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Thomas Brox Røst › Likes

Shannon Jiménez
Mastering the Art of French Cooking (2 Volume Set) - http://www.amazon.com/dp...
Mastering the Art of French Cooking (2 Volume Set)
Sorry guys, no beacon inside :) - Jérôme Flipo
Karen James
I wish there was a universal format for submitting peer-reviewed papers; authors could post papers (once!) & then the journals bid on them.
Oh, now that's an interesting idea, Karen. - Graham Steel
Cyndy Parr tweets ( http://twitter.com/cydparr... ) "This is kind of what PLOS One envisions -- it goes up there, and then it could get chosen to be part of a hub". Iz true? - Karen James
Thanks, Graham. Having just had a paper rejected by two journals in a row, I'm fed up to here *points to own eyebrows* with spending hours if not days re-formatting to meet the ridiculously precise but in no way substantive guidelines of different journals. It's not even rewriting, it's just pointless fiddling and a silly waste of time. If the taxpayers only knew... - Karen James
There are two issues at hand here. One, a universal format for submission, Two, a bidding process on papers. The Neuroscience Peer Review Consortium points to how the second part of this kind of deal is working right now in some disciplines (http://nprc.incf.org/), the really really sad part about the first issue here is that the big publishers don't care what format you submit in (let... more... - Ian Mulvany
+1 for more standards for paper submissions, starting with reference styles. And for allowing submissions in the NLM DTD format. - Martin Fenner
Ian, you may say they don't care, but when one is submitting a manuscript, one is trying to do everything one can not to give the publisher any possible little excuse to reject your paper without review. - Karen James
Second time in a week that someone stated "publishers don't care about format of submissions". Again I ask: if that's the case, why do all journals make a huge deal about it in their instructions to authors? - Neil Saunders
As for universal format: easily solved by writing our papers on the web. Imagine a simple forms-based interface with fields for title, authors, abstract, introduction... Imagine a button in Google Docs that says "submit this document to <insert journal here>" !! But currently, we all like to use our own word-processing software on our own machines, then upload a document in a multitude of formats. It's going to take a big shift in thinking and work practices. - Neil Saunders
What Neil said: if journals don't care, why do they make such a damn song and dance about it? Why not explicitly say you can *submit* in any basic AIMRAD format? Worry about format after acceptance: either the journal can send it to India per Ian above, or if they make the authors do it at least they only have to do it once. My next paper (quit laughing) is going out in basic AIMRAD... more... - Bill Hooker
Note: this is easier for me to do than many, because I've basically given up on an academic career as currently constructed. - Bill Hooker
"it's just pointless fiddling and a silly waste of time. If the taxpayers only knew" I think they should / deserve to know! - Björn Brembs
+1 Neil "why do all journals make a huge deal about it in their instructions to authors?" and +1 Björn "I think [the taxpayers] should / deserve to know!" - Karen James
Neil & Bill: maybe "don't care" is to strong a phrase. A manuscript does need to be structured correctly to fit into the journal's content management system (an application note looks different to a letter looks different to a research paper), have images properly resized and references in the right format so that they can be processed by systems that convert to them links etc. - Euan
Also: what happened to that Wolfram word processor for papers that was supposed to do what Neil mentioned above with Google Docs? - Euan
Ah, http://www.wolfram.com/product... but doesn't look like there's a great deal of support for life sci journals (BMC aside) - Euan
the publishers i know would be delighted to standardise to NLM DTD for submissions -- would save lots of editorial time and production costs -- the publisher i know best sends accepted papers to be manually turned into xml which can then be used for PMC deposition and the semi-automatic generation of the HTML and PDF versions. But things like the Publicon app have taught publishers that implementing the technology to do something doesn't mean that it will happen in significant quantities! :) - Joe Dunckley
I used Publicon when it was released a few years ago. Essentially a dead product now. Lemon8-XML does what Neil describes as "Imagine a simple forms-based interface with fields for title, authors, abstract, introduction... ": http://network.nature.com/people.... - Martin Fenner
These interviews (about eXtyles and Editorial Manager) might be interesting to those that care about submitting papers in the NLM DTD format, as I specifically asked that question: http://network.nature.com/people... and http://network.nature.com/people... - Martin Fenner
There is a nascent version of that working in neuroscience http://nprc.incf.org/. Journals have formed a consortium where if an author submits to one journal and it gets rejected, the author can specify that the reviews follow the paper to another journal so that it doesn't need to be re-reviewed. This was viewed as a way for papers that have nothing wrong with them but which don't fit the scope of the journal can be published more quickly and easily. - Maryann Martone
What about replacing "papers" and "journals" in the subject line with "proposals" and funders? - Daniel Mietchen
What if journals said here's our LaTeX template. Put the right text in the indicated field, lotion in the basket, and anything else won't be accepted. - Mr. Gunn
@Daniel Mietchen: Yes, that too! @Mr. Gunn: What I'm advocating is that there's a single LaTeX (or whatever) template - not that you'd re-paste for each journal. - Karen James
karen, yes. The idea being you give them the text and they do whatever they like with the formatting. - Mr. Gunn
Zee.
