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alexholehouse

3,113 karma · joined August 3, 2011

My lab studies how biological function is encoded into disordered proteins using a combination of theory, simulations, informatics, and experiment.

https://holehouse.wustl.edu

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alexholehouse··on Why Learning to Code Is So Hard – and Why It Gets Easier
I'm looking at running an intro to CS/programming short course for biologists (graduate students) at my university. I may drop you an email at some point to pick your brains, if that's OK?
alexholehouse··on Europe approves high-price gene therapy
I'm torn here. On the one hand, this is a great development, and could represent an effective way to treat a whole range of diseases.

On the other, and I speak from experience, we really don't fully understand what goes on in terms of gene expression regulation. We have ideas which generally work in vitro, mostly in vivo with model organisms (drosophila, yeast, etc) but relatively little basic research looking at fundamental mechanisms of regulation is done in higher eukaryotes. The upshot is that we may have ideas of what's happening, but those ideas may be one of several possible explanations which lead to similar outcomes. Moreoever, the impact of gene therapy in terms of a long term cellular (and immune) response is poorly understood.

I'd be intrigued to see what longitudinal data have been generated to show Glybera's safety over the kinds of timeframe relevant here.

alexholehouse··on Goldeneye 64's inspirational startup story
It was all about the race to the RCP90 on stack in multplayer - that white corridor of death...
alexholehouse··on Show HN: Built my resume as an interactive website, version-controlled on Github
Great to see a fellow Wash U student on here - nice work. One thing - is there any way to export it as a pdf?

I know this kind of defeats the purpose, but some people/companies may still want to print these things out, or at least have them on file where they have a static copy (as in it won't change automatically), so having control over what that pdf looks like might be useful.

Just a minor point though, love the design.

alexholehouse··on How To Land Any Major Brand For Your Startup
If I were the event company I'd just bar Virool from future events. I'd have though making enemies would be more detrimental than gaining a finite number of clients, but equally, I may not be the most informed person to make a judgement in this situation.
alexholehouse··on Gary McKinnon saved from extradition to the US
So does this not mean that a white person in (say) Nigeria would not be able to claim they were experiencing racism if they were targeted because of their skin colour? [I'm not, in any way trying to be inflammatory]

I actually agree with a lot of what you're saying, but I'm not sure historical context gives a perfect mechanism to categorize racism or banter, but it does give a lot of weight, certainly.

alexholehouse··on Gary McKinnon saved from extradition to the US
but in most cases these days it's more a more casual comedy thing, similar to the way the English dislike the French - they don't really but it's fun to have a frenemy.

I think this is totally accurate, but I worry this subtly is lost on some people, and especially kids. I'm English, and lived in Scotland between the age of 10 and 14, and the genuine anti-English victimization I received both at school and out and about was ridiculous. It never bothered me, perhaps because I don't really consider myself, "English" having (at that point) never lived there, but I remember being genuinely shocked. I expect it's much the same a French child would experience coming to school at that age in the UK.

Kids see their parents or comedians mock the English/French, but don't necessarily distinguish between, "banter" and genuine disdain. Hopefully those kids grow up to identify that difference, although some of the experiences I had would suggest this may not always be the case.

alexholehouse··on Paul Graham: Silicon Valley Favors Obama Over Romney 2 To 1
I'm not sure you can have a "landslide" with a sample size of 24...
alexholehouse··on AndroidKickstartR: Start your next Android app in 10 seconds
I'm about to buy a new phone, and I'm going to get an iPhone 5. The primary reason is not because it's (necessarily) a better phone than any Android phones, or because iOS6 is better, but because I can't spend three weeks building an iPhone app anywhere nearly as I could an Android one. I don't have the time, or even close to having the time, but I know with an Android phone I would do it anyway, and it would probably just derail the other 30 things I don't have time for. (For the record, I have built an iPhone app before and it's not that it's harder than building for Android in terms of code/framework, but I don't have a Mac, a developer licence etc).

I wonder if anyone else is motivated to get an iPhone because of this? It's a kind of bizarre situation, but one I'm so glad I identified before buying a phone.

alexholehouse··on Show HN: LearnStreet - The Best Place to Learn How to Code
Looks great, really nice. Minor point, I have a feeling (and can't find evidence to the contrary) that Twitter's stack is actually Java, not Ruby [1]. They may have changed back since then, but I can't find anything about it. Maybe I'm totally off though, and other parts of their stack are rails. I don't know - I'm not really a webdev guy...

[EDIT] - any reason for the downvote? I'm totally fine with being wrong, or have I just completely missed something?

