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Neil Saunders › Likes
FriendFeed: "We will make sure that people do non-computer-y things tonight, such as hang out with people in person. To do this, we will inflict duck hunt on everyone using FriendFeed." Me: "AAaaaaaahhhhhhhhhhhhh"
MVB (Curmudgeon of FF), Josh Haley, T. Brent, technopeasant and 7 other people liked this
:(
- Derrick
I shot one to see if it would go away.
- Mike Nencetti
It's been duck carnage over here, but the thing just. won't. die.
- Imitation lris
If you're running Adblock, kill everything with "themes/newyears" in it. Works.
- D0r0th34
That dog isn't popping up to laugh or whatever.
- Julian
Mr. 4 was disappointed that when you shoot it, the duck doesn't fall to the bottom of the page and stay there.
- s t e v e
And you cannot shoot it multiple times as it falls.
- Polly Potter
How do you shoot it? Can I just poison it?
- Rochelle Rochelle
Oh...duh...just figured it out. The shooting part, anyway.
- Rochelle Rochelle
Is it like with zombies? Will I inevitably become a duck? *quack*
- Rochelle Rochelle
I'm so glad we didn't have to do wood cuts. http://usefulchem.blogspot.com/2009...
Christina Pikas, Dan Hagon, carolh and 5 other people liked this
the next generation will note that they are glad they don't have to extract knowledge from human-only readable documents
- Jean-Claude Bradley
+1 Jean-Claude. A few more "information generations" and working scientists will consider our current methods functionally equivalent to woodcuts. I hope.
- Bill Hooker
Strictly speaking woodcuts were an extravagance in Newton's time since it was only used for inline figures within the text (itself composed of metal type) so each figure had to be individually, skillfully and laboriously hand-crafted. Also since it was wooden it had an extremely short lifespan compared to the rest of the text block which meant that only short print runs were possible...
more...
- Dan Hagon
timoreilly: How do you whittle down your number of online accounts? (Good New Year's task) http://bit.ly/6oVGrd Some good advice already, need more. - http://twitter.com/timorei...
Neil Saunders liked this
timoreilly: How do you whittle down your number of online accounts? (Good New Year's task) http://bit.ly/6oVGrd Some good advice already, need more.
- Richard Akerman
Bird Sites On The Web Over The Last Decade - http://www.burdr.com/2009...
Neil Saunders and Deepak Singh liked this
Yet another year is in the can - http://mndoci.com/2009...
Björn Brembs, Pawel Szczesny and Neil Saunders liked this
Peter Miller, Andrew Lang, Neil Saunders and 2 other people liked this
Happy 2010 from Copenhagen! These pictures were shot through my kitchen window a few minutes after we entered the new year.
- Lars Juhl Jensen
RT @seamuscooper: At The Mountains of Madness-- it's really good. I take back everything I said about Lovecraft not being good at longer stories.
Neil Saunders liked this
molmodelblog: 17 Protein disorder prediction servers http://bit.ly/8F86H7 - http://twitter.com/molmode...
Neil Saunders liked this
Public PhD defense - http://www.slideshare.net/yannick...
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joergkurtwegner, Steve Koch, Deepak Singh and 6 other people liked this
It's almost too nice to be a thesis defense!
- Benjamin Tseng
Laurent Keller: great work and apparently also great lab!
- Björn Brembs
is there supposed to be audio?
- Jean-Claude Bradley
Santa's a Health Menace? Media Everywhere Are Falling for It—But the Study Was Meant as a Joke - NurtureShock Blog - Newsweek.com - http://blog.newsweek.com/blogs...
Neil Saunders liked this
Media competence for the media.
- Roland Krause
Ruby on Rails Tutorial: Learn Rails by Example - http://www.railstutorial.org/
Mike Chelen, Bronwen Dekker and Neil Saunders liked this
If you want to learn Rails, you could do a lot worse. Integrates Git from the get go, introduces Github and uses Heroku for deployment.
- Deepak Singh
Good, practical advice and a promising start - only 4 complete chapters out of 10 planned, so far.
