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Biological Circuit Design

biocircuits.github.io

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Re: Biological Circuit Design

#21

Post by nextos »

BalinKing wrote: post #10
dekhn wrote: post #8

Earlier quoted context omitted.

Not for biologists; typically, they will do multivariate calculus but not so much diffeq (although depends on the school and the student).

At Caltech specifically FWIW, the biology major requirements include intro to diff eq (Ma 2),[0] which is usually taken in the first quarter of sophomore year. [0] https://www.bbe.caltech.edu/academics/biology/undergraduate-...

It's a fantastic and atypical program. It's not surprising faculty there wrote and teach from this masterpiece: https://www.routledge.com/Physical-Biology-of-the-Cell/Phill...

Re: Biological Circuit Design

#23

Post by RheingoldRiver »

dekhn wrote: post #5
max_ wrote: post #3

Earlier quoted context omitted.

What do u mean "graduate level"?

I mean that PhD candidates would be the primary target, rather than undergraduates, although talented, advanced undergraduates would also be welcome (this being Caltech, I'd expected there to be plenty of juniors and seniors in the course). I say this because it drops into diffeqs and fairly subtle/complex behavior quickly.

Caltech alum.

difeq is part of the common core that everyone must take to graduate and taught to sophomores first term, although a few (maybe 10-15 or so each year? out of about 200-250) (as of about a decade ago) students will test out of ma1a and then take ma2a first term freshman year instead of sophomore year. Testing out of ma1a requires knowing both calculus and also proof techniques.

courses numbered 100-199 are taken by both undergrads and graduate students, and because of Caltech's "rigorous" core often (but not always) the undergrads have an easier time.

I don't know this class specifically, but you would probably have a couple super motivated sophomores but mostly juniors and seniors taking a course numbered like this. Occasionally a few people will take 100-level courses freshman year (I took one such full-year and 1 one-term class, and I wasn't the only frosh in either).

(humanities/social science courses numbered 100+ are a bit of a different matter and tend to be super easy, but no one really takes those classes seriously for obvious reasons)

Re: Biological Circuit Design

#24

Post by epgui »

brcmthrowaway wrote: post #16

Can anything be made out of this?

Yes, just google "biological computer". There's been research on this for decades, and there are many promising therapeutic avenues for many pathologies. And people have built real-world toy biological computers that do cool things.

Re: Biological Circuit Design

#25

Post by epgui »

j7ake wrote: post #6
dekhn wrote: post #2

I sure hope this is a graduate-level course.

The difference between graduate and undergraduate level is that graduate is often easier (ie less work load) than undergrad… This is because graduate students main focus is their research, and courses are a distant second.

This is often (but not always) true. Not sure why you're getting downvoted so much.

Re: Biological Circuit Design

#26

Post by outlace »

Highly relevant book: Modeling Life by Alan Garfinkel. Assumes only knowledge of algebra and teaches the foundational skills of differential equation modeling. Best book I bought this year.

Re: Biological Circuit Design

#27

Post by Terr_ »

throwup238 wrote: post #17
brcmthrowaway wrote: post #16

Can anything be made out of this?

The individual techniques described in the class are in use all over the pharmaceutical and biotech industries (especially biosensors) but we're still in the early stages of biological circuits, akin to where electronics was right before the vacuum tube was invented. We've got stuff that operates sort of like basic logic elements like relay switches did in electronics, but we're far from designing any complex integra…

> We've got stuff that operates sort of like basic logic elements like relay switches did in electronics, but we're far from designing any complex integrated circuits.

Somehow this makes me think of the griping of background NPC scientists in the classic game Deus Ex, which I think has a rather high quality of year-2052 technobabble.

_________

DONOVAN: It's really a question of abstraction. [...] You can't be dealing with this sort of thing on the base-pair level.

LUNDQUIST: Essentially what I told Miss Chow. Tissue augmentation... it's not a matter of twiddling bits.

DONOVAN: We need to stay focused on tools.

LUNDQUIST: In principle... Yes, I agree.

DONOVAN: The older scientists don't grasp what it means to have so much data.

LUNDQUIST: Still, we have to throw them a bone once in awhile.

DONOVAN: With the right software, organism design should be indistinguishable from CAD/CAM.

Re: Biological Circuit Design

#29

Post by Demonoculus »

cge wrote: post #19
dekhn wrote: post #5

Earlier quoted context omitted.

I mean that PhD candidates would be the primary target, rather than undergraduates, although talented, advanced undergraduates would also be welcome (this being Caltech, I'd expected there to be plenty of juniors and seniors in the course). I say this because it drops into diffeqs and fairly subtle/complex behavior quickly.

I TA'd BE/CS/CNS/Bi/etc 191 years ago, we had some freshman in the class, and there was definitely the expectation they'd have some familiarity with differential equations; for example, the mass-action model of chemical reaction networks relies on them. These sorts of classes tend to get students in a broad range of levels, and I think there's the expectation that they'll figure out whatever they're unfamiliar with.…

I'm hoping this is a typo '191 years ago'. Don't mean to sound pedantic just interested when this was. My friend was in Caltech for his MS + PhD in Electrical engineering from 2008 onwards. I think he graduated in 2014-ish.
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