Geek looking to get fit? Seriously consider getting one of these. - http://thenextweb.com/shareab...
Geek looking to get fit? Seriously consider getting one of these.
Show all
But Zee. You're gonna get all this yucky sweat on the MBP. I really don't want you want that. It's kinda gross. - John Wang
I would bust my arse if I tried to exercise while on my computer - Shevonne
Amund Tveit
Post: Tornado Web Framework In Production With Django And Nginx | Jeremy Bowers | St. Petersburg, Florida - http://www.jeremybowers.com/blog...
Erik Pitzer
Reducing One Amino Acid Could Increase Lifespan (slashdot) - http://science.slashdot.org/story...
Michael Nielsen
An interesting attempt to establish a virtual market associated to scientific publications. - Michael Nielsen
Fulaan, inna Hebel
Science: The looming crisis in human genetics | The Economist - http://www.economist.com/display...
Science: The looming crisis in human genetics | The Economist
Science: The looming crisis in human genetics | The Economist
"Human geneticists have reached a private crisis of conscience, and it will become public knowledge in 2010. The crisis has depressing health implications and alarming political ones. In a nutshell: the new genetics will reveal much less than hoped about how to cure disease, and much more than feared about human evolution and inequality, including genetic differences between classes, ethnicities and races." - Fulaan, inna Hebel from Bookmarklet
we'll know more than before - surely a good thing....... - winckel
For a different perspective, see the Nature article "Let's celebrate human genetic diversity" http://ff.im/9PbOx - Ruchira S. Datta
Uh-Oh... - Christopher Harley
Sprague D
David Bowie’s Response To First American Fan Letter - http://revivl.com/news...
David Bowie’s Response To First American Fan Letter
Assuming it's legit, he was 20 years old at the time. Very sweet. - Sprague D from Bookmarklet
John Resig
Mike Chelen
Fwd: "Wikipedia for academic research". Post a summary of your research to increase its impact. http://acawiki.org/Home (via http://friendfeed.com/plosone...)
it looks like semantic mediawiki? - Mike Chelen
ah thanks, interesting to see which extensions they are using - Mike Chelen
Noteworthy: so far, 18 summaries of articles in PLoS Biol., 12 in PLoS Med. (None in PLoS ONE). - Jim Till
Perhaps noteworthy: the vast majority of edits in the last thirty days are by two people. It's hard to build critical mass... http://acawiki.org/index... - Andrew Su
the site looks pretty new, sometimes starting fresh produces the best results, although it can be useful to find some existing data to import initially - Mike Chelen
The site launched this week. The PLoS articles were seeded using the Editor Summaries that PLoS Bio and PLoS Med routinely publish - Peter Binfield
Peter: wondering if the data was converted from another format, or does PLoS supply RDF directly? is there any description of the process used? - Mike Chelen
We didnt work with them on this (other than to have some early meetings). I suspect they just copied and pasted... However, it can be extracted from our XML file of course. - Peter Binfield
Yes, it's copy and paste at present. A better workflow would be a good enhancement to Semantic MediaWiki if anybody's looking for a project! - Jodi Schneider
here is a guide to import data (TSV, tab separated values) to Semantic MediaWiki with a script: http://semantic-mediawiki.org/wiki... and some extensions for XML import: http://semantic-mediawiki.org/wiki... - Mike Chelen
Simon Willison
A PostgreSQL client library (that speaks the wire protocol) in pure JavaScript for Node.js http://github.com/creatio... - neat
edythe
Portable Chicken Coop by ChickenCoops on Etsy - http://www.etsy.com/view_li...