- Neil Saunders
thesimplerlife.net » Blog Archive » developing an autotelic personality, or, how to enjoy everything - http://www.thesimplerlife.net/2009...
Peter Miller, Jean-Claude Bradley, Jenny Morman and Neil Saunders liked this
The true test of an autotelic personality [...] is being able to enter that state of flow even while doing things that many people may consider boring. A person with an autotelic personality can take something as mundane as mowing the lawn and turn it into an opportunity for growth. Therefore, the argument that developing an autotelic personality will directly impact your quality of life is quite easy to make. Deriving true enjoyment out of every aspect of is the key to separating the quality of our lives from external (and therefore uncontrollable) forces. Becoming somebody with an autotelic personality is not something that can be done overnight. It must be actively practiced until it becomes part of your personality.
- Meryn Stol
Mike Elgan: 10 obsolete technologies to kill in 2010 - http://www.computerworld.com/s...
Neil Saunders liked this
"The fax machine was obsolete 15 years ago. When someone says "fax it to me," I always feel like I'm being punk'd. A fax machine is nothing more than a printer, scanner and an obsolete analog mode that work together to waste time, money, paper and electricity."
- Chris Miller
I'd like to see the end of articles that are 2-page solely to increase page views ;-)
- Neil Saunders
Priceless! The 25 Funniest Vintage Tech Ads - Network World Slideshow - http://www.networkworld.com/slidesh...
Neil Saunders liked this
"My oh my, how things have changed. These 25 vintage tech ads are guaranteed to take you back -- and, in most cases, remind you how truly terrible our tastes once were."
- Peter Murray
Google Open Source Projects You Probably Don't Know - http://blogoscoped.com/archive...
Neil Saunders and michael sean wright liked this
The 0x1fff blog published a list of 35 open source projects from Google. Included are Google Glog, Google CRUSH, Google Update aka Ohama Omaha, the Google Feed Server and many more.
Daily #fail RT @mjrobbins: Daily Mail: Mistletoe cures cancer. *facepalm* http://www.dailymail.co.uk/health...
Joe Dunckley, Egon Willighagen and Neil Saunders liked this
No doubt will be added to http://dailymailoncology.tumblr.com/ and/or http://kill-or-cure.heroku.com/.
- Neil Saunders
Duncan Hull to Duncan's feed, The Life Scientists, Semantic Web for Health Care and Life Sciences IG
The Semantic Biochemical Journal experiment « O'Really? - http://duncan.hull.name/2009...
Mickey Schafer, Hope Leman, joergkurtwegner and 19 other people liked this
"There is an interesting review [1] (and special issue) in the Biochemical Journal today, published by Portland Press Ltd. It provides (quote) “a whirlwind tour of recent projects to transform scholarly publishing paradigms, culminating in Utopia (http://www.getutopia.com) and the Semantic Biochemical Journal experiment”. Here is a quick outline of the publishing projects the review describes and discusses: Blogs for biomedical science Biomedical Ontologies – OBO etc Project Prospect and the Royal Society of Chemistry The Chemspider Journal of Chemistry The FEBS Letters experiment PubMedCentral and BioLit [2] Public Library of Science (PLoS) Neglected Tropical Diseases (NTD) [3] The Elsevier Grand Challenge [4] Liquid Publications The PDF debate: Is PDF a hamburger? Or can we build more useful applications on top of it? The Semantic Biochemical Journal project with Utopia Documents [5] The review asks what advances these projects have made and what obstacles to progress still exist....
more...
- Duncan Hull
from Bookmarklet
Am I missing something here? I only seem to see a few popups when mousing over references?
- Cameron Neylon
Interesting though getting started wasn't entirely transparent. Figs are interactive (pink background and menu) so, for example, data from Fig 9 can be replotted. Tended to spawn popups at an alarming rate. Fig. 13e appeared unable to load into popup.
- Peter Miller
@Cameron, you need to download the Utopia client to get the full effect http://www.getutopia.com the animations are embedded in the PDFs and viewable within the client. It's not a browser based thing (yet).
