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Rajarshi Guha › Likes

Graham Steel
Message in a (Digital) Bottle http://www.science3point0.com/mcblawg... Some #S3.0 thoughts ahead of #scio12
Michael Kuhn
Prediction of drug combinations by integrating molecular and pharmacological data. - http://www.ncbi.nlm.nih.gov/entrez...
Cameron Neylon
The stupidity of SOPA in Scholarly Publishing - http://cameronneylon.net/blog...
It was Michael Kuhn who pointed out to me over the holiday break that both Elsevier and Macmillan (parent company of Nature Publishing Group) were listed as supporters of the Stop Online Piracy Act. If you don't know about SOPA and why it is one of the most politically and legislatively incompetent actions of ... - Cameron Neylon
We should start collecting such instances right away - if SOPA comes, we'll take down all these sites and post the papers that we've secretly downloaded before in our libraries :-) - Björn Brembs
I am a bad, bad person. Trolling the big pigs for SOPA violations seems like an awful lot of fun. - RepoRat
This is why we need to be able to "like" comments, RepoRat, - Mr. Gunn
note, Macmillan US and Macmillan Ltd (our and NPG's parent company) are separate companies ... Macmillan US being the one listed, if I'm reading correctly ... - Kaitlin Thaney
I don't mean to poke you in the eye about this, Kaitlin. I think you're one of the good ones, but if Nintendo can reverse their support, so can Macmillan (US). I think people understand that SOPA is a US law, too, even though it would have widespread effects. - Mr. Gunn
Completely understand :) Just clarifying that this is not our parent company, nor Nature's. Still doesn't make it right, but just to make sure the 2 aren't conflated (common mistake often made). - Kaitlin Thaney
If you look at the publishers "supporting" SOPA through the Association of American Publishers it gets even more insane, a whole bunch of university presses and smaller societies that could be at real risk from this. http://publishers.org/members... I can't help but feel that a bunch of members telling the AAP to withdraw would be a good thing. - Cameron Neylon
Abhishek Tiwari
Woo! R on JVM 60% complete, contributions wanted http://t.co/mTh4ftyy
Egon Willighagen
I have created a G+ Page for the CDK... - https://plus.google.com/1041867...
I have created a G+ Page for the CDK... Chemistry Development Kit - Egon Willighagen
Michael Kuhn
RT @rands: Captivating account of what happens when smart and well trained people panic: http://t.co/nRJloOVF
Noel O'Boyle
peter murray-rust
Textmining: NaCTeM and Elsevier team up; I am worried - http://blogs.ch.cam.ac.uk/pmr...
Egon Willighagen
I use something similar to record/plot temperatures in one minute increments on the server in my garage. Want to make sure I know in advance when it wants to catch fire! - Orion Jankowski
Euan
The Sugru story is pretty amazing http://t.co/mhIMWaWM
+1 for taking names from Irish ;-) - Noel O'Boyle
Abhishek Tiwari
How Pursuit of Profits Kills Innovation and the U.S. Economy - http://t.co/Aq8nwgw0
Abhishek Tiwari
RT @noahi: All of the Excel defaults are wrong. Here's one way to make graphs look better. http://t.co/bI8FJqWQ
Noel O'Boyle
Displaying pharmacophores from Pharao in Avogadro - http://baoilleach.blogspot.com/2011...
Displaying pharmacophores from Pharao in Avogadro
Amira
"Twitter is a linguist's dream come true: it compiles millions of messages in hundreds of languages daily, making the question "Who speaks what languages where?" easy to answer. That is the question taken up by self-described "map geek" Eric Fischer. He has created a map of the world's languages used on Twitter by pulling together data collected by Google Chrome. (...) It’s as if someone took one of those composite satellite maps -- you know, impossibly showing the whole world at night, the darkness broken by hubs and strings of artificial light ... and gave it the power of speech." - Amira from Bookmarklet
this is super ! here's the huge 4.2MB map directly for high resolution: http://farm7.static.flickr.com/6050... (check the legend carefully else you may think the entire country of Japan tweets in French :-) - Adriano
oh wow :-) - Maitani
Interesting. - Son of Groucho
here's a close-up of Europe, http://i.imgur.com/XfugE... -- centered on the French / German border: language != geography. - Adriano
great, Adriano :-) - Maitani
In close-up it looks like another amazing network https://lh5.googleusercontent.com/-vBVC0d... :-) Thanks Adriano! - Amira
to clarify how languages are networked, see directed graph http://1.bp.blogspot.com/-icTwf3... -- which sheds light on where the color coding overlap on the tweets map. - Adriano
Thanks! - Amira
Björn Brembs
Egon Willighagen
improved the CDK fingerprint by changing the hashing approach → http://chembioinfo.com/2011...
That's interesting, isn't it. OB has a simple hash function also, so it looks like there is room for improvement. - Noel O'Boyle
Noel O'Boyle
Egon Willighagen
CDK 1.4.5: the changes, the authors, and the reviewers - http://chem-bla-ics.blogspot.com/
pn
pn
Open Access means people die - http://www.pawelszczesny.org/2011...
