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Deepak Singh › Likes

Amr Awadallah
Disk failures in the real world: What does an MTTF of 1,000,000 hours mean to you? - http://www.cs.cmu.edu/~bianca...
Ilya Grigorik
eventmachine channels are pretty awesome. ex.. multicast all ruby tweets to all websocket clients: http://github.com/igrigor...
Neil Saunders
The worst scientific idea of the decade: vaccines cause autism - http://genome.fieldofscience.com/2009...
Paul Buchheit
If anyone at Google is looking for something to open source, the core machine learning infrastructure (like Seti) would be very good for the world.
I agree, SETI would be great. But whoa, it would be a huge amount of work to open-source it. - Daniel Dulitz
Search for Extra-Terrestrial Intelligence? - Gabe
Har har.... I assume there is ZERO chance of this ever happening. - Jay
@Jay - I suspect Paul wouldn't ask if he thought there was zero chance. Last time I remember Paul asking for something from Google to be open sourced it was their JS compiler. That took a while, but http://code.google.com/closure... - Nick Lothian
@Jay: Remember that Paul's referring to (relatively) generic infrastructure here, not search ranking code. But I think Daniel's right that it would be a *lot* of work, since most Google infrastructure is not "productized" and easy to wrap up in a bow for public release. Like any company with a lot of infrastructure, there are a lot of interdependencies that would be difficult to untangle. I think it would probably be better to simply publish papers on how it works, as with GFS, BigTable, etc. - Joel Webber
Boy, that would be a bold move Paul. Agreed that it would help out many though! - manielse (Mark Nielsen)
How about just dumping the source to the web without all the dependencies, even if it doesn't even compile? If it looks useful enough there's a good chance someone would adopt it. - Jim Norris
I suspect you're right about that, Jim. But Google would probably catch more crap about a "throwing it over the wall and letting it stagnate" open-sourcing than it's worth. But maybe I'm just down on it because Google catches crap no matter what these days... - Joel Webber
It's hard to open source distributed algorithms -- there's no obvious public standard to use, and the reasonable choices (TCP sockets? MPI?) are nothing like Google's internal infrastructure. I think a paper would be more useful than source code, the way MapReduce papers lead to Hadoop. Paul, have you looked at Vowpal Wabbit (http://hunch.net/~vw/)? It has experimental support for cluster parallelism, and I hear good things about it. - ⓞnor
Well, it doesn't have to be an either/or issue. - Jim Norris
If the code is too hard to separate from the infrastructure, then maybe a compute service like EC2 that provides an application interface specifically for solving problems with SETI could be good for both the world and good for the Google. - Bill Strathearn
@Bill: Now *that* sounds like a good idea to me, especially if accompanied by a paper describing the algorithms in use. - Joel Webber
Although technically really interesting and usefully, I do think that Google will not open source or even give inside information about such a key differentiating technology in the hands of their competitors. But I agree that it would be really great for the world. - yusuf arslan
I saw mention of JS open sourcing, did you folks see CoffeeScript yet? great stuff from Jashkenas, http://jashkenas.github.com/coffee-... - Mark Essel
The value of "differentiating technology" is not in novel algorithms, but in the thousands of places where implementations of these algorithms have been fixed and customized and tuned to solve the problem at hand -- which wouldn't have to be described in a whitepaper. - Tudor Bosman
@Tudor Bosman: I do not agree that the competitive advantage is the knowledge of fine tuning and implementing the algorithms. The concept/design of Google's machine learning infrastructure is very important. Don't get me wrong, I do think that Google SHOULD open source this. But I think they WILL not because of business considerations. - yusuf arslan
I think even just a paper would be very useful and fruitful. - Ruchira S. Datta
Ruchira, do you have particular biological datasets in mind? Are they too large even for a single machine version of Vowpal Wabbit to comfortably cope with (say, several tens or hundreds of billions of labeled instances)? - Simon
Simon, my comment was just general. Now that you mention it, I could use Vowpal Wabbit on some of my projects, which are not anywhere close to that big. Thanks for the tip! - Ruchira S. Datta
"The need for opensource in machine learning" http://jmlr.csail.mit.edu/papers... (author affiliations of relevance) - Amund Tveit
Trevor F. Smith
There's still time to the Creative Commons this year: https://support.creativecommons.org/donate Think of what CC licensing enables.