Portable Chicken Coop by ChickenCoops on Etsy
"The Portable Chicken Coop covers less ground space than other chicken coops. As well as space efficiency, the covered run gives both hens and costly feed good weather protection. The traditional design satisfies your natural instincts, allowing them to go up at night to roost. The coop has one full-length door allowing easy access to the lower run for feeding and watering and lets chickens exit and roam free. The nesting box, located at one end of the ark, has its own external egg collection door. A removable side door allows for easy cleaning of the upper roosting chamber. All Chicken Arks come with sturdy carrying handles for easy portability. Moved every couple of days, your chickens will mow and fertilize your lawn." - edythe from Bookmarklet
Orli Yakuel
Javascript scroll clock - AMAZING! http://toki-woki.net/p... (via @eyalshahar)
Berci Mesko, MD
Ho John Lee
Daring Fireball: A Liberal, Accurate Regex Pattern for Matching URLs - http://daringfireball.net/2009...
A common programming problem: identify the URLs in an arbitrary string of text, where by “arbitrary” let’s agree we mean something unstructured such as an email message or a tweet. I offer a solution, in the form of the following regex pattern: \b(([\w-]+://?|www[.])[^\s()<>]+(?:\([\w\d]+\)|([^[:punct:]\s]|/))) This pattern should work in most modern regex implementations. I can vouch for it working in Perl, Ruby, and with the PCRE regex library (which in turn means it works in PHP and BBEdit, both of which use PCRE). This pattern attempts to be practical. It makes no attempt to parse URLs according to any official specification. It isn’t limited to predefined URL protocols. It should be clever about things like parentheses and trailing punctuation. - Ho John Lee
Deepak Singh
Automate EC2 Instance Setup with user-data Scripts - Alestic.com - http://alestic.com/2009...
The Ubuntu and Debian EC2 images published on http://alestic.com allow you to send in a startup script using the EC2 user-data parameter when you run a new instance. This functionality is useful for automating the installation and configuration of software on EC2 instances. - Deepak Singh
I used this feature last year - it's really handy to be able to pass a script to "apt-get install" various things after startup. In my case I also pulled a BLAST database from s3 using s3cmd. - Andrew Perry
user-data scripts are compatible with official ubuntu amis, and can be used to boot strap other startup utilities like runurl - Mike Chelen
Deepak Singh
When “good enough” just doesn’t cut it - http://mndoci.com/2009...
