Jean-Claude Bradley
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33 minutes ago - jottit.com - Link
From Aaron Swartz - Deepak
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“David is watching the Canucks vs Oilers.”
1 hour ago - Link
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4 hours ago - smashingmagazine.com - Link
nice hacks, thanks, hope it works for any version of WP - Alexey
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Detecting Communities in Science Blogs - SlideShare
20 hours ago - slideshare.net - Link
by Christina K. Pikas, PhD student @ University of Maryland - Enro via Bookmarklet
Interesting stuff. But where's the associated blog post? :-) - Bob O'Hara
I second Bob - Bora Zivkovic
um, which associated blog post? - Christina Pikas
one you will write, that explains the slides in more detail ;-) - Bora Zivkovic
Ok-will do- the videos are supposed to be on the site today, but wasn't loading for me - Christina Pikas
Christina - Nice project! I'd be curious to know if you included mathematical blogs in your study? In my opinion, they are some of the most interesting around, yet they seem to form their own little world, mostly cut off from the rest of the science blogosphere. Were they maybe a separate cluster? - Michael Nielsen
using the spin glass community det algorithm - they fell in with physics and CS (CS blogs were more like theoretical, math-heavy...). I definitely had a bunch of math blogs by both grad students and professors... They weren't completely cut off... - Christina Pikas
This is fantastic and fascinating work, Christina. Loved the note about the cluster of female bloggers talking about work climate, and dearly hope you follow it up. - D0r0th34
What is the best place to link to your post and slideshow on the SO'09 wiki? Your session is not about blogs, really, but there are a couple that are - one about networks, for instance. People should see this before coming to the conference. - Bora Zivkovic
Did you find any graph theoretic cliques? - Andrew Lang
@Andrew - tons of cliques (maximal complete subgraph of 3 or more nodes), tried also LS sets, Lambda sets, k-cores..... many of the standard cohesive subgroups in Wasserman and Faust - there too many so not informative. Unlike the typical sparse network, this network is a hairball. - Christina Pikas
@D0r0th34 - I'd love to, even had sketched it out as a diss idea, but *really* want to stay away from gender and all that, and it's a slippery slope. @Bora - not sure where to link it from, maybe start a generic page on what we know about science blogs? - Christina Pikas
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1 hour ago - scienceblogs.com - Link
2 hours ago - scienceblogs.com - Link
a linkfest of responses by some medbloggers, sciencebloggers and political bloggers - Bora Zivkovic
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“Thinking about a trip to Europe in May. So many options. Make your case here :)”
23 hours ago - Link
Where have you been in Europe already? - Chris Lasher
Up-and-coming parts of Eastern Europe (Latvia, for example) may be surprising and enlightening in a changing world - Joe Davison
Me, too. Last year: London, Cambridge, Trieste, Belgrade, Berlin. This year I hope for a repeat of Belgrade plus some other places if I can, e.g., Stockholm, Amsterdam, Barcelona....any meeting there where I can get invited? ;-) - Bora Zivkovic
Stockholm and Berlin (let me know if you come to Berlin). - Björn Brembs
I've always wanted to do the Dalmatian coast and the Adriatic. And Spain. - Chris Cotsapas
Chris, on business extensively to the UK, France (mostly Paris), Switzerland (mostly Basel), Germany, Holland, Belgium, Spain (Madrid), Italy (Milan, Trieste, Venice) and I am sure I am missing some. With my wife, Vienna is the only place we've spent enough time. I've been to France and the UK for non-work a few times - Deepak
Just to clarify, this is for a weeks vacation :) - Deepak
several friends have been to Croatia recently and raved. Pictures were amazing... - Andrew Su
How about Norway? - Amund Tveit
Have not been to Norway. Should add that I've been to Denmark and Sweden as well - Deepak
Barcelona, Spain is worth looking. - Pierre
Pierre, Barcelona is definitely on the short list - Deepak
Cities: Praha, Firenze, Roma, Lisboa, Istanbul - Alain Pierrot
Deepak - put it this way. Where else in the world can you stand on a 2000 year old pavement in a building which is pretty much still standing except Bath...on the other hand England in May...bleark! - Cameron Neylon
From the list of places which you haven't yet visited, I put another vote on Barcelona. - Pawel Szczesny
if it is late May you can go midnight golfing in Trondheim, Norway :) - Amund Tveit
Cameron, Exactly. I have been to England too often in May :) - Deepak
berlin, poland (eg warsaw, krakow) - laura
Barcelona is excellent, Amsterdam isn't half as good as it was and depending on your taste Brugge is a popular destination. - Toby Graham
