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pn
RT @infoecho: "collective wizdom".. Like to see how well it works... http://www.ox.ac.uk/media...
So far, three colleagues have gleefully emailed that link to me to wind me up... - AJCann
And I can't use it. - pn
Mr. Gunn
Mendeley, the ‘Last.fm for academia’, holds $10,001 ‘Battle’ to boost its API - http://thenextweb.com/uk...
... or another way to get development for cheap. - pn
Pawel Szczesny
How many times you can publish the same service? http://www.ncbi.nlm.nih.gov/pubmed...
All three articles are describing slightly different aspects of the service, but it's still _the same_ service (!). - Pawel Szczesny
Well papers are academic currency. Any way to increase your wealth (utility be damned) :) - Rajarshi Guha
But three? Within six months? 200% inflation rate is going to kill this system... :) - Pawel Szczesny
@Pawel... agreed. This is the same paper. It is not uncommon for biology groups to publish the 'tool' separetely from the 'science', but this sounds ridiculous... plagiarism it is... actually, all journals I have been reviewing for in chemistry, do not allow results to be published before... I can't believe there are so many angles to this tool that those journals would have allowed it... within 6 months... that means they must have been submitted simultaneously :) - Egon Willighagen
Actually they're doing themselves a major disservice. By publishing the same thing 3 times they effectively divide their citations by 3, which harms their H-index. - Paul Gardner
And none of these 3 papers cite Jmol! Or even mention it... - Egon Willighagen
NAR often includes previously published databases and software. - Matt Hodgkinson
I've also heard of a rejection to the NAR webserver issue b/c of a Bioinformatics Application Note. But I'm not sure if this is a general policy. Once you're in the NAR db / webserver issue, you can re-submit after 2 years. - Michael Kuhn
I'll play devil's advocate. Apart from the reaction against CV stuffing is there any good reason not to do multiple publications for a service? If the argument were, for instance, to reach a series of different audiences? - Cameron Neylon
multiple pubs in multiple venues are fine. But pubs are currently a currency and basis of competition (amongst other things); from this POV, spamming journals with multiple articles devalues the individual articles - Rajarshi Guha
Agreed but surely its the author's choice to balance that devaluation against potential value gain of reaching new people? I guess what I find interesting is that people feel that protecting against publication inflation is a bigger concern than getting information out efficiently. Similar case where a piece in PLoS Currents was subsequently published elsewhere and everyone got their... more... - Cameron Neylon
I checked the website, and the have an attribution clause... I could not find the attribution requirements, but nothing stops them from asking people to cite all *3* papers... - Egon Willighagen
@Cameron... I think it's a problem of inflation, and devaluation. 3 papers is simply more rewarding, and everyone not publishing more or less the same thing trice is effectively punished. - Egon Willighagen
Perhaps, but is that not a symptom of measuring the wrong thing? If we actually measured re-use (e.g. citations) and three papers meant the number of citations were cut in three for each paper and the total number was the same then we'd be ok right? No devaluation? The problem here is not that its being published three times but that we value the wrong things (number of papers) in a system that enables (or even encourages) cheating. - Cameron Neylon
What @egon said. My basis for this argument is that, in principle, multiple pubs in different venues are fine (I'm not sure how different the venues were for this case). And in a world where the nuances (or lack thereof) of these multiple pubs are taken into account, this would be fine. But in the real world, where jobs/grants/promotions are (unfortunately, frustratingly) based on a... more... - Rajarshi Guha
@cameron - absolutely! We are measuring the wrong thing. But, that's what we're measuring. So to stay in the race, we (well, not me, it doesn't matter to me much anymore) play the game, whose apparently best strategy is to publish as much as we can. I'm sure that with your and others' efforts this will change one day - but people still want to get their jobs/grants/promotions ... - Rajarshi Guha
Agreed - and this isn't a case where I'd argue much in their favour. But the thing with PLoS Currents was a bit different but got a very similar response. Interested whether people feel that's as egregious a case. - Cameron Neylon
is there a link to the PLoS Currents discussion? - Rajarshi Guha
Not sure if these particular 3 papers are what I usually think of as duplicate papers. The "Acta Crystallographica Section F" one is part of a special issue about the JCSG pipeline, so I think it's reasonable there even if it's duplicating things. And my opinion is that the NAR database/server issues are also a special case - as they provide a resource to the community and often describe websites that have been published elsewhere. In short, not the most straight forward example of duplicate publications. - Mickey Kosloff
Cameron, if you're playing devil's advocate, don't forget to send an invoice to NPG, because they will profit the most from perceived inflation of papers outside of Nature* ecosystem. :) But let me play the game as well - if we allow for such marketing strategy, it gives yet another advantage to people who use English natively and have no problems to write five different stories on the same discovery. Yet another penalty for not being British? Thank you so much, Cameron ;). - Pawel Szczesny
Pawel++ - Egon Willighagen
Mickey, while I agree these are "special cases", not clear duplications, I still don't really get it why it's allowed in a first place. When I was reviewing a manuscript for NAR special issue I'd asked authors to improve the service in comparison to the original (published few months earlier) despite clear policy on allowing duplicates. Today, probably I would refuse to review for NAR special issue at all... - Pawel Szczesny
Incredible how people behave like you expect them to behave in these comments. Very revealing and eye opening. - pn
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7 ways Github has changed the open source world - http://honza.ca/2011...