Is this a symptom of writing software for publication and then moving on? - Michael Barton
It's a symptom surely of what the measured endpoint is - getting the data out for the paper - not producing something that has real utility. It's the good enough _for what_ bit that is the problem here surely? - Cameron Neylon
It's all of those things. Worth remembering that in many cases, academic researchers who write software are not professional software developers. I think in the past and to some extent now, many people would answer "yes, good enough is just fine". I'm encouraged to see a new generation of computational biologists who clearly have been trained in software development and care about things like re-usability, reproducibility, testing, version control, distribution and so on. It is getting better. - Neil Saunders
That's fair - constant suprise to me that I seem to know more about software development best practice than the academic researchers I talk to. I blame Greg Wilson of course...need to get Software Carpentry or similar course made compulsory for all science undergraduates :-) - Cameron Neylon
And to those who don't get why this is important: we should spell out the cost (both financial and in time) to a research project, every time a new person starts on a project and has to clean up the mess of files and code left by their predecessors. I've seen this time and time again. - Neil Saunders
Or write it into the grant conditions. That spells out it out pretty clearly... - Cameron Neylon
Neil, I agree with you. I think that's going to change, as more and more software developers enter the life sciences, folks who care about maintenance, quality, etc. But the PIs are still a problem. Of course, this is not just academic research though. I've seen it in companies and perhaps that's the difference between between someone who stays middle of the road and someone (someone could be an entity) who excels - Deepak Singh
couple of off topic things: I think your RSS is not working, or you might have changed it. It doesn't show up on my GReader. Also your Fork Me link to GitHub is not pointing to your account. - Paulo Nuin
Paulo, the feed seems to be OK at this end. and yep, do need to fix that Fork Me link. Thanks - Deepak Singh
Survival of the fittest will show how good things are. In the (free) open source world quality/time_to_invest will show, and for commercial world the quality/price will do the same. - joergkurtwegner
Joerg, I think that's beginning to happen, especially with open source alternatives pushing purchasing behavior. Plus expectations have changed. No one is going to use an internal search engine with a several millisecond response time, when you are used to Google - Deepak Singh
Perhaps I'm the pessimist, but if all scientific software were merely 'good enough' I'd be in heaven. Good enough would at least imply that it compiles/runs/etc. - Paul J. Davis
I think "good enough" in software is favored when an individual needs to get something done and faces limitations in terms of time or financial resources in accomplishing the task. Within those constraints, "good enough" is the best way of making progress rather than waiting 'til someone writes the best possible code. It shouldn't remain that way, but if its cutting edge research, a clear market demand may not have been established as an incentive for some one to create a particular piece of software. - Jill O'Neill
Jill, I've seen enough evidence where that's not the case. PI's tend to lose interest when they have papers published, or if a grad student or postdoc leaves. In the case of commercial entities, it's a cultural thing. Constraints can lead to phenomenal code. - Deepak Singh
Isn't it similar to the evolutionary selection, with academics having a set of "pressures" different from those needed to develop #1-type software? Once the paper gets published, there is no pressure for researcher to improve the code, and things remain "good enough". While in a commercial setting there is always strong pressure from the side of the customer/competition, which drives the development further. I.e. to solve the problem one needs to bring some kind of pressure element to the academic setting. - Yaroslav Nikolaev
T. Brent, technopeasant
"Since 1953, when the first issue of the magazine appeared with an interview of E. M. Forster, our Q&A encounters with the great writers of our times have come to be recognized as a sort of literary genre unto themselves: the Paris Review interview." - T. Brent, technopeasant from Bookmarklet
The range from good to very, very good... - T. Brent, technopeasant
Thank you for this! - Véronique Rabuteau
Ca me fait plaisir, cherie! :) - T. Brent, technopeasant
this is brilliant. thank you. - Mycaptain
I spent a couple of weeks reading nothing but these interviews. - T. Brent, technopeasant
