donovanr

6 ms·

1.
by donovanr 1y ago
Yes! Units are up to you (with some constraints)! Physicists do this in practice a lot: https://en.wikipedia.org/wiki/Natural_units
2.
by donovanr 1y ago
Yes, this. A lot of work in this field is missing from that timeline. Just circa 2010-2020, Les Loew's VCell 3D PDE approaches, Faeder et al.'s BioNetGen / ODE work, Luthey-Schulten Shulten's grid based cell models, the
3.
by donovanr 2y ago
it's uncreative/tired but at least to the point. Too many papers are confused / opaque agglomerations of a year's worth of research shoehorned into a paper. At least with these you can fairly easily assess whether the cl
4.
by donovanr 6y ago
This rings _so_ true. While I was in grad school I got bored sitting behind a computer all day, and my wife and I decided to build a tiny house on a trailer as a way of venting our pent-up DIY urges. We'd just build it in our spare ti
5.
Why no black bar for John Lewis(usatoday.com)
5 points by donovanr 6y ago|1 comments
6.
by donovanr 6y ago
Allen Institute for Cell Science | ONSITE Seattle | Full-time | software engineer / ML / computer vision | https://alleninstitute.org/ The modeling team at the Allen institute for Cell Science is hiring for two so
7.
by donovanr 7y ago
Allen Institute for Cell Science | software engineer / ML / computer vision | ONSITE Seattle | Full-time The modeling team at the Allen institute for Cell Science is hiring for two software engineering positions -- a data generali
8.
by donovanr 8y ago
Very nice. It might be worth worth weighting each data point in proportion to the population it represents.
9.
by donovanr 8y ago
1. All of the above. The label free tool in particular gives you such a big free lunch at the microscope that the combination of it and good visualization has the potential to massively impact research workflows. 2. We are very interested
10.
by donovanr 8y ago
That's at least close to true. It might be better to think of it as a smoothed "segmentation" of a 3D image, i.e. some algorithm decided what pixels are officially part of e.g. the mitochondria set, and outlined them. That
11.
by donovanr 8y ago
Characterizing cellular variation is exactly what we're interested in, e.g when and why are the mitts clustered around the nuclear vs not. Lots of images in our data have them packed around the nucleus -- you can look at the localizat
12.
by donovanr 8y ago
not sure about specific plans but it's definitely something we're interested in
13.
by donovanr 8y ago
just saw this; I'm part of the computational modeling team that worked on this -- can try to field any questions or find more qualified people to do so.
14.
by donovanr 8y ago
would be happy to, but I don't see your email there -- mine's in my profile (I think!) if you'd like to get in touch
15.
by donovanr 8y ago
Some feedback on the quiz: - a few of the questions were very good, and either spoke to key high level concepts, or were specific while being language agnostic. (e.g which one of these layers wouldn't you need, why wouldn't this t
16.
by donovanr 9y ago
specious extrapolations aside, the plot itself is deceptive -- exponential growth in a log-linear plot should be a straight line, not one accelerating upward super-exponentially.
17.
by donovanr 10y ago
Sedgewick's 1978 paper[0] on implementing quicksort has some interesting hand optimizations of the assembly code -- loop rotating, unrolling, etc. I wonder if modern compilers do the same? [0] http://penguin.ewu.edu/cs
18.
by donovanr 10y ago
Zee's QFT in a Nutshell is a very readable, high-level view of what's going on in QFT. Griffiths' book is his one text I haven't read, but I love his others so much I can't help but second the recommendation.
19.
by donovanr 10y ago
Right, but it's the 'every once in a while" part that I wonder about, i.e. the variance of that distribution. Maybe you could argue that since the Maxwell-Boltzmann distribution is narrower the lower its mean, if kT is small
20.
by donovanr 10y ago
I've always been curious: I understand that h.nu from cell phone radiation isn't big enough to ionize (say) DNA, but since the molecules in our body are in thermal equilibrium, can't h.nu + kT get it done every once in a whil
21.
by donovanr 11y ago
I enjoyed reading this as written rather than as (I assume) intended: "The enormity of defining any job they want can be overwhelming..."
22.
by donovanr 11y ago
These results seem unconvincing without any error bars / confidence intervals, or even a mention of the number of replicates performed (though the downloadable data set seems to indicate that each test condition was performed only once
23.
by donovanr 11y ago
Have to rep for my favorite math text that pretty much no one else has heard of: Ray Mayer's Introduction to Analysis [1]. It's rigorous, compellingly readable, and accessible to college freshmen. It was never published commerci
24.
by donovanr 11y ago
I work at the cellular/molecular scales in a computational biology program; musculoskeletal stuff can often find a home in bioengineering departments. Not sure how much insight I can offer, but feel free to shoot me an email, my conta
25.
by donovanr 11y ago
I am a 5th year computational biology student, and have yet to take any real coursework in theoretical biology, despite the fact that most of what I do could be broadly classified as exactly that. Theoretical biology seems to be the black s
26.
by donovanr 11y ago
Massless GR is sometimes called "pure gravity", and is something people are still interested in (or were, last time I was paying attention) [1]. Kind of remarkable that even the base-case has so many open issues. I should re-rea
27.
by donovanr 11y ago
The author only encountering to 10^500 sting vacua/landscape issue in 2013 raises some serious crackpot alarm bells [0]. That was common knowledge in the community by 2005 at the latest. http://math.ucr.edu/home/b
28.
by donovanr 11y ago
I don't mind profanity at all per se, but the tacit misogyny of that one does bum me out. I'm from the US, if it matters.
29.
by donovanr 11y ago
I'm a CompBio PhD student, and my experience is that folks in that field are much more careful with statistics than in, say, molecular biology labs, but it varies from lab to lab. My PI is exceedingly meticulous about stats -- for ins
30.
by donovanr 11y ago
A lot of the low-hanging fruit, in terms of statistical significance for heritable disease, has already been picked, in the sense of a naive search for SNP X in gene Y that causes disease Z. The more people continue to look for single SNPs

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