Rajarshi Guha
all set to head of to India for vacation, been 3 years since I visited . Merry christmas and a happy new year to all
have a great time Rajarshi - which city? - Jean-Claude Bradley
calcutta - Rajarshi Guha
Have fun!!! And eat lots of rasmalai - Deepak Singh
Have fun! Will miss your patch reviewing powers! - Egon Willighagen
joergkurtwegner
Mining Drug Space: Sky-rocking graphics in new MOE release - http://miningdrugs.blogspot.com/2009...
The Molecular Operating Environment (MOE) has a new graphics functionality allowing protein visualization in Ray-Tracing quality by using GPU programming. - joergkurtwegner
Matt Wood
Woo - just got engaged!
Congratulations. - Michael Barton
Michael Nielsen
Median age of NIH grantholders - http://dl.dropbox.com/u...
Median age of NIH grantholders
Stunning graph: the median age has increased by nearly half a year per year for the past 35 years. - Michael Nielsen
I guess librarianship isn't the only field eating its young. - D0r0th34
It's a horrible graph. If I hadn't heard other facts consistent with this, I'm not sure I'd even believe it. It does suggest that the NIH granting system is badly broken, at least if creating a new generation of researchers is anywhere on their agenda. It also suggests a great topic for a PhD - figuring out a good explanation for what's going on. I imagine someone with an interest in... more... - Michael Nielsen
Incidentally, there is more background here, including links to the original data: http://metamodern.com/2009... - Michael Nielsen
I would like to see this plotted against tenure-track line numbers in the relevant disciplines. I don't necessarily think it'll be a gluelike correlation because NIH research goes on in industry, but it *might* be. - D0r0th34
If this trend continues, by 2072 the median age will exceed life expectancy in the U.S.... - Adam Ratner
Similar story in Australia. Head here - http://www.arc.gov.au/ncgp... - scroll down to the ECR (early career researchers) section and weep. - Neil Saunders
Dislike. :-( - Ruchira S. Datta
Um. I don't know what I'm talking about of course, but if grantholder's keep their grants for more than a year wouldn't you expect to see some increase? Isn't this graph just showing that grantholders tend to get their grants renewed? - Nick Lothian
in a healthy ecosystem, young people would be filtering in as older people retired. doesn't seem to be happening. - D0r0th34
actually, now that I think about it, other things to graph against this are time-to-degree and number/length of postdoc positions - D0r0th34
I've heard the median age of _1st_ NIH grant is an even steeper curve but have not seen data. and who is to say this isn't a healthy system: just miserable for those who can't get grants (raise hand). - dubbio
Drexler addresses my issue in a follow up comment in the link that Nielsen posted above. Yes, there is a skew in the age of first granting. - dubbio
Anders Norgaard
Roderic Page
http://biostor.org now has over 4000 articles from #bhl Still on the hunt for sources of bibliographic metadata...
Andrew Perry
Mmmh, is some scripting not easier? - joergkurtwegner
I'm be inclined to script most of my own PDB munging operations but, from what I can tell, occasionally people still hand edit parts of them. I received an edited PDB file back from a curator at the PDB a few years ago that had some problems introduced by what appeared to be typos from hand editing. Maybe this tool would have helped :) - Andrew Perry from Android
Merry Xmas FFeeders - AJ
I just watched Up. **Sniff** Someone poked me in the eye. :'( **Sniff** - http://weheartit.com/entry...