I will save it for after November. - Mycaptain
lol I understand, my fellow scribe. :) - T. Brent, technopeasant
its very tempting but I have to put it for another time cause I am behind already:) - Mycaptain
my faves include: Kurt Vonnegut, Jr., Dorothy Parker and Truman Capote - T. Brent, technopeasant
This is totally amazing! - lev nikolayevich myshkin
And they all talk craft. And Hemmingway talks about his slippers. A lot. Weird. - T. Brent, technopeasant
Mona Nomura
Paul Buchheit
An early birthday present: The Gmail Javascript compiler was just open-sourced! http://code.google.com/closure... (it compiles JS into smaller, faster JS)
We first started work on it almost 8 years ago. It has come a long way since then :) - Paul Buchheit
Happy Birthday Paul! - AJ Batac
Today is actually just my internet birthday. - Paul Buchheit
Well, thanks :) But for a verbose API I'll stick with YUI :P Have to inspect the power of templating and compiler, though. - Claudio Cicali ♋
I wonder what happens when you apply it recursively -- can you get down to 1 byte of code that takes no time to execute? ;=) - Brian Sullivan
Finally! This is great. - Tudor Bosman
Happy Birthday! - Robert Scoble
Nice! - Micah Wittman
Unfortunately it looks like the internationalization features may be missing. I wonder why those were removed? (or if I'm just not seeing it) - Paul Buchheit
Paul you are my best-friend :`( - Onur Gündüz
if you were starting a new site today, would you use this over jquery (which friendfeed uses)? - Karl Rosaen
Karl, jquery is a library, this is a compiler. I would use them both. - Paul Buchheit
well, i mean closure library :) but yeah, they could be used together - Karl Rosaen
ah, i see this is a link closure compiler, not the broader closure tools. - Karl Rosaen
Refactoring, JS style. - Gabe
Now, this is a good news - Ozkan Altuner
@Paul the Closure project has three components: compiler, library, and template language. Looks like the Closure/library might be competing with jQuery. - Shakeel Mahate
this is sweet! - Jay
I think jQuery does a lot of stuff that might confuse the compiler, e.g. iterating over an array of string function names and creating new function wrappers (look at the way the parent/child/next/prev/etc functions get installed) The Closure library is also full of type annotations that help the compiler make better optimization choices, so you're likely to get a better compiled outcome using Closure than jQuery + fixes + compiler - Ray Cromwell
@paul -- I know you've been wanting this opensourced for a long time. sorry it took such a long time. Nick Santos and the jscompiler team has finally done it! Cheers! - Jing Lim
Happy Birthday - ashish
Many happy returns!! - Cozy geta
Happy Birthday, Paul! - Andrew Terry
Happy Birthday Paul - Sandeep Kalidindi
Happy B'day Paul! don't be evil :) - sirishkumar
Congratulations to the team (and @Paul & Jing) -- I know everyone's been waiting a long time for this. For anyone considering whether to use jQuery vs Closure, consider that they're meant for largely different purposes. jQuery's good for enhancing static web pages; Closure's much better at building large apps. And as Ray points out above, Closure the library is going to get much better results from Closure the compiler than an arbitrary js library would, because of all the type annotations. - Joel Webber
Paul Buchheit has been at the top of my best of pages all month. Rock on, Paul. - Donald C. Lindsay
Hey HAPPY BIRTHDAY PAUL !!! Cool present!! <insert CAKE> :D - Susan Beebe
Paul, any comment on this write up? http://www.sitepoint.com/blogs... - Sachin
That writeup is trolling for traffic IMHO. Nit picking 50 lines out of 200+ thousand (written for readability, which get compiled and optimized), providing no benchmarks for claims, and spending half the time bashing Java, it just seems to be struggling to find something wrong with Closure. - Ray Cromwell
Sachin: he seems to be commenting on Closure the JS library, not Closure the JS compiler (that Paul's post was about). And he may be a douchebag, but I haven't seen anything I disagree with. - Gabe
@Sachin: I hate to be too harsh, but that post is pretty much garbage. From what I can tell he's pretty much managed to enumerate some of the worst things about Javascript -- nitpicking the code for referencing "undefined" directly without declaring it as an uninitialized local? That's insane. Following this advice is mostly a recipe for an unreadable mess. Also, look in the comments for several refutations of the idea that some of these are even optimizations. - Joel Webber
Joel, you're just not man enough to handle a language where 'top' is an implicitly reserved keyword, and 'undefined' which should be, isn't. But it could be worse, 'null' could be something you could override. :) - Ray Cromwell
Daniel Mietchen
