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Simon Cockell › Likes

AJCann
Woo hoo!
YouTube - ‪Upload your video‬‏.png
I assume the CC is new, not the standard YT license? - Egon Willighagen
Yes, this is new. Only one CC licence at present though - but this is progress. - AJCann
It's just that the NEW is placed at the same hight as the YT license... - Egon Willighagen
Phil Lord
WebPrints – ePrints within knowledgeblog. - http://www.russet.org.uk/blog...
Heather Piwowar
You go, #jiscmrd :) Got email from SS: "7 data citation challenges" tweeted more than anything else on SlideShare right now, on front page
F.A.B. :) - Graham Steel
Any chance there is an audio file for this? - Brian Westra
Brian, unfortunately not. See ff thread http://ff.im/A3XZn for a brief overview, and I'll try to add some notes to the slides in the next few days. - Heather Piwowar
Martin Fenner
Heather Piwowar
ok, I'm a big fan of this kblog idea. Use wordpress for scientific publishing. check it out: http://knowledgeblog.org/ #jiscmrd
AJCann
You have no idea how happy this graph makes me or what I have had to go through to make it :-) #Rgasm - http://yfrog.com/h8on7pj
You have no idea how happy this graph makes me or what I have had to go through to make it :-) #Rgasm
Nice, but don't the numbers need to be rotated 90° clockwise? - Mr. Gunn
Ah, but look at the error bars! :-) - AJCann
did you check out ggplot2? http://had.co.nz/ggplot2... - Michael Kuhn
Those are very nice error bars indeed. - Bill Hooker
ggplot2 is great, except for plotting a function - Dahaniel from Android
Inspired by your last post, I started to write an errorbars function allowing optional arguments, including help page, etc. I hope to finish it Friday (too many meetings tomorrow) and share my code then... - Jan Wessnitzer from iPhone
Sadly, because of institutional constraints, I can't use R packages on this introductory course, but building objects like this from scratch has merit to it for R beginners. - AJCann
I looked at the graph and the first thing I thought was: "where are the axes labels" :-) - Mickey Kosloff
Björn Brembs
The future of scholarly publishing is bright - if you think long term - http://bjoern.brembs.net/news...
pq -- "The future of scholarly publishing does look bright - just not for publishers." It even looks pretty good for publishers who aren't insanely greedy. :-) - Bill Hooker
I wonder if they've overdone it so much, that the backlash will wipe for-profit publishing from scholarly communication entirely. IMHO they have... - Björn Brembs
@Björn: you quote "...accompanied by an apparent decline in the quality of peer review." The lack of journal / editorial standards should not be underestimated... refereeing would have been very much better, if the editors properly trained and/or corrected them. They don't. Anyone: feel free to post a poll on who ever had his referee report rejected. One layer here is editorial... more... - Egon Willighagen
BTW, coulnd't leave this comment in your blog: STOPPED: KEY_FILES FOLDER NOT WRITABLE - Egon Willighagen
Sorry, Egon, moved servers and haven't ironed out all the permissions yet! Thanks for the info!! Should be working now... - Björn Brembs
Confirmed: it works now. - Egon Willighagen
Thanks, Egon. I replied there (basically agreeing with your point about peer-review standards). - Björn Brembs
Martin Fenner
Papers 2: the reference manager made with love - http://blogs.plos.org/mfenner...
Pierre Lindenbaum
XSLT+XML+geolocation=KML "BioStar users on a world map" - http://plindenbaum.blogspot.com/2011...
Egon Willighagen
Installing Diaspora on Debian Linux | achton.net - http://achton.net/2010...
Egon Willighagen
wondering when #biostar will stop being in 'bootstrap mode'... http://biostar.stackexchange.com/
Martin Fenner
How to use Citation Typing Ontology (CiTO) in your blog posts - http://blogs.plos.org/mfenner...