- Duncan Hull
Done that, looking at both the paper online in enhanced version and pdf I'm not seeing any visual cues or anything that take me anywhere much. Do I need to have the utopia client running as well? Ok you need to open the pdf in Utopia. That's really not immediately obvious I have to say, particularly with the "enhanced online version" getting billing front and centre. Ok I could have read the instructions but its only the mention that Utopia is a "pdf reader" that tells you what to do. Could be clearer.
- Cameron Neylon
Have to say that the idea of a semantically enhanced pdf I have to download and open up in a particular viewer seems to be somewhat missing the point :-)
- Cameron Neylon
Also seems odd that the enhanced online version doesn't at least include the links that are in the enhanced pdf
- Cameron Neylon
@Cameron I see your point, I'd like to see a more web friendly version but there are some limits to what you can do in a web browser (especially when it comes to sequence alignment and molecular visualisation)
- Duncan Hull
Yes, and that is all fair enough - you need to start somewhere but you'd think the links could be translated across pretty easily (e.g. Caspase-3 in paper 1, fig-1 legend is linked in the PDF to a wikipedia entry, why not in the online version?). Bring on HTML5 is what I say :-)
- Cameron Neylon
@Cameron ... and yes, its an "experiment" too (normaly caveats apply!). The thing to look for is the little Utopia Documents icon embedded in the text once you've opened up an article (e.g. the review) in Utopia documents. Thanks for the rapid feedback...
- Duncan Hull
Yep, found it eventually. I'd suggest changing the instructions to be much more explicit. i.e. Download Utopia, then download pdf, then open in Utopia. Most people will have pdfs set to autoload in something else so its not an obvious path - particularly to people used to plugins and overlays. Heh, next quetions can I leave a comment on the journal article to suggest this....mmmm.....that would be a "no" then... ;-)
- Cameron Neylon
Dear Santa, Please can you provide Utopia for Ubuntu/Debian/Linux. Thanks :)
- Allyson Lister
I just skimmed it initially - didn't note the requirement for this odd piece of software. Puts paid to it for me, I'm afraid.
- Neil Saunders
From Philip McDermott: "ubuntu version in the works but just slightly delayed for launch. I'd have thought it'll be available next week sometime"
- Allyson Lister
The idea of a specialized PDF reader for this means it's just a proof of concept at this stage. I'll mention it to the Mendeley people and see if they might like to incorporate some of this into their internal PDF reader.
- Mr. Gunn
@Mr. Gunn thanks...
- Duncan Hull
@Mr. Gunn thanks. Be interesting so know what they think of it, feel free to put them in touch with us :o)
- Philip McDermott
I think that the initial confusion of PPLs website has confused a lot of web-oriented users. Try grabbing the app, the paper, and working through it, and you should get a feel for what we're trying to do. We're not saying web-based is bad, it's just that this is a little different.
- Philip McDermott
@Philip see also commentary here http://digitalcuration.blogspot.com/2009...
- Duncan Hull
As I understand it the PDF reader software is just an initial client for the backend which lets you annotate whatever - and from where all the annotations are fetched. If (when?) it gets opened up you could extend the existing client to read other files, write your own client, write a Firefox plugin, whatever...
- Euan
@Euan yes that's right (and you put it much better than me). As for opening it up, you'd have to ask the Utopia team... it would make a lot of sense.
- Duncan Hull
I like the concept of the Utopia reader. But the integration of references could have been done better. Why not use DOIs instead of linking to a Google Scholar search?
- Martin Fenner
Dear Santa, like @Allyson I really hope your reindeer's can still pull the Linux version, too.
- joergkurtwegner
Besides, how does it compare to the interactive ICM in PLoS ? http://ff.im/acHs9
- joergkurtwegner
PLoS Computational Biology: A Quick Guide for Developing Effective Bioinformatics Programming Skills - http://www.ploscompbiol.org/article...
Dave Lunt, Piotr Byzia, Steve Koch and 6 other people liked this
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
My new Nature paper: A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea (w/ CC license - yay) - http://www.nature.com/nature...