I just watched Up. **Sniff** Someone poked me in the eye. :'( **Sniff**
yeah... It's like a magic poke. I got poked through my 3D glasses more than once during that movie. - Rasmus Lauridsen
I cannot wait to own this one... even if I suffered the same fate as the husband. Tough to keep the sniffling sound quiet in the theatre. - Bette Cooper
**Sniff** http://www.youtube.com/watch... <- listen to this once more. **Sniff** - Merry Xmas FFeeders - AJ
Loved this movie!! - Roberto Bonini from iPhone
The first scenes made me cry, too. - April Buchheit
We went out and bought it yesterday so my parents could finally see it. It's just as good the second time. Can't wait to watch it again and again and again!!! - Junebug (aka Sarah Jill)
We just watched it tonight too. Not at all what I had expected. Sob. - adf
this was the sweatest most affectionate story i've seen so far. i cannot help envying them :) - asli subasi
Honestly, I've never seen couples like that IRL. :| - Merry Xmas FFeeders - AJ
well i hope you'll AJ, b/c i want to believe that i will become one, sooner or later . . .(probably much much later) =) - asli subasi
Another movie I'd love to see. - Kol Tregaskes
saw this a few times on the planes i took to and from M'sia this year. my face got wet each time. - Joe Silence
Jonathan Gitlin
Security theater at the airports is about to get even more nonsensical. Next time I go to Europe I'm going by sea.
April Buchheit
My Christmas present!!!!!
photo.jpg
OMGCOOL! w0000t! - Merry Xmas FFeeders - AJ
wow - mohammadk
Jealous! - Joe Pierce
Congratulations. Santa loves you! - Louis Gray
YAY!!!!! I want that too! Let me know what you think of it! - Susan Beebe
م.ب.! ..دی - کاوشگر
Thanks for my awesome new laptop, Paul! I love it!! xoxoxoxoxo - April Buchheit
Cool! - Mycaptain
nice gift - Mehmet Fatih YILDIZ
vaoww ) - Me fallit ஐ
Congrats - I got one too :) Love it....... - Tyson Williams
اینم دلش خوشِ ‏ها! - کاوشگر
Wladimir Labeikovsky
PLoS Computational Biology: A Quick Guide for Developing Effective Bioinformatics Programming Skills - http://www.ploscompbiol.org/article...
Good, but very basic. Looks like they're just trying to bring standard OSS techniques to bioinformatics. - Donnie Berkholz
It is basic, but you'll be surprised how little of that happens. - Deepak Singh
I think publishing these very basic guides is "A Good Thing" - but I don't know that bioinformatics/computational biology journals is the right place. The readership of those journals tends to be those who find the information too basic. Might be better to publish such material in biological science journals - Nature Biotech, for example, runs a very good introductory maths/stats/computing series. - Neil Saunders
Amr Awadallah
Saw Avatar, stunning visuals (the art, not tech per se), story is Pocahontas with a Matrix twist, the scenes come from WoW. Go Stanford :)
Ilya Grigorik
I really hope Avatar makes a killing, maybe that'll convince someone to invest $3+ trillion to do the Dune trilogy.
April Buchheit
nan braun
Anyone who has not yet seen avatar should run there at their first free chance.
Mark A Jensen
Edwin Krebs Dies at 91; Discovered a Crucial Bodily Process - Obituary (Obit) - NYTimes.com http://www.nytimes.com/2009...
PLoS ONE in the Media/Blogs
A year of incredible developments @ PLoS ONE - congrats to Pete Binfield and his team http://everyone.plos.org/2009...
Iddo Friedberg
This is full of WIN: Microscopic gears powered by bacteria. - http://www.reportergene.com/2009...
By conventional photolitography, Sokolov and colleagues from Argonne National Laboratory, report on PNAS the design of microscopic gears (6 ug mass) able to extract useful work from swimming Bacillus subtilis. According to their calculations, few hundred bacteria work together in order to turn the gear at a velocity of 1-2 rpm, generating femtowatt power. - Iddo Friedberg from Bookmarklet
Comment posted on Blog: You say, "Here the concept is that brownian motion can generate directed motion..." I'd say it's not Brownian motion that is creating the directed motion...The bacteria actually have flagellar motors that propel the bacteria. So the bacteria provide the energy (via ATP). Non-swimming bacteria (which would undergo Brownian motion) would not propel the gears, as I... more... - Steve Koch
96well's response: "Yes, thanks. Bacteria are swimming (and not floating) because of flagella, and yes: ATP and not real Brownian motion is responsible to the movements. I feel sometimes 'brownian motion' is used (non very properly) to describe bacterial motility just because the linear trajectory operated by the flagellar motor turns rapidly into new directions with a pattern which... more... - Steve Koch
The Brownian thing made me think: is there any demonstration of behavioral swarming in microbes, the kind we get in locusts, bees & college students? - Iddo Friedberg
I guess the answer is "yes"... http://www.rowland.harvard.edu/labs... - Iddo Friedberg
bob
bob
Plane overshoots Jamaica runway; more than 40 hurt - http://www.breitbart.com/article...
