oligopool-based DNA assembly method?

Option A: open-source it because the genie is out of that bottle already

Option B: don't open-source it because improved algorithms solving this problem will add more biosecurity risk

[Howard Salis @hsalis]

I want my super intelligent AGI to be like Vic Fontaine (Deep Space 9).

An emotive superintelligent hologram, but no need to lord it over the corporeals.

[Justin Blethrow @JBlethrow]

At @plasmidsaurus, we discovered our $50, 3 day TAT RNA-seq service can also detect mycoplasma contamination from several prominent species, and we've already alerted over a hundred labs to likely contamination. We're working on adding this to the service for free very soon.

[Howard Salis @hsalis]

@ProfTomEllis @SynBio1 A research org that only expects to exist for <10 years will absolutely cut all sorts of corners because why not?

[Howard Salis @hsalis]

@ATinyGreenCell What's your typical LLM workflow to accelerate writing tests & harnesses?

[Howard Salis @hsalis]

@SynBio1 This is what happens when GPT plays the Reverse UNO card on your image request.

[Howard Salis @hsalis]

@SynBio1 My cat *loves* whipped cream from the can, but not if you whip it yourself w/o the sugar. It could be the texture, or perhaps he’s a mutant.

[Howard Salis @hsalis]

@rlacombe @MoAlQuraishi @gembioworkshop @iclrconf You're thinking that more states = more complexity, but it's actually not that difficult to compute. We're developing whole-cell models & solving grand canonical ensembles involving 100s of DNA binding factors to calc binding probabilities. Much easier @ isotherm + isobaric!

[Howard Salis @hsalis]

@rlacombe @MoAlQuraishi @gembioworkshop @iclrconf There are more chemical reactions taking place inside a refinery than in the human body.

[Howard Salis @hsalis]

@rlacombe @MoAlQuraishi @gembioworkshop @iclrconf Then by induction, biological systems have state functions. What's your point?

[Convoke @Convokebio]

Today we're publishing our index of unmet needs in human disease: 2443 indications scored and ranked on burden of disease, prevalence, pipeline activity, and treatment burden. We hope this will help drug developers identify overlooked medical problems

https://t.co/OX4BKC8cfI

[Howard Salis @hsalis]

@Avi_Marcus @ATinyGreenCell @_inc0_ Nitrogenase uses ATP and electrons to catalyze its reaction. And they are high potential electrons that require special carriers (ferredoxins).

[Howard Salis @hsalis]

@beaverd the funny thing is that nitrogenase isn't just a single enzyme

and the rate-limiting step is not N2 binding

so ....

[Howard Salis @hsalis]

@anshulkundaje IMO it's herd mentality to train a transformer or two with genome sequence info. It's not a novel concept anymore, it just requires compute. I'd love to see AI people take a real big swing and develop better algorithms for training physics-informed NNs. Weights could have meaning