Ruchira S. Datta, Christopher Fields, rowlikeagirl and 16 other people liked this
Kudos for getting the CC license!
- Bill Hooker
Absolutely =)
- Graham Steel
I note that the data for the project, in addition to being in Genbank and at the JGI IMG sites, is now available in Biotorrents at http://www.biotorrents.net/details...
- Jonathan Eisen
Jonathan - How did you get the CC license?
- Michael Nielsen
I wrote briefly about the CC license thing on my blog a while ago here: http://phylogenomics.blogspot.com/2008... ... I think it is only done for papers reporting new genome sequence data.
- Jonathan Eisen
Ah, very nice. It's useful to know about that policy from Nature. When I publish material related to open science I usually have a chat with my editor about licensing - this is the kind of thing that will be useful to bring up in future discussions.
- Michael Nielsen
Nature announced a Creative Commons license for all genome papers in December 2007: http://dx.doi.org/10...
- Martin Fenner
Worth noting that this was in response to strong community demands coming out of the controversy over the public and private genome projects as I understand it. Other communities take note (looking at you structural biology...)
- Cameron Neylon
Two cancer genomes published in Nature last week also have Creative Commons license: http://dx.doi.org/10... and http://dx.doi.org/10...
- Martin Fenner
Well, for many years (dating way back ...) Nature made genome papers available for free - and amazingly to me they have stuck to this. I do not think this was due to the public vs. private debates per se but I guess we could ask some of the old timers. Chris Gunter, who was an Nature back then and handled many of the genome papers, was involved in some way with this "openness" policy. The move to CC licenses in 2007 was a pleasant surprise too ...
- Jonathan Eisen
Kudos also for getting the Nature paper. Merry Christmas.
- Matthew Todd
I wrote a bit more about the paper and the story behind the story here: http://phylogenomics.blogspot.com/2009...
- Jonathan Eisen
Thanks for the fascinating blog post. As one commenter said, longer than the Nature paper itself. I wish we had more blog posts like this where authors write about their just published papers.
- Martin Fenner
from iPhone
+1 Martin! Even better if authors were allowed to write to write their papers the way they want and wouldn't have to write blog posts - hint: paper: four pages, supplement: 10 pages. Supplements must be among the most absurd outgrowths of our decrepit publishing system...
- Björn Brembs
Well, Bjorn and Martin, I agree and disagree. Certainly, forcing papers to be a certain length, to me, is silly, and is Yet Another Reason I like PLoS, since they have no specific restrictions on page lengths in most cases. And I completely agree that supplemental material is mostly inane. In fact, in my PLoS One, PLoS Bio and other PLoS papers I have tried to put as little as possible...
more...
- Jonathan Eisen
@Jonathan: I wrote the comment before I read the largely biographical blog post :-) Either way, being forced to be concise is indeed (often? sometimes?) a good thing, but can be done without the insane page limits of some journals. On the other hand, who but the author would have the right to force brevity? Put another way, shouldn't an author be allowed to completely spoil their work...
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- Björn Brembs
Unfortunately there is still a lot of work to be done before we can easily find all blog posts talking about a particular paper. Nature and other journals should follow the lead of PLoS with linking to blog posts directly from the paper webpage. And tools such as Researchblogging.org, Nature.com Blogs or Streamosphere should do a better job of aggregating all blog posts about a particular paper together.
- Martin Fenner
Bjorn: 1) Author should indeed be in charge of length in my opinion as well as form in many other ways 2) Does not hurt to have editors who suggest things that might make a paper better. 3) As for understandability, I think part of the review of a paper, including in journals like PLoS One, should be whether or not what is written correctly explains what was done and correctly explains...
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- Jonathan Eisen
Loosely coupled tools: BWA - http://mndoci.com/2009...
Michael R. Bernstein, Neil Saunders and Brad Chapman liked this
The BWA/SAMtools separation is great. Other aligners like Bowtie are now producing SAM as well, so you can swap aligners in and out of analysis pipelines a little more freely. Absolutely the right direction to go.