Plane overshoots Jamaica runway; more than 40 hurt
Plane overshoots Jamaica runway; more than 40 hurt
"KINGSTON, Jamaica (AP) - An American Airlines flight carrying 154 people skidded across a Jamaican runway in heavy rain, bouncing across the tarmac and injuring more than 40 people before it stopped just short of the Caribbean Sea, officials and witnesses said. Panicked passengers screamed and baggage burst from overhead bins as Flight 331 from Miami careened down the runway in the capital, Kingston, on Tuesday night, one passenger said. The impact cracked open the fuselage, crushed the left landing gear and separated both engines from the Boeing 737-800, airline spokesman Tim Smith said." - bob from Bookmarklet
Looks pretty bad. I wonder why it broke up? - Paul Buchheit
It was one hell of a bumpy ride from the looks of it, Paul. - Alex Scoble
That's one old 737. That's why. - Roberto Bonini from iPhone
It has winglets, doesn't seem all that old to me. Planes just aren't designed to land like that one did. - Alex Scoble
I heard on CNN that the passengers were clapping at the smooth landing before the accident. This runway has poor drainage, so the plane's brakes may have been ineffective. The bouncing and damage may have happened after it left the tarmac. I don't know whether the report I heard or this article (citing turbulence) is accurate. Wait for RISKS Digest. - Bruce Lewis from fftogo
And the break pattern seems consistent with the nose, fuselang and tail being separate components - Deepak Singh
Roberto: The 737-800 has only been around since 1997, so the plane couldn't be more than 12 years old. - Gabe
So was this a Boing 737? - Gabe
Yes. Its first flight was November 2001 http://aviation-safety.net/databas... - Ken Sheppardson
See http://www.maxtrescott.com/max_tre... for an AFAICT purely speculative suggestion of what may have happened. Anyway the simplest explanation now is that it broke up because it ran off the runway. Why did it run off the runway? Good question. - Daniel Dulitz
Running off the end of an 8700 foot runway takes more than one or two factors... - Daniel Dulitz
Ok not so old then. I wonder what the crash investigation will turn up. - Roberto Bonini from iPhone
On CNN a pilot said that this runway lacks grooves for drainage. Hydroplaning and the tailwind are two factors. We'll have to see what other factors were involved. - Bruce Lewis
http://aviation-safety.net/photos... roadside bank looks brutal - Thomas Page
Alex Iskold
I can't get my Inbox to zero no matter what. Oh well, its time for another glass of Malbec then.
Kathy E Gill
#avatar 3d. Did not think it could live up to hype. It did. More later.
Neil Saunders
Every time you open a sequence file in Word, a bioinformatician cries out in pain - http://rrresearch.blogspot.com/2009...
The original has dying angels... I wonder about the death rate cause scientists are so bloody sloppy... - Egon Willighagen
That is... if we were more accurate, would science have progressed further, finding earlier and better cures? - Egon Willighagen
Maybe not, but we might avoid spending money on useless things. - Paulo Nuin
Cameron Neylon
Fwd: The need for clear data licenses :: High Earth Orbit - http://highearthorbit.com/the-nee... (via http://friendfeed.com/cavlec)
Via D0r0th34 - Cameron Neylon
recommendation of CC0 and ODbL is nice, funny to consider how few appropriate licenses there are, especially compared with open source - Mike Chelen
early days yet :) - D0r0th34
Chris Messina
RT @dalmaer: Jetpack 0.7 gives you some First Run Action http://mozillalabs.com/jetpack...
Lars Juhl Jensen
Eventual Consistency Explained for Non-techies - http://practicalcloudcomputing.com/post...
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