skysight-inc/HackerNews huggingface dataset:
> I think if you have objects and a reference-counting GC already this problem is pretty easy, but I assume the C programmers don't want that for performance or portability or some other reason.

Uh. Every large C code base I've worked with has had this in some form, usually fairly pervasively. I've mentioned glib as a library that exercises this heavily. In the Windows world this would also include COM. Kernel mode stuff on various platforms tends to do a lot of refcounting as well.

Note that "reference counted object" is just a fancy word for "struct with an integer" - I feel like your phrases like "if you have objects" and "GC" strikes me as confusing this with other features in other languages, a sign that we're not entirely talking about the same thing.

Edit after more time spent away from it: I guess to restate the original comment, what I was trying to say is that to an experienced C programmer closures don't make anything "more hard" - it's just the same memory allocation strategies that you'll be dealing with anyway, and there are already well understood solutions (such as having one of your struct fields be a reference count).
I wasn't appalled by AWK language but the blind switching of two lines which were assumed to be paired reads when many reads are not paired. It is precisely lack of checking that is a problem. I have nothing against AWK, although personally I use Python for massaging data.
Ronald Bradford's http://www.slideshare.net/ronaldbradford/my-sql-idiosyncrasi...
is worth reviewing for anyone who runs MySQL.

I especially like how he explains SQL_MODE bit by bit and ends up recommending

SQL_MODE =
ALLOW_INVALID_DATES, ANSI_QUOTES, ERROR_FOR_DIVISION_ZERO,
HIGH_NOT_PRECEDENCE,IGNORE_SPACE,NO_AUTO_CREATE_USER,
NO_AUTO_VALUE_ON_ZERO, NO_BACKSLASH_ESCAPES, NO_DIR_IN_CREATE,
NO_ENGINE_SUBSTITUTION, NO_FIELD_OPTIONS,NO_KEY_OPTIONS,NO_TABLE_OPTIONS,
NO_UNSIGNED_SUBTRACTION,NO_ZERO_DATE, NO_ZERO_IN_DATE,
ONLY_FULL_GROUP_BY, PAD_CHAR_TO_FULL_LENGTH (5.1.20), PIPES_AS_CONCAT,
REAL_AS_FLOAT, STRICT_ALL_TABLES, STRICT_TRANS_TABLES

I also recommend "MySQL 5.1 vs. MySQL 5.5: Floats, Doubles, and Scientific Notation" http://blog.mozilla.org/it/2013/01/17/mysql-5-1-vs-mysql-5-5... for anyone who working with non-integer numerics.
Quirky are really pushing the "David & Goliath" angle in their latest response.

http://www.quirky.com/blog/post/2013/01/quirky-stands-strong...
Regarding samtools, it doesn't sound very good from what I'm hearing:

"Look at the disgusting state of the samtools code base. Many more cycles are being used because people write garbage. For a tool that is intimately tied to research, the absence of associated code commentary and meaningful commit messages is very poor. The code itself is not well self documenting either."

commit log:

http://samtools.svn.sourceforge.net/viewvc/samtools/trunk/sa...

code:

http://samtools.svn.sourceforge.net/viewvc/samtools/trunk/sa...
Off topic, but since you mentioned jgrahamc's article in Nature, interestingly, this was what I read last night on Simply Statistics: http://simplystatistics.org/2013/01/23/statisticians-and-com...

It's a similar issue. I think statisticians are taking constructive steps to correct their path, since you know, ML is the new sexy thing. Bioinformatics could take a much longer time to self-correct though.

Although, as I mentioned in an earlier comment, Fred seems to be in a prime position to disrupt the bioinformatics field since he seems to know all the problems that afflict it
I bet there are farmers in Minnesota, too. So there bound to be rednecks.
This is pretty hilarious, from my brief experience with bioinformatics I can very well imagine someone writing the opposite rant, about CS people getting into bioinformatics not knowing sh*t about biology. I mean, browse through bioinformatics textbooks, those are either written by computer scientists and those are little more than string algorithm textbooks or by biologists and then the layer of jargon for someone coming from CS is just impenetrable. Same with bioinformatics teachers, I come from a CS background, but spent one solid month seriously trying to understand the basics of molecular biology and my bioinformatics seminar instructor sometimes seemed to know less about it than me. Terrifying, no wonder nonsense results are produced.
The fine print of H264 says as a consumer you can implement the codec without paying a license fee for non commercial personal use. That does, however, mean all the free implementations like in FFMPEG are liable because since they are open sourced they are not restricted to consumer use.
Open source projects can't pay royalties. But people who use them can be forced to.