The reason I brought it up was because when you select Ruby, one of the motivational messages opens with, "Twitter uses Ruby to power 400M incredible tweets every day."

http://www.readwriteweb.com/cloud/2011/04/twitter-drops-ruby...

alexholehouse··on Myths about Hash Tables
I think at the point of having 1000 items in each bucket, a hashtable was never a good idea. I read it more as like, "Don't worry if you have collisions cos it'll be OK" as opposed to "Collisions have no impact on performance".
alexholehouse··on Linux 3.6 released
OK, so here's a question. I've always wanted to spend some time reading through the Linux kernel - I really enjoyed operating systems when I studied it (and reading through MINIX src) but I don't really know where/how to start with Linux.

I mean, I guess I can just dive in, and maybe that's the best approach, but is there a strategy anyone would recommend for reading the Linux source in terms of it making sense as a combined unit of code (as opposed to a collection of algorithms, if that makes sense)?

alexholehouse··on Male DNA Commonly Found in Women’s Brains
This story already made the rounds on wednesday http://news.ycombinator.com/item?id=4582655

I'm yet to read the paper, but the comment highlighted in the thread from Wednesday raises some points[1]. For ease of access I'll re-replicate it here;

"This is just a PCR study. No evidence that the foreign human DNA even entered host cells, much less that it was expressed. Probably shows only that minute quantities of foreign human DNA can hang around a host body for a while. Most likely explanation is that it gets bound up in the extracellular matrix. Being that the DNA is of human origin, it would not trigger an immune response, but rather, it would just be slowly degraded like the host's own DNA when it is released from dead cells (part of the normal, perpetual turnover of cells). DNA is hardy stuff; people have sequenced DNA from Neanderthal bones. Study co-author J. Lee Nelson's comments are ridiculous hype. He should be ashamed of himself. That those comments were published in this newspaper uncritically is also an embarrassment. This work was published in PLoS ONE. PLoS ONE articles are peer reviewed only for the validity of the methods used, not for the importance of the subject matter or the validity of the conclusions drawn. This is where you can publish all sorts of meaningless crap."

I disagree with the extremity of the commentor's view on PLoS ONE articles, and feel they should perhaps have noticed that Dr. Nelson is a lady, not a dude, but still something worth considering.

[1] - http://www.latimes.com/health/boostershots/la-heb-women-brai... , comment 2

alexholehouse··on Re: Hakin9's new Nmap Guide
Outstanding. My personal favourite is,

"Our experiments soon proved that exokernelizing our fuzzy Knesis keyboards was more effective than making autonomous them, as previous work suggested. Our experiments soon proved that microkernelizing our PDP 11s was more effective than exokernelizing them, as previous work suggested. We note that other researchers have tried and failed to enable this functionality."

alexholehouse··on Remove your alarm safety net and fix your sleep
I didn't used to know people used snooze at all - it always seems so futile - you have two options (at least in my mind);

alarm @ 8:00 --> get up at 8:00

alarm @ 7:45 + snooze --> painfully lose 15 minutes of good quality sleep and hate every second of it.

Why is that even a thing?

alexholehouse··on Sons' DNA remains in mothers' brains
Paperlink: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjourna...
alexholehouse··on Tesla reveals Supercharger network, Free Fill Ups
Sorry - just a typo, meant profit. It was late.
alexholehouse··on Tesla reveals Supercharger network, Free Fill Ups
I remember talking to a friend who worked for an oil company, who told me that the shops at gas stations actually make 2-3 times more than the revenue generated from the gas. If you were an oil company which dealt exclusively with the consumer (which of course non of them are) you would in fact be a catering business which sold gas on the side.
alexholehouse··on Mypy - An experimental Python variant with dynamic and static typing
Reminds me a bit of Julia[1], which allows optional static typing.

[1] http://julialang.org/

alexholehouse··on Zimbabwe residents synchronize toilet flush
> The example you give was a harsh yet necessary action due to the fact that low-IQ humans require brutality to understand when they've done wrong, because nice words and the rule of law just don't cut it with them.

I can't believe this just happened.

alexholehouse··on The Apple Reaper
Agreed this makes no sense? If this is correct, does this not represent a [significant] financial incentive from Apple to not have an iOS only app?
alexholehouse··on Everything's broken and nobody's upset
Clearly some of these are life choices, and important ones which almost certainly make sense to you, but one thing;

No dishwasher?