I would suggest Berlin, Poland and Tallinn, Estonia. Helsinki is just ferry ride away as well - Zaki Manian
Stockholm, London and Paris - Christopher Harris
City-vacation: definitely Barcelona (or Amsterdam, but for entirely different reasons) Hiking, outdoors and nature-scenery: - come visit Norway as Amund says - we've got fjords, mountains and lots and lots of isolated strange local people. - Nils Reinton
Living here most of my life, I wonder what people find appealing in Poland ;). - Pawel Szczesny
Polish girls - Leather Donut
city vacation? countryside vacation? - Richard Akerman
+1 for Norway! Studied there for a while - absolutely amazing country. Love the coast and the fjords... - Victor / Mendeley Team
+1 for Norway, and you could add Sweden and Denmark too. One option is the Öresund, Copenhagen Malmö, Lund, Roskilde, Helsingor (=Hamlet's castle), Gothenberg etc. They're all fairly close, so travel isn't difficult. - Bob O'Hara
Oh, and the Tallinn/Helsinki idea (include Tartu too!) is good. I live in Helsinki, so I might be biased. - Bob O'Hara
Do let me know if you come by Copenhagen! :) - Lars Juhl Jensen
Amsterdam. I have a google map of some of my favorite places can't link to it now from phone, but will later when I get back to pdx - Maureen
if ever you set foot in France, let me know: Paris, Bordeaux, Lyon... - Alain Pierrot
Stockholm/Uppsala... love to talk with you about ODOSOS drug discovery... - Egon Willighagen
I love Lisbon and Portugal. - Sarah
Deepak, you should just make a Tour de FriendFeed: European Edition. - Chris Lasher
Sorry, can't help, busy working - David Dobbs
Good point Chris :) Deepak, feel invited to Poland, if you plan to make the Tour de FriendFeed. - Pawel Szczesny
@Chris: Excellent ! :-) Deepak, I can be your guide in the garden of Versailles :-) - Pierre
You're always welcome to visit Hungary. I'm ready to be your guide. :) - Berci Mesko
lol ... that would be fun wouldn't it. I shall present options to the boss and see what she has to say. I miss my 10-15 weeks a year in Europe (from a few years ago) - Deepak
The list above from Alain Pierrot has most of my favorites but I would substitute Lisbon with Porto (Oporto) and add Berlin. If you do go to Portugal tell me in advance and I can give you some tips. - Pedro Beltrao
@Deepak re: england in May - to be fair the last few years summer has been the first two weeks of May... - Cameron Neylon
But seriously if there is a work angle on this and you want to hook up some talks or visits then drop me a line (or hassle me at Science Online). - Cameron Neylon
Growing up in Yugoslavia, I spent every summer on the Croatian coast, so for me that is "the norm", but spatially and temporally removed now I agree that it is stunningly beautiful, especially the islands. - Bora Zivkovic
Having spent 5 days in Italy, specifically Sorrento and Capri, as well as Rome, just this last spring, I would love to return there. So much to see, so much good food and people. - Bob M. Montgomery via twhirl
At last someone said Italy! Venice, Rome, Sorrento, Florence, Padua, Sienna - all more wonderful than anywhere? I have never been to Bali or Vigata (Sicily) where Gianrico Carofiglio and Andrea Camilleri, respectively, set their books, but I would love to visit them. - Maxine
Go to the non-Paris part of France! Auvergne! Midi! Provence! May is just before the annual influx of loud Dutch and British tourists take over the areas. - Eva
If I'm still in the country by then, you should definitely come by Lisbon, Portugal. Otherwise I may just as well need a tour of Seattle if I'm near by :) - Ricardo Vidal
Eva ... lol. One reason for going in May, although looks like I might be in Europe for conferences in March ... hmmm - Deepak
Ricardo, if you make it here, just holler - Deepak
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1 hour ago - the-scientist.com - Link
A shortage of donated brain tissue is hampering research into diseases such as Alzheimer's, Parkinson's, and dementia, a team of British scientists warned yesterday (Jan. 6). About 10,000 brains are used for scientific research in the UK. But researchers say that they need thousands more fresh organs from donors with both diseased and healthy brains. There are currently only 20 brains to study autism and 30 brains to research Alzheimer's in the country. "There's a great opportunity to facilitate important research to discover cures and treatments which would go unfulfilled if we don't increase the number of brains available for research," said Paul Francis, a neurochemist at King's College London, at a press conference in London. - Alexey via Bookmarklet
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“Oznur Tastan: Prediction of interactions between HIV-1 and human proteins using information integration”
3 hours ago - Link
current HIV therapies not optimal bc not accessible to all people, cannot eradicate from body, and drug resistance. - Shirley Wu
Target the biology of HIV, which requires use of host cell machinery - need to predict novel direct physical interactions between HIV-1 and human proteins. - Shirley Wu