The idea that VP8/VP9 will gain traction and remain royalty free is laughable.
In this case, that isn't what he's referring to. The midwestern accent is the one that national newscasters are taught.
I always send my apk via email, and my friends will install it. what's the problem with that?
apk is a file, just like jpeg, mp3. rename it to whatever you like and then transfer.
What movies have this?
Ask HN: Will you watch a shuttle launch in Google Earth? 
HN community,

I am trying to get feedback on my Google Earth Video sharing website, sorry I know this is not the first time. But today is big, the first video, other than my own was uploaded and it is a shuttle launch from 5/11/09.

Anyone in the HN community who might enjoy a shuttle launch or checking out the concept of videos inside Google Earth please watch this.

*You must have the Google Earth Plug-in
1. Visit www.ommageo.com; 2. Zoom in on Kennedy Space Center(the closer you zoom, the cooler it is); 3. Click the geotag (yes, it is the geotag with the guy kissing the giant Grey Goose bottle - I know what your thinking, sweet first user); 4. When the geotag opens click play on the YouTube player; 5. Any feedback would be awesome, I am not looking for feedback on the video just the website, but feel free to comment on the shuttle launch.
Where does the Rosalind project (rosalind.info) fit into all of this, I'm wondering? It seems to be written by people who have actual understanding of the mappings between biology and informatics, with clear explanations of problems in terms of the programming challenge involved.

Surely they can't get that far without having some kind of sensible method?
In certain circumstances, people smell blood like sharks. If you're a 'normal' and successful person, with a functioning ego, you will either naturally or semi-consciously put out a vibe that lets other people know you're going to hold your own. Your personality and sense of humor will interact in some reasonable way that strikes a balance with the egos of others.
With mental illness, it's as if people smell it on you. You become a target. People sense your vulnerability, and they can become angry with it, attack it as if they're attacking the spectre of insecurities or uncomfortable truths in their own shadow-selves.
The fact that people will use the socially plausible explanation of your mental illness to explain away such bullying becomes one of the impossible double-binds that mentally ill people live with.
One man's analysis.
I also recommend reading what Stephen Fry has to say: http://www.pgwodehousebooks.com/fry.htm
It would be interesting if they included people who sound 'blue collar' and people who sound like they're from the sticks (hillbilly) in the mix. Not sure what the results wold have been, but it'd be interesting to know. As control, they could add English speaking African immigrants.
Children now a days
Awesome! I hope it isn't marred by an attempt to close the default-open nature of web applications (they're looking for feedback on "potential missing functionalities to deploy secure web applications." Echoes of HDCP. Ugh.)
Pulled from the App Store in 3, 2, 1...
That's an interesting proposition, I'll see what I can do to offer the alternative of making f ambiguous instead of using s. I don't think it could be the default because most users wouldn't be as quick to type the three letters, at least at first, and it would need to timeout really fast so as to keep f's original responsiveness to single letters.
Douglas Adams on Wodehouse

""" Who are your favorite authors?
Charles Dickens, Jane Austen, Kurt Vonnegut, P. G. Wodehouse, Ruth Rendell.

...

Master? Great genius? Oh yes. One of the most blissful joys of the English language is the fact that one
of its greatest practitioners ever, one of the guys on the very top table of all, was a jokesmith. Though
maybe it shouldn’t be that big a surprise. Who else would be up there? Austen, of course, Dickens and
Chaucer. The only one who couldn’t make a joke to save his life would be Shakespeare.
...