I don't really understand this. My dishwasher has a single wheel and a switch. The switch is "heated dry" [ON|OFF] and the wheel sets to one of three positions ("light wash", "normal wash", "medium wash"). If you're only washing dishes for one then I guess this makes sense, but I fail to grasp how an example of a bad dishwasher user interface is a barrier to all dishwashers (at least in terms of UI - clearly you may have environment reasons).

alexholehouse··on Self-Taught Developers: Are You Missing Your Foundation?
I think this is just it though. You don't necessarily need to be able to sit down and formally write out the exact amortized big O complexity, (or little O, [O|o]mega or theta) but equally it's good to have some idea of how something would scale.

I feel like self taught developers who are serious just learn this by intuition because, frankly, if you're writing software where it matters then very quickly it becomes an obvious concern. If your self taught and it doesn't matter then it doesn't matter!

With a formal background you may or may not use it, but I'd say the only difference is knowing the formal notation makes talking about it with other programmers who also know that notation easier, but even then it's not like algorithmic complexity is (at it's heart) at particularly difficult concept when directly applied to a project. I always found it much harder as an abstract idea rather than when working with a specific algorithm.

alexholehouse··on MIT overtakes Cambridge and Harvard to top spot in QS world university rankings
I have two degrees from the UK, and am currently doing a PhD in the US. During the application process I visited 8-10 different graduate schools in the states, and honestly, I felt like any one of them would be comfortably in the top 5 in the UK.

Maybe that's a totally superficial assessment, but in terms of the quality of facilities, research going on and the interaction I had with professors they were awesome. I don't think this is surprising though - the US is a lot bigger (and I visited a lot of the top universities) so you'd expect there to be more high quality institutions, because there are simply a lot more students/faculty.

This is why I find the UK occupying a lot of the top ten to be someone dubious. No slight against the British academic world, but four out of the top six when adjusted for funds and population just seems ridiculous.

alexholehouse··on MIT overtakes Cambridge and Harvard to top spot in QS world university rankings
Honestly, these rankings are [always] ridiculous.

Clearly there is a need to capture certain metrics and display that as quantitative information, and the difference between, say, the top 10 and the 90-100 is probably relevant, but the difference within the top ~20 is so minimal its largely irrelevant.

It really galls me when people make decisions about undergraduate or graduate schools (or, probably employees, although this is a position I'm yet to be in) based on these kinds of rankings. Clearly it should factor to some extent (i.e. Harvard vs. Jeremey's University of Rubishville[1]) but there are MANY much more important factors to consider.

The irony is that the rankings are 50% opinion based, which basically amounts to identifying where people think are prestigious. I wonder what people use to identify which the prestigious universities are - they can't possible go and visit them all, but if only there were some kind of online ranking they could use to get an idea...

[1] When I went to undergraduate, this was the fictional university my younger brother suggested he might end up going to.

alexholehouse··on Hybrid graphics support in Nvidia 's Linux driver
I <heart> Bumblebee. I just got an Optimus laptop (Lenovo U410 ideapad) and was appalled to discover I couldn't even run VMD [1].

Having installed Bumblebee, I can just use use optirun to provide CUDA enhancement just by initializing VMD using

$ optirun VMD

It's just that easy, and while it is a bit hacky, if you live on the command line it's not a major issue (especially when combined with aliases).

[1] - http://www.ks.uiuc.edu/Research/vmd/

alexholehouse··on Bruce Willis to fight Apple over rights to music collection after his death
Please don't ever post anything from The Sun. It's a worthless, sensationalist pit pandering in majority to festering idiots who live vicariously through a bizarre mix of celebrities and "real-life-tragedies".

[Edit - This is, perhaps, an extreme view, and The Sun is in no way alone in using this modus operandi. However, as a Brit I feel an impulsive need to warn those who didn't grow up with The Sun!]

alexholehouse··on Show HN: My Github résumé
Matt Brown's resume template[1] really gets around (which is no bad thing, I use it myself[2]). I hope he realizes how widely it's used.

1 - [http://resume.github.com/css/resume.css] 2 - [http://www.holehouse.org/CV.html]

alexholehouse··on My Python Code for the Netflix Prize
Netflix had to pull the dataset after a researchers at U Texas were able to de-anonymize the dataset, shown in their paper Robust De-anonymization of Large Sparse Datasets.[http://www.cs.utexas.edu/~shmat/shmat_oak08netflix.pdf]
alexholehouse··on Evernote Smart Notebook by Moleskine
I don't know why you should need stickers at all - just have some unique symbol you can draw, train evernote on the symbol and get rid of the stickers all together. It can't be that hard to do if you train it on your own symbol, as opposed to trying to learn to copy one or whatever.
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