Updated my Link to Link Wordpress plugin to now use a simplified version of CiTO. - Martin Fenner
You guys are doing cool things in WP... makes it tempting to change... - Egon Willighagen
Thanks Egon. I think that Wordpress is an excellent platform for scholarly tools. But we are just at the beginning. - Martin Fenner
Martin, this is fantastic, and thanks for the how-to post. Can't wait to see what is coming next. Looks like my days at hosted wordpress.com are coming to an end... - Heather Piwowar
@Egon @Heather - Come to S3.0 ;) - science3point0
Heather, what Mark said. I can also give you a blog at my testing site blogs.xartrials.org. - Martin Fenner
Also a good option, I have my own wordpress dev playground there :) - science3point0
I'm sold on this stuff already! I set up a free hosted site on wordpress.com to play around, but switchet to my own installation hosted elsewhere so I could play with plugins (which wordpress.com won't allow). I'll certainly give Martin's plugins a go shortly. - 'Mummi' Thorisson
PS I'm historically a Drupal (http://drupal.org) man through-and-through when it comes to building websites. But WP is such a nice, super-user-friendly toolkit for this sort of thing. - 'Mummi' Thorisson
Mmm... has anyone spoken with the people from ResearchBlogging? I guess it should be part of the HTML snippet the create too.... - Egon Willighagen
Egon, I thought about this too. It makes a lot of sense to create the code ResearchBlogging needs with a Wordpress plugin. I will look into this when I start working on a plugin that creates a bibliography in March. - Martin Fenner
Lars Juhl Jensen
Matt Wood
Papers 2, available from 8th March from @mekentosj, with 85 new document types and more: http://mekentosj.com/
Phil Lord
Bill Hooker
Publish and perish: why the current publication and review model is killing research and wasting your money - http://ubiquity.acm.org/article...
tldr (yet) but thought folks around here might be interested - Bill Hooker from Bookmarklet
Fabio Casati is doing some interesting stuff... - Cameron Neylon
"Highly Inefficient Publishing Process. This model is incredibly inefficient under every perspective, and results in a colossal waste of public funding, and forces researchers worldwide to waste countless hours that could be devoted to better research (or to have fun with family and friends). It is a system deeply rooted in the past, oblivious to the advent of the Web and related new... more... - Daniel Mietchen
It is interesting that the ACM Digital Library entry (http://portal.acm.org/citatio...) for this article has a broken DOI number and requires an account for full text access. The authors note that: "this is preliminary work (version 1.0, or rather 0.9). We release it anyway according to the concepts proposed in this document." This is a nice illustration of the point that the ACM Digital Library does not handle versioning well. - Don Pellegrino
Lars Juhl Jensen
Commentary: Intel’s take on GPU computing - http://larsjuhljensen.wordpress.com/2011...
A week or two ago, I published a post in which I argued that most papers, which report order of magnitude speedup of a bioinformatics algorithm by using graphics processors (GPUs), did so based straw man comparisons: Massively parallel GPU implementations were compared to CPU implementations that did not make full use of the multi-core [...] - Lars Juhl Jensen
Pierre Lindenbaum
Champagne ! Our paper is accepted in "Nature Genetics" :-)
Congrats! What's it about? Or doesn't that matter? :) - Egon Willighagen
@Egon, I'm going to wait for the publication of this article before talking about it :-P - Pierre Lindenbaum
Congrats!! - Björn Brembs
I'm glad you got a paper out, but I'm sorry you couldn't get it published in a real journal. - Bill Hooker
@Pierre... ah, embargoed... obviously increases dissemination of scientific results :) - Egon Willighagen
Congrats !!! - Mitsuteru N
Martin Fenner
Jochen Weile
Yay! My OndexView paper got accepted by Bioinformatics. (Subject to minor revisions)
Björn Brembs
I hate that different journals must have different citation styles!
Wondering what the first journal will be to accept DOIs and do the viz themselves... - Egon Willighagen
And the differences are often so totally arbitrary: Smith, J (2005) or Smith J. 2005. or some irrational crap like that. I say: author-date in the text and I don't care how you format the bibliography, as long as it includes all authors, title and source. - Björn Brembs
Having not writtem a paper yet (except for homework), but having read A LOT of papers, i think the bibliography should at least be arranged either alphabetically (my favorite for purely aesthetic reasons) or by year. Some papers have haphahazardly arranged bibliographies and its a pain in the derrier to go through the references. - Shanthi Bradley
But Björn, if journals didn't dictate which font and font size to use in your figures and how to format the bibliography, how would they justify that they have dramatically improved the value of your paper and that you should thus sign over copyright to them? >:-) - Lars Juhl Jensen
Egon, I don't think DOIs alone are enough. A citation should contain some redundancy to allow alternative routes to the object, eg if the DOI had a typo! - Chris Rusbridge
We had a discussion about this at the #scio11 conference two weeks ago. We felt that DOIs alone are not enough, and that we will never agree on a single citation style. So just use whatever you like, as long if the basic info (eg. Title, DOI) is there. - Martin Fenner
Sure... redundancy is good... but with any citation style in the .doc, together with a DOI, they can figure out the styling... with author prefered citation, there should be more than enough redundancy to 'checksum' the DOI... that is, it does not have either or... - Egon Willighagen