We Wodehouse fans are very fond of phoning each other up with new discoveries. But we may do the
great man a disservice when we pull out our favourite quotes in public, like “Ice formed on the butler’s
upper slopes,” or “. . . like so many substantial Americans, he had married young and kept on marrying,
springing from blonde to blonde like the chamois of the Alps leaping from crag to crag” or (here I go
again) my current favourite, “He spun round with a sort of guilty bound, like an adagio dancer surprised
while watering the cat’s milk” because, irreducibly wonderful though they are, by themselves they are a
little like stuffed fish on a mantelpiece. You need to see them in action to get the full effect. There is not
much in Freddie Threepwood’s isolated line “I have here in this sack a few simple rats” to tell you that
when you read it in context you are at the pinnacle of one of the most sublime moments in all English
literature.

Shakespeare? Milton? Keats? How can I possibly mention the author of Pearls, Girls and Monty
Bodkin and Pigs Have Wings in the same breath as these men? He’s just not serious!
He doesn’t need to be serious. He’s better than that. He’s up in the stratosphere of what the human
mind can do, above tragedy and strenuous thought, where you will find Bach, Mozart, Einstein,
Feynman, and Louis Armstrong, in the realms of pure, creative playfulness.
From the Introduction to Sunset at
Blandings (Penguin Books)

"""
A can of refried beans is cheaper, healthier, and tastier than a dollar burger.
Some thoughts on this article:

- This guy clearly has a limited understanding of the field. This quote is laughable: "There are only two computationally difficult problems in bioinformatics, sequence alignment and phylogenetic tree construction."

- As a bioinformatician, I feel sorry for this guy. Just like any other field, there are shitty places to work. If I was stuck in a lab where a demanding PI with no computer skills kept throwing the results of poorly designed experiments at me and asking for miracles, I'd be a little bitter too.

- Just like any other field, there are also lots of places that are great places to work and are churning out some pretty goddamn amazing code and science. I'm working in cancer genomics, and we've already done work where the results of our bioinformatic analyses have saved people's lives. Here's one high-profile example that got a lot of good press. (http://www.nytimes.com/2012/07/08/health/in-gene-sequencing-...)

- I'm in the field of bioinformatics to improve human health and understand deep biological questions. I care about reproducibility and accuracy in my code, but 90% of the time, I could give a rat's ass about performance. I'm trying to find the answer to a question, and if I can get that answer in a reasonable amount of time, then the code is good enough. This is especially true when you consider that 3/4 of the things I do are one-off analyses with code that will never be used again. (largely because 3/4 of experiments fail - science is messy and hard like that). If given a choice between dicking around for two weeks to make my code perfect, or cranking out something that works in 2 hours, I'll pretty much always choose the latter. ("Premature optimization is the root of all evil (or at least most of it) in programming." --Donald Knuth)

- That said, when we do come up with some useful and widely applicable code, we do our best to optimize it, put it into pipelines with robust testing, and open-source it, so that the community can use it. If his lab never did that, they're rapidly falling behind the rest of the field.

- As for his assertion that bad code and obscure file formats are job security through obscurity, I'm going to call bullshit. For many years, the field lacked people with real CS training, so you got a lot of biologists reading a perl book in their spare time and hacking together some ugly, but functional solutions. Sure, in some ways that was less than optimal, but hell, it got us the human genome. The field is beginning to mature, and you're starting to see better code and standard formats as more computationally-savvy people move in. No one will argue that things couldn't be improved, but attributing it to unethical behavior or malice is just ridiculous.

tl;dr: Bitter guy with some kind of bone to pick doesn't really understand or accurately depict the state of the field.
> Exactly the patent threat will come from the MPEG-LA or the members directly. Because if VP9 is indeed similar to H.265

Why would they design the codec to be vulnerable to patent attacks? VP8 was designed to work around threats from H.264. They surely applied the same logic for VP9 since they intend it for practical use and not as theoretical brain exercise. MPEG-LA spits threats all the time, including against Theora and VP8, but they have no teeth to bite.
This illustrates the fundamental problems of C very well, which are the requirements to be very specific about types and manually manage memory.