- Brad Chapman
Brad, that's great. I was a little concerned about the "use this aligner for this pipeline" model
- Deepak Singh
Harsh Reaction to Chemistry Claims Cast Doubt on Reactome Paper : ScienceInsider - http://blogs.sciencemag.org/science...
Jean-Claude Bradley, Steve Koch, Neil Saunders and Cameron Neylon liked this
Issues with peer review here, but it sounds like open data might have helped. "In private chats and online postings, chemists began expressing skepticism about the reactome array as soon as the article describing it was published, noting several significant errors in the initial figure depicting its creation. Some also questioned how a relatively unknown group could have synthesized so many complex compounds. The dismay grew when supplementary online material providing further information on the synthesized compounds wasn’t available as soon as promised. “We failed to put it in on time. The data is quite voluminous,” says co-corresponding author Peter Golyshin of Bangor University in Wales, a microbiologist whose team provided bacterial samples analyzed by Ferrer’s lab."
- Matthew Todd
from Bookmarklet
Maybe we should do a round-up of high profile peer review "failures" from this year? Between this, hydride oxidation and the withdrawn crystal structures its not been a good year really...
- Cameron Neylon
Yes, on that note see http://www.coronene.com/blog...
- Matthew Todd
Developing effective bioinformatics programming skills - http://mndoci.com/2009...
Khader Shameer and Neil Saunders liked this
The FriendFeed app for Facebook is really starting to piss me off, and I'm one step away from removing it.
Neil Saunders, Roberto Bonini and April Russo (app103) liked this
1. I don't want it setting my Facebook status, but it's doing so anyway.
- Chris, Taskerrific Guy
2. I don't like how it spams my wall with all my reddit comments, yet it continues to do so even after I've tried to get it to stop posting _anything_ at all to my wall.
- Chris, Taskerrific Guy
Y'know what? Looking at all the complaints about the app on its own wall, *BAM* gone. I'm dropping this app from Facebook.
- Chris, Taskerrific Guy
Chris: If the application is updating your status then you provided the application with permission to update your status. If you don't want it to you should uninstall or just revoke the permission at http://www.facebook.com/editapp...
- Benjamin Golub
There was no option for setting/unsetting any permissions related to status. If there were, perhaps I wouldn't have uninstalled it.
- Chris, Taskerrific Guy
I gave permission for the app to post to my wall, not update my status. This is a new "feature", separate from wall posts, it cannot be turned off and is annoying a lot of people. I wouldn't mind if it didn't update my status with stupid things (like twitter @ replies).
- Neil Saunders
Synthetic Biology 4.0 : highlights and reflections - http://blog.pansapiens.com/2008...
Deepak Singh and Neil Saunders liked this
Amazing technologies introduced here. I think it is interesting that marine microbes can help create gasoline. This <a href="http://marinefuel.com/dock-pr..." title"marine gasoline" name="marine gasoline">marine gasoline</a> shows a lot of promise.
- Marine Fuel
Glass Microbiology | Luke Jerram - http://www.lukejerram.com/project...
Neil Saunders liked this
Pretty.
- Bill Hooker
from Bookmarklet
You need a Data Asset -- not a Data Warehouse http://feeds.feedburner.com/~r...
Neil Saunders and Deepak Singh liked this
The Future - http://twitpic.com/1faqu
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Steve Koch, Ruchira S. Datta, Neil Saunders and JoeCamel liked this
Update: The BuzzCloud for 2009 - http://larsjuhljensen.wordpress.com/2009...
Steve Koch, Neil Saunders, Peter Miller and 2 other people liked this
Google Geo Developers Blog: The Maps Data API: Bringing Geospatial Search to Google's Cloud - http://googlegeodevelopers.blogspot.com/2009...
Richard Akerman and Neil Saunders liked this
"adding geospatial and attribute search to your maps"
- _alf
RT: @NatureNews: Rage against the paywall: Nature, set your news free http://www.finestructure.com/2009... & facebk grp http://www.facebook.com/group...
Nils Reinton, Björn Brembs, Alun Salt and 2 other people liked this
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