This reminds me: we're planning to publish our little open science project http://buridan.sourceforge.com soonish. Should we move it from sourceforge to github or does it matter? - Björn Brembs
Doesn't matter. - Egon Willighagen
I would go to GitHub. - pn
Ricardo Vidal
RT @seanconnell: Here are some OSX terminal tips. Many were new for me. http://apple.stackexchange.com/questio...
... or welcome to Unix, Mac fanboys. - pn
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Re: Trapped in the USA: The Reification of Data: from the Printing Press to the Web-centric API - http://boscoh.com/science...
"Are you still trapped in US?" - pn
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Re: Trapped in the USA: The Reification of Data: from the Printing Press to the Web-centric API - http://www.disqus.com/people...
"Are you still trapped in US?" - pn
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30 Fantastic Geeky Tricks to Get The Most From Your Mac | Mac.AppStorm - http://mac.appstorm.net/roundup...
30 Incredible Safari Extensions Available Now - pn
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Work in a Swedish company? Self-employed American in Sweden needs your helps - http://www.dalkescientific.com/writing...
immigration laws are a pain. Hope things work out for Andrew - Rajarshi Guha
yep, I have many stories of immigration laws - pn
Jeff Habig
Anyone with recommendations on portable hard drives (1TB+)?
Western-Digital are quite good - pn
Rajarshi Guha
Man places his genome in public domain, on Github - http://manu.sporny.org/2011...
*cough* his SNPs are public domain *cough* - pn
Good point about the need for better search and analysis tools - Mr. Gunn from YouFeed
He's braver than me....not sure I want to go there. I did share my Paternal Haplogroup and projections of what I might look like fat, bald and old though: http://tinyurl.com/5upk6p9 - Antony Williams
Just wondering how the type of data placed into the public domain here differs from that in Genomes Unzipped? http://www.genomesunzipped.org/project In the latter case it also appears that at lot of care was put into the ethical considerations of the people concerned plus there's strength in numbers. - Dan Hagon from Android
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Crate is to sharing files, what Dropbox is to storing them. - http://thestartupfoundry.com/2011...
Would be great... if it worked. No go with FireFox, at least not without signing up. - Bill Hooker
Works for me, check http://lts.cr/Mqp - pn
I actually did register for it, it was quite straightforward, simple. I'm on Firefox. - pn
An option would be http://www.dropitto.me/ - pn
pn
Oh dear a little more like 1.9 methinks... "Error occurred: The following PMID is not available: 21221106" ;-) - Cameron Neylon
guess this is a PubMed problem... sometimes the newest PMIDs seem to have problems. Guess this is the article: http://www.nature.com/nbt... - Michael Kuhn
Yep, sorry, just starred on my list and was going to read it later. Thanks, Michael. - pn
Chris Miller
Does anyone know of an easy way to stream presentation slides to a remote collaborator while I give audio on the phone? Required: I've got to be able to advance the slides from my end, at least 640x480 resolution, and can be either linux or windows based
webex? They have some free trials. - pn
I did this recently using GoogleDocs. I was able to share my powerpoint and advance the slides while I talked over Skype. - Elizabeth Brown
Skype has desktop sharing. - Donnie Berkholz
I've used GoToMeeting (free version) with good success. - Bill Hooker
Have done such with Skype, worked fine. - Daniel Mietchen
Adobe also offers a free desktop sharing option called Adobe ConnectNow. Also include video-conferencing but is limited to three participants per session. Worked fine when I tried it. - Arnulf Köhncke
Yes, you can do this in Google Docs and Skype. Skype works especially well for a single user. My favorite, though, is Zoho Show http://show.zoho.com - Patricia F. Anderson
Mary Canady
Wow @nuin taught me a new acronym today: NSFW
there's NSFL too - pn
You live a sheltered life. You can see more acronyms here: http://is.gd/Q61Q23 - Mr. Gunn
do not click, do not click - pn
Mary Canady
Anyone know what the platform behind this is, if any? Nice, every blog post represented by pic only on home p. http://cuteanddelicious.com/
it uses wordpress + http://fthrwght.com/autofocus - pn
Matt Wood
Wishing everyone a very happy and successful 2011.