Of course those things aren't a problem in cases where you need to do those things, but that isn't the case for most applications.
That was a tongue-in-cheek thingy. I write extensive tests for all my code. But when I look for a job, people counts papers not weight software quality. It is not easy.
I bet you said the same thing back when VP8 was released, no such patent lawsuit has occured.

Also, On2 which Google purchased holds lots of video compression patents, patents which codec's like h.264 and h.265 just as likely violates.

MPEG-LA does not offer any patent indemnification either.
>You should really put a comma between "penalty" and "speak".

It's optional.

>Oh, and there is no standard English.

This is wrong. There absolutely is a standard American English. Jesus Christ, no wonder young people can't get jobs. They don't teach English in school any more.
Which of these scenarios do you think is more likely?

That a group of nonprofits and academic institutions all colluded over a decade or three to make money in a very roundabout way for groups they don't have any direct involvement with?

-or-

That a group of oil industry types, in a nod to the junk science used by big tobacco for years, colluded over a decade or three in an attempt to discredit something that will directly impact their bottom lines in a bad way?

Follow the money. Hell, follow human nature.
Software engineering is important for bioinformatics, in my opinion. But it's important to identify the things that are important and aren't:

Reproducible code: extremely important.
Correct code: extremely important.
Readable code: very important.
Efficient code: often not as important.

Even today, the UCSC Genome Browser is an example where efficient code is important. It is interactive software, has many human users who can work much efficiently when the browser is responsive. And with projects like ENCODE, there are now incredible amounts of data available from the browser that would not be easily possible with a less efficient system.

Very different from an analysis system that will be run a handful of times in batch mode.
To steal an idea from and in the spirit of pg's "What You Can't Say" essay:
http://www.paulgraham.com/say.html

We might look at smug, entitled "aristos" in a period French Revolution film, or look at slave owners in a pre-Civil War period piece and think ourselves better. We might look at those characters treating the urban poor like dirt or see a smug and shortsighted slave owner talking about the music of black slaves as if it were a primitive sign of their inferiority -- and shake our heads and feel smart knowing what we know as 21st century persons. But in the spirit of "What You Can't Say" let me say that there is just as much shortsighted abusive smarminess, smug superiority, and shallow judgment of people by their superficial features in our day as in those times past. And yes, this includes the West Coast, the Bay Area, and no small part of the startup scene.

Remember that the historical persons such that characters mentioned above were based on thought of themselves as cultured, enlightened, and sensitive, much as many of today's knowledge workers do. Remember also that many of them were utterly blind to their own shallow judgements and earnestly thought of themselves as winners in a meritocracy, as many persons do today. Now note that only a minority of such individuals were actually as enlightened as they thought they were.

And lastly, there are those among you who have or will overcome the blindness of your own subculture and time, but remember that only very rarely does this come without some form of shock, surprise, or pain.

EDIT: Another instance where we can relate some media to the subject -- the powerful executives portrayed in Mad Men equated sounding like a top-tier university white male with "sounding professional." They equated looking like one of them with "looking professional." Just as much of that goes on today as did back then, it's just that the styles have changed.
>If your test was to compare an intraframe between vp8 / baseline h264 / and Theora, you would have concluded Theora was the best by a wide margin.

But it wasn't. I was comparing the visual quality of the whole video, and provided the full encoded clips for people to download and compare for that reason.

I am willing to do further test encodes, but have no interest in doing something like encoding all 28 HD test clips available on derf's test clip page[1], since as a purely visual comparison, especially with the actual encodes, it would be incredibly exhausting.

EDIT: I added a notice about the downsides of single clip comparison to the top of the post.

[1] http://media.xiph.org/video/derf/
The cloud is a marketing buzzword. You can determine a lot for a product by who is pushing for it - it was coined and promoted by the big corporations that had resources to spare and sell them with a 3-400% markup

http://www.codinghorror.com/blog/2012/10/building-servers-fo...

While I see the value in making things more flexible and cheap like the open compute initiative, my cynicism has taught me to assume every time that what is heavily promoted this way by a entity that tries to position itself as the middleman - it may not be bad for you, but it rarely will be the best for you.