I am inclined to submit a proposal for a session on Open Science. If any of you plan to go there or wish to contribute to the session, let me know. - Daniel Mietchen from Bookmarklet
Update (a few months later): The main deadline for session proposals is gone, but Eurodoc ( http://www.eurodoc.net/ ) are planning to submit a session for the "young scientists" part, for which the deadline is Sep 30 (next Wednesday). Preliminary title (possibly familiar to some of you): "What would science look like if it were invented today?" Would any of you be available to join the... more... - Daniel Mietchen
People from the Oxford Internet Institute put in something on Science and the internet - can't remember the exact details but could put you in touch. - Cameron Neylon from twhirl
Yes, Cameron, please do. But participation in our session would not be limited to pre-selected themes or people - we plan to do it as open as possible. - Daniel Mietchen
Absolutely. Just a case of demonstrating that the thinking is connected up :-) - Cameron Neylon
The current draft of the proposal is at http://etherpad.com/What-wo... . - Daniel Mietchen
Seems to me that a session on Open Science could fit well within theme #10 ("Policy - what follows?") of the http://www.esof2010.org/themes... : "European science, research and innovation policies; the role of EU and national institutions; European science policy in a global context; international S&T cooperation policies; the changing landscape of European... more... - François Dongier
The deadline for the Scientific Programme (and also the "Policy what follows" theme) has already passed, it will be submitted in the Career Programme. So as Daniel wrote, it should be for young scientists to inform them about developements and also to involve them in a debate on new developments. For now, it is most urgent find people for the list of speakers which will be connected online to talk about Science 2.0. - weppens
session accepted: http://ff.im/bi8Mb . - Daniel Mietchen
Well done. - François Dongier
Still, if any of you would like to join the session remotely (or perhaps even physically), please let us know. - Daniel Mietchen
Renato Albano
Search in Django, Large Problems, Mostly Solved | Surfing in Kansas - http://ericholscher.com/blog...
RAPatton
Harry Truman and Poker in the White House - WSJ.com - http://online.wsj.com/article...
Harry Truman and Poker in the White House - WSJ.com
Harry Truman and Poker in the White House - WSJ.com
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"When Harry S. Truman was sworn in to office, his poker buddies from the previous war were afraid he might stop playing now that he had been "promoted." They need not have worried. The new chief executive even requisitioned a set of chips embossed with the presidential seal for use in the White House, though he tried to avoid being photographed gambling on its premises. The prudes of America would put up with only so much. Truman had learned to play cards from his aunt Ida and uncle Harry on their Missouri farm back in the 1890s. In a letter to Bess Wallace, the woman he was courting, in February 1911, the sincere 26-year-old suitor wrote, "I like to play cards and dance . . . and go to shows and do all the things [religious people] say I shouldn't, but I don't feel badly about it."" - RAPatton from Bookmarklet
"hroughout his 88 years, Truman used poker as both a personal and political means of expression. His motto, "The buck stops here," refers to the dealer's button or placeholder, because during the 19th century hunting knives with buckhorn handles often served that function. It was the president's folksy way of letting Americans know he was responsible for what happened on his watch. That... more... - RAPatton
Werner Vogels
The upcoming Economist Debate is on Cloud Computing: "This house believes that the cloud can't be entirely trusted" http://www.economist.com/debate...
Shevonne
M F
M F
British political posters 100 years ago - http://emmeffe.posterous.com/british...
British political posters 100 years ago
British political posters 100 years ago
British political posters 100 years ago
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Ashalynd
RT @timoreilly:The Unreasonable Effectiveness of Data,IEEE Intelligent Systems(2009)PDF: http://www.computer.org/portal... How Google works its magic.
Czar
Awesome Pic, "Hubble Unveils Stunning Star Birth in M83 WFC3 view of M83. Credit: NASA, ESA, and the Hubble Heritage Team (STScI/AURA) – Universe Today" - http://www.universetoday.com/2009...
Awesome Pic, "Hubble Unveils Stunning Star Birth in M83 WFC3 view of M83. Credit: NASA, ESA, and the Hubble Heritage Team (STScI/AURA) – Universe Today"
Amund Tveit
Amund Tveit
RT @atbrox Preliminary Experiences Crawling with 80legs - http://atbrox.com/2009...
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