Dyer et al Bioinformatics 2007, Davis et al Protein Science, Konig et al Cell 2008 previous work. But no study doing global analysis - Shirley Wu
Supervised learning. Dah, that slide went by too fast. HIV-1 and human protein pairs represented with set of features - Shirley Wu
Use decision trees, random forest classifier with majority vote out of possible trees - Shirley Wu
Training and test data taken from keyword search of proteins and relationship terms. Differentiated between direct relationships ("binds to", "acetylates" etc) and indirect ("regulates", "affects") - Shirley Wu
35 features including expression data, PPI data, sequence motifs, etc - Shirley Wu
motif example: does human protein contain ligand domain or belong to ligand protein class? does HIV protein contain binding signature? - Shirley Wu
Also use similarity of HIV-1 protein to human protein's interaction partner - sequence, cellular localization, post-translational modifications, etc - Shirley Wu
evaluation: AUC 0.92 and Mean Avg Precision 0.23. - Shirley Wu
Results recapitulate observation that pathogens tend to interact with host proteins with high degrees of connectivity to other proteins - Shirley Wu
Resulting predictions: Tat interacts with Pin-1? - Shirley Wu
I'd be a bit surprised if that were true, since a quick look at Tat sequences in GenBank indicates that it contains only one consensus Pin-1 recognition motif (ser/thr-pro), and the thr at that position is not well conserved (it's not, for instance, present in the refseq). - Bill Hooker
Also, Tat is one of those miserable proteins (small, charged, ?globular) that will *interact* with pretty much anything. Whether the interaction means anything is another matter. The NCBI Gene entry for HIV-1 Tat lists well over a thousand protein-Tat interactions... - Bill Hooker
I didn't really catch it hence the question mark. It was definitely Tat interacts with something, which doesn't really help - Shirley Wu
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December 31 at 12:36 pm - i117.photobucket.com - Link
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2 hours ago - nytimes.com - Link
"“R is a real demonstration of the power of collaboration, and I don’t think you could construct something like this any other way,” Mr. Ihaka said. “We could have chosen to be commercial, and we would have sold five copies of the software.”" - Ricardo Vidal via Bookmarklet
Open Source / Free Software FTW! - Michael R. Bernstein
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2 hours ago - blogs.usyd.edu.au - Link
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2 hours ago - network.nature.com - Link
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2 hours ago - hcrenewal.blogspot.com - Link
Is the field of bioinformatics in trouble? I ask this due to two disturbing trends. The first is the misuse of bioinformatics for "dubious" purposes. The second is, has bioinformatics itself reached a wall of stagnation due in part to disciplinary insularity and resultant inadequate collaboration with its medical counterpart? - Paulo Nuin
In "A Professor and an Anti-Aging Tonic", Roy Poses commented on an academic who misused bioinformatics to violate the trust of patients and also violated their trust by getting entangled with commercial interests, in this case with what seems a magic potions operation. - Paulo Nuin
Bioinformatics appears to receive more media attention and offer more status, career opportunities, and compensation than the less-prestigious medical informatics. - Paulo Nuin
This is exactly the issue I raised in my Merck letter. I fear in the field of Bioinformatics, this occurs frequently, and in fact billions of investor dollars are going down the drain in the pursuit of cybernetic in-silico miracles as a result. - Paulo Nuin
Pure gold!!!!! - Paulo Nuin
quoting the title from a recent paper from Lincoln D Stein:"Bioinformatics: alive and kicking" http://genomebiology.com/2008/... - Pedro Beltrao
See also Shirley's notes on the currently going panel session at PSB on this http://friendfeed.com/e/1d7391... - Cameron Neylon
Stein's paper was commented here http://friendfeed.com/e/53b9cc... - Paulo Nuin
That blog post is all over the place - a lot of incoherent ranting, I don't see the main message. - Neil Saunders
I had to read three times to understand it. Found it on Reddit programming and it has 10 votes there. - Paulo Nuin
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4 hours ago - scienceblogs.com - Link
cloning of a bull; super-fast fungal spores; fast repopulation from oceanic reserves; pain is easier to bear when paired up. - Bora Zivkovic
Great summary! Reads like a tweet. - Neil Saunders
LOL! Perhaps that's how press releases should be written - on twitter - Bora Zivkovic
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“We are the best Sneetches on the Beaches!”
3 hours ago - Link
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