We didn't get into this specific issue at Beyond the PDF, but I always felt like citations should be links with embedded metadata and that the "list at the end" style was just a holdover from print which has of course maintained through to PDFs. Were we using HTML instead, I think you'd see the current manner of representing citations fade more rapidly. - Mr. Gunn
William, I stopped liking the "list at the end" style a few weeks ago. Citations should be embedded in the text. "List at the end", aka bibliography should be supplied as separate file in BibTeX format. - Martin Fenner
What martin said - Kubke
well, yes, let me put it this way: authors should not be in charge of journal branding... but make publishers and their database allies self-organize with the aim to save authors time - Claudia Koltzenburg
@Egon, > accept DOIs and do the viz themselves < well, at CTT, we're ready to do this, let's look for the authors :-) -- we say nothing about the format a submission should be in, I am actually looking forward to the day we get a contribution in xml :-) - Claudia Koltzenburg
That's the spirit! Changing styles is just a click of a button anyway - the problem arises from the ridiculous number of different styles and that one author can't have all of them. So if we can change styles at the click of a button, why can't publishers? Why do authors still have to do that? - Björn Brembs
well, maybe authors do not get together well enough to form a strong lobby of PRODUCERS :-) - Claudia Koltzenburg
Fractioning authors into 24,000 different groups is one way to prevent strong lobbies :-) - Björn Brembs
well, let me take some steps, then, and make explicit CTT's longstanding policy: http://friendfeed.com/claudia... - Claudia Koltzenburg
Lars Juhl Jensen
Only in a bioinformatics group do people use Doodle to decide when to eat cake
Jonathan Eisen
Cool paper, & winner of "worst new omics word award": Predatosome - http://phylogenomics.blogspot.com/2010...
Perhaps authors are now deliberately baiting you in order to get publicity for their paper :) - nlomioni
Yes, sure that would be a good strategy. May have to rethink whether I write about the paper in the future. - Jonathan Eisen
Eisenome: the set of all papers profiled in the "worst new omics word" series... - Andrew Su
Oh man, I can't believe I never thought of Eisenome before --- I am definitely going to find a way to use that - Jonathan Eisen
Eisenome. Brilliant !! :-)) - Graham Steel
Liking for "Eisenome". :-) - Bill Hooker
@Jonathan The geek element in me can confirm that http://eisenome.blogspot.com is freely available. Just sayin' ;-) - Graham Steel
Wouldn't that be the "ironome" ... i.e. all genes involved in iron metabolism? Someone is already researching "you", Jonathan: http://www.chem.tamu.edu/faculty... - Iddo Friedberg
perfect Iddo - my baseball nickname for years was "Ironman" - Jonathan Eisen
Graham - not anymore. - Mr. Gunn
Mr. Gunn you are in deep trouble if that was you - Jonathan Eisen
"It Wasn't Me" - Shaggy :- http://www.youtube.com/watch... - Graham Steel
I was kidding, but is it really not avail. anymore? Could be the evil speculative domain parking stuff practiced by the likes of GoDaddy et al. - Mr. Gunn
1 Gazillion points to Mr/Dr./Prof J. Eisien for creating these soon to be, infamous Eisenome and Eisenomics blog sites via this humble FriendFeed thread !! - Graham Steel
Despite my use of twitter for the #scio10 meeting, I continue to be amazed by how awesome friendfeed is --- friendfeed - I am back - Jonathan Eisen
Not that I wont still tweet - but I do love friendfeed - Jonathan Eisen
Make good use of it. It's a rare scientist that can play this trick of a self-named -ome. "Suome" doesn't quite roll off the tongue. "Lindenbaumome"? "Steelome?" "Szczesnyome"? None quite have the same ring. "Hookerome" is close, but I'm sure that's just putting a nerdy spin on a third-grade playground taunt (just a guess Bill)... - Andrew Su
Andrew, I think we all have to hand this one to you for coming up with the idea in the first place :-) - Graham Steel
@Andrew "Iddome"? Going back to the hiring and P&T discussion, an inner joke in my department says I was hired only because one of the senior researchers there is working on indoleamine 2,3-dioxygenase (IDO). Hey, it's as good a metric as the ISI impact factor... - Iddo Friedberg
+1 Iddo - thanks for a hilarious discussion Andrew, Graham, Johnathan.... - Mr. Gunn
Andrew, even the judge at our wedding made fun of my name, pointing out that well, of course my wife wasn't going to take *that* name. I'm just wondering how I get a grant to study my own -ome... :-) - Bill Hooker
The Koch a doodle doo -ome is unveiled http://kochadoodledoo-ome.blogspot.com/2010... - Steve Koch
Thank you all for this great discussion. Just changed my name in all public registers to "Nils Reintome". - Nils Reinton
"Lindenbaumome" may not work, but surely it would be the "Lindenbome", which kinda does.. I'm not even going there for my own name... - Simon Cockell
@Steve Koch... kochpostulates.blogspot.com is still free... - Iddo Friedberg
To keep the fun/discussion going, I have commenced http://prionomics.blogspot.com/2010... - Graham Steel
Maybe we should do homeopathomics - Jonathan Eisen
Absolutely :-)) Now't on goog so far in that regard !! - Graham Steel
@Iddo -- good idea. I snapped it up, and tried to use it for good, not evil :) Maybe someday I'll know what to do with it http://kochspostulates.blogspot.com/ - Steve Koch
As requested, I'm officially adding the Björnome: http://bjoern.brembs.net/news... - Björn Brembs
pn
pn
Sharing proteomics data, trickier than it seems - http://blog.dannynavarro.net/2010...