How many people think twice before handing sensitive info to google after the David Petraeus situation.

The cloud infrastructure is just a tool - it has its limited uses, its gotcha-s etc. It is good for prototyping, rapid deployment but after that - not so sure.
Wow, does instagram illegally solicit and publish personal data from preteens?
I didn't realize spot instances were so much cheaper than on-demand. A small on-demand instance is ~47$/month
tptacek (original author of the OP here) and I responded to the draft here: http://news.ycombinator.com/item?id=4549504 The tl;dr is: the trust model is broken, and low-level primitives exposed in the way that they are is begging for pain.

Not a lot has changed since then, sadly.
As someone in the field, let me assure you: This article does not accurately reflect the state of the field.
I have seen (and shot down) people floating ideas of doing AJAX HMAC. It's a great idea if you think about it. But if you really think about it... it is a OHGODSWHY idea
There are racial accents in addition to regional accents. Sometimes they are subtle, but humans are good at identifying subtle patterns.
Interestingly, the fraudsters were caught because of a false claim on a CV, and that finally destroyed their creditability.

It is intentional fraud, no doubt about it; they restarted halted clinical trials. I was just pointing out they did sloppy work too.
Seriously? Fire up picasa or iphoto or Facebook and then tell me whether facial expression is any part of facial recognition all. Recognition works because it uses immovable bone structure.
I won't disagree that they say both are equally important, but I hear libertarians talking about economic issues much more than I hear them talk about social issues.

And on top of that, they seem to caucus with the republicans much more so than the democrats despite the republicans' horrible (from a libertarian perspective, at least) stances on social issues like gay marriage, abortion, and marijuana. Can you think of any libertarians caucusing with democrats? I can think of at least the Pauls caucusing with the republicans.
There are a lot of problems in bioinformatics. Mainly, lack of reproducibility (ie "custom perl scripts"), poorly organized and characterized data and plenty of wheel reinvention (I heard Jim Kent, who first assembled the human genome, created his own version of wc [word of mouth, citation needed]).

The fact of the matter is that through high-throughput sequencing, microarrays, what have you, generation of biologically-meaningful results is possible.

There are a lot of problems in bioinformatics that need to be solved. Github has helped. More of bioinformaticians are learning about good software development practices, and journal reviewers are becoming more enlightened of the merits of sharing source code.
The devil is in the details. Will children be able to create and use, load and write proper data structures without hunting down some extension that works with all browsers? Will they be able to create networking protocols or reading and writing serial ports when robotics is becoming so much more important right now? The answer is no.
You keep bashing anything not h.26x in multiple threads. MPEG-LA threatened to assemble an anti-VP8 patent pool ages ago, and that has yet to materialize. Show us the goods, and give a really darn good reason why the ideals behind wanting a royalty-free codec don't matter.
The point of HATEOAS is to build software whose abstractions are stable across evolving server and client implementations. Software that spans decades, for example, such as HTML, in the face of many different browsers and web frameworks (from CGI through PHP to Ruby/Python/Node).

The client (browser, in most cases) is independent from the specific servers, it just knows the media types and link relations. The server has to bind to that media type (i.e. generate HTML).

This is a subtle thing for API developers as we mostly just have the HTML web as the big success story for HATEOAS, and haven't done this as much for machine to machine communication... But as an example, the Google crawler is an example of a non-browser that took advantage of the HATEOAS for browsers and built a new application around it that took advantage of the genericness of HTML. i.e. it didn't have to develop an API to each website, it just understood the difference between the links embedded in <A> tag, <IMG> tag and <FORM> tag, and can traverse the links that help it improve its search index.

One of the closer attempts to HATEOAS was Facebook and the Open Graph protocol, attempting to describe social data through link relations in a way that's completely independent of specific clients & server implementations.

The limiting factor to HATEOAS in practice for API developers is the lack of programming model & tooling for describing & linking API actions together on the Web, which is something actively being experimented over at RESTfest, the W3C REST workshops, etc. There's HAL for example, http://stateless.co/hal_specification.html