Same to you! - pn
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borga on how did we miss this? Europe warming Gulf Stream current completely broken down. "the breaking of... the Loop Current may generate a chain reaction of ... serious consequences on the dynamics of the Gulf Stream thermo-regulation activity of the Global Climate. - http://www.reddit.com/r...
"might add a PDF warning at the end of the title." - pn
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borga on Someone please help me understand EBI blast's visual output. I have looked everywhere, there's no help or reference. - http://www.reddit.com/r...
"I would bet that you might not be getting a long alignment then. Try the same on NCBI's blast and compare it to check." - pn
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borga on Someone please help me understand EBI blast's visual output. I have looked everywhere, there's no help or reference. - http://www.reddit.com/r...
"on the right side you have the sequences that your query sequence matched to and where on those sequences you got the match (between positions 1 and 7000+). On the left side, on each row you have the alignment of the subject sequence over your query sequence (between positions 1 and 1000+). The colour of each alignment represents an E-value that is the probability of that alignment happening by chance. You can get the actual value from the lagend on the bottom." - pn
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borga on US Government censors 70 websites for whole world. Redditors we need to fight for our freedom! - http://www.reddit.com/r...
"change we can believe in" - pn
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borga on Curious what other bioinformaticians on Reddit do, how much they make, degrees, advice on career growth, etc... - http://www.reddit.com/r...
"Yes, it's kinda fun, until you need to write grants! I get your point, it's a different life style, and the not-so-good salary is compensated by other perks. I'm in Canada, and I'm not Canadian, and the biotech industry in Canada is smaller (and less rich) than the US, and it's quite difficult to get a visa to make the jump. If you want PM me and we can exchange email and contact." - pn
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borga on Curious what other bioinformaticians on Reddit do, how much they make, degrees, advice on career growth, etc... - http://www.reddit.com/r...
"76k a year it's pretty good for a small biotech, I wish I was making the same when I was 25. I'm 37, have a MSc and PhD, two post-docs and just recently start making close to that. But that's the price to stay in academia. I do a bit of everything, from research, development, tutor students, etc. Use from C++ to Python, Ruby, Django, Pylons, R, you name it." - pn
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Re: Trapped in the USA: The End of Natural Evolution - http://boscoh.disqus.com/trapped...
"I agree with you, and I know many researchers made a career on the so-called human evolution. With so many effects and phenomena working on the genotypes and phenotypes, it's basically intellectual forgery to believe we are still evolving in the classical sense (natural selection)." - pn
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Re: Trapped in the USA: The End of Natural Evolution - http://www.disqus.com/people...
"I agree with you, and I know many researchers made a career on the so-called human evolution. With so many effects and phenomena working on the genotypes and phenotypes, it's basically intellectual forgery to believe we are still evolving in the classical sense (natural selection)." - pn
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Re: Trapped in the USA: The End of Natural Evolution - http://boscoh.com/science...
"I agree with you, and I know many researchers made a career on the so-called human evolution. With so many effects and phenomena working on the genotypes and phenotypes, it's basically intellectual forgery to believe we are still evolving in the classical sense (natural selection)." - pn
Lars Juhl Jensen
The Absolute Minimum Every Scientist with Data Absolutely, Positively Must Know About Unicode and Character Sets (No Excuses!) - http://wwmm.ch.cam.ac.uk/blogs...
this post seems a bit lengthy for an 'absolute minimum' but a good idea nevertheless - Attila Csordas
"every scientist with data" -- can you *be* a scientist, without data? - Bill Hooker
not today Bill, quite passé if you're not doing humungous data. - pn
The original Spolsky article (which for whatever reason, was not linked to): http://www.joelonsoftware.com/article... - Chris Lasher
@Chris, the link is in there but sorta buried, about a third of the way down. - Bill Hooker
It's perfectly possible to avoid that problem with LaTeX. You would just type -{}- - Ruchira S. Datta
Ruchira, PMR will be glad of the correction if you get in touch with him. - Bill Hooker
I don't actually think any of this SHOULD be known by everyone. People should rather know the difference between a text editor and a word processor. - Mr. Gunn
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borga on With Apple's $51b in cash and securities, takeover rumors ignite ... Facebook, Adobe, Disney, Sony, Akamai, ARM, nVidia ... place your bets! - http://www.reddit.com/r...
"Exxon-Mobil, Macbooks at the gas station." - pn
Pedro Beltrao
Introducing 'The Fourth Paradigm' - the blog - http://blogs.nature.com/fourthp...
"nice" banner, very Microsoftie. - pn
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