Think the rub is both a) standards are still lagging behind users (formats for marking up identications and quantitations are still in development), and b) mass spec manufacturers and key software tools are still not fully supporting the standards that already exist. - Neil Swainston from iPhone
Pedro Beltrao
Episode 02 – Systems Biology with Pedro Beltrao - http://nodalpoint.org/2011...
its so weird to hear my own voice :) - Pedro Beltrao
Wow, I didn't realize nodalpoint was revived (and in podcast form). Love! - Chris Lasher
Cameron Neylon
I'm not usually much for #followfriday but an awful lot of v clever people, many quite new to twitter, in the #beyondthepdf stream
Cameron Neylon
Just for info. Another project in this Wordpress love in is the #JISC funded #knowledgeblog project http://knowledgeblog.org/ #beyondthepdf
Amused at the mailing lists. JISC, you rascals! - AJCann
Cameron Neylon
Hoist by my own petard: How to reduce your impact with restrictive licences - http://cameronneylon.net/blog...
I was honoured to talk at the symposium to celebrate Peter Murray-Rusts' work. I didn't want to give the usual kind of talk to this audience. I wanted to focus on what I think are the big risks and opportunities for the research community and why I believe that a focus on maximising research impact might be a way to bring the community together in a positive way. However I made my own point by inadvertently putting up a permissions slide that prohibited livestreaming, live blogging, and recording. By using a restrictive licence I very effectively reduced the potential impact of my talk about impact. The message is pretty clear. If you want to make a difference, use an open licence and give people permission to re-use your work. If you want to make no impact at all then restrictive licences are a great way to achieve that. - Cameron Neylon
How interesting, Cameron. Thanks for sharing the story. Kudos to everyone for respecting your (inadvertent) wishes. Curious: you have that slide in some other slidedeck on purpose? Is it for when you are talking about institution-specific issues internally, or ??. Not judging, I'm interested. - Heather Piwowar
Great story, Cameron. - Michael Nielsen
@Heather the slidedeck has two slides, one for people like me and one for people that didn't want liveblogging etc If I had a brain they'd be in the opposite order (see under "nudging") but that was just the way I originally did it... - Cameron Neylon
Gotcha. Thanks! - Heather Piwowar
What Neil said -- I'd have heckled you! (If I'd noticed.) - Bill Hooker
Thing was, Cameron started off by discussing his early career. I assumed that he was talking about issues he didn't want broadcast around the world (I couldn't tell if the video was streaming or not). Either that, I thought, or else he was going to make a point at the end of the talk about how no-one can prevent live discussion of talks. - Noel O'Boyle
Egon Willighagen
unless I find a way to hide questions, it is exit #quora ... #noise #fail
Just had a quick glance at the bioinformatics questions there. It looks like at least half of them could be answered by pasting the question into Google. - Lars Juhl Jensen
I have seen mention of Quora Gurus and blog posts along the lines of "How to market your brand on Quora", so there is plenty of noise coming and I have no idea how they're going to handle it. - Mr. Gunn
a simple Hide function as here on FF may be just enough, though an adaptive 'priority' function as on gmail could be really useful too... - Egon Willighagen
Martin Fenner
RT @zotero: Zotero Standalone Alpha with support for Chrome and Safari now available! Part of #ZoteroEverywhere http://www.zotero.org/support...
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