Central thesis: "open access means that there will be more potentially harmful papers available to general public". We should get rid of the internet too, perhaps? - Noel O'Boyle
Noel, that's not central thesis. That's example of reasoning to which Peter's approach leads. - Pawel Szczesny from iPhone
Pawel, I agree with your point, but I disagree with your example... allowing people to make mistakes I value more than believing you know better and disallow things... your argument is like disallowing freedoms because some cannot handle them... that makes your argument quite different from those of PMR, even though both anecdotal of shape... - Egon Willighagen
Egon, I get the difference very well and that example was chosen on purpose (I had some less "nuanced" as well, but didn't decide to use them). However, if a scientist is using unscientific arguments, the remaining nuances don't make a difference anymore. How we can improve the quality of public discourse if we allow for such argumentation? - Pawel Szczesny
Well, theoretical sciences I guess :) PMR formulated a hypothesis, that is worthy of empirical validation... which effect is larger: that of foolish people, of that of people kept uninformed... (I don't know; I'm not a social scientist...) Where would science be if we cannot hypothesize anymore.... You provided an important alternative hypothesis... null hypothesis, perhaps? - Egon Willighagen
Ok - I get you now. Central thesis: "Anecdotal evidence is irrelevant to a scientific argument." And other things besides OA can help more. - Noel O'Boyle
Egon, the problem I see is that PMR's own words: "I don’t think anyone can deny the truth of that conclusion." are not a formulation of hypothesis, but a populist language. This unfortunately has many implications, none of which I like. - Pawel Szczesny
I agree that PMR's blog posts are often short on links to further detail. I personally prefer linking in my blog to further info to back up my story and improve the 'learnability'... I personally think 'learnability' is the more important aspect, and Open is the means. PMR is an established Cambridge scholar... they can do with bold language, leaving things to be worked out by others.... more... - Egon Willighagen
Egon, you've touched a few very important issues. One thing is that if you don't have a leverage, you use the leverage of the community of which you're a member. So, PMR comments might influence position of people relying on the community in certain situation where trust in a discussion depends on the community's 'brand'. The other thing is that from perspective of people in less... more... - Pawel Szczesny
And finally, the biggest win of OA will be when the general public actually cares about open access to knowledge, not when scholarly communication will be open and still nobody cares. That will translate to _rational_ public discourse, because fact checking and hypothesis testing will be a normal mode of coming to conclusions on public issues. Indeed, there's a place for anecdotal evidence, but they serve as a starting points of coming to conclusions, not end points. - Pawel Szczesny
Noel O'Boyle
Noel O'Boyle
S. Lott: VMware, VIX and PyVIX2 - http://slott-softwarearchitect...
Control VMWare using Python - Noel O'Boyle
Egon Willighagen
Noel O'Boyle
Abstract | Open Data, Open Source and Open Standards in chemistry: The Blue Obelisk five years on - http://www.jcheminf.com/content...
...the new Blue Obelisk paper - Noel O'Boyle
Wondering who will take the opportunity to comment... I expect some people to disagree at points... - Egon Willighagen
Such as? - Rajarshi Guha
PMR is nearly an author of every paper on the front page. He missed one - slacker. - Andrew Lang
Already (i.e. Monday morning) in top 10 most accessed articles in last 30 days. How's that? I'm only writing the blog post now. (Hmmm...could be the nice graphic - most of the other articles didn't provide one) - Noel O'Boyle
It's those dratted tweeters again!! (Rajarshi, Egon, Tony) - Noel O'Boyle
Yeah, don't underestimate the power of graphics :) But will some deliberate asynch blogging, it will soon reach the first position... - Egon Willighagen
Hah! I will use my secret powers to get mine to the top of the list...or....not.... :-) - Cameron Neylon
Quick - stop him! - Noel O'Boyle
Dr Nylon is using his secret #electron powers again - we are DOOMED..... - Graham Steel
John Wilbanks now p0wning OB/BO paper. Should be a separate list for rock stars :-) (http://www.jcheminf.com/article...) - Noel O'Boyle
Amira
"What I'm about to tell you is gonna change your life forever. Are you really sure you want to know it?"
the truth.jpg
:) - Winckel
Jim Henson is amused. - Xabaras (G.O.)
Geoffrey Hutchison
by Lemony Snicket | OccupyWriters.com - http://occupywriters.com/by-lemo...
Thirteen Observations made by Lemony Snicket while watching Occupy Wall Street from a Discreet Distance - Geoffrey Hutchison
Blue Obelisk
Similarity-Potency Trees (Depth-First) - http://depth-first.com/article...
A colleague has just sent you a 500-record SD File containing structure-activity relationships (SAR) that youve never seen before. What are the first steps you take to begin to make sense of it?The approach a medicinal chemist would take might involve:opening...
Apparently uses the CDK... - Egon Willighagen
Good for smaller SAR analysis. Doesn't scale that well for larger collections due to the need for a pairwise similarity calculation. Could be speeded up by using approximate NN though - Rajarshi Guha
Egon Willighagen
The Blue Obelisk Shoulders for Translational Cheminformatics - http://chem-bla-ics.blogspot.com/
The Blue Obelisk Shoulders for Translational Cheminformatics
Egon Willighagen
not using an independent test set and using Q^2 for model selection in QSAR is just institutionalized cherry-picking #fail
peter murray-rust
Animal Garden: An allegory on scholarly publishing and walled gardens - http://blogs.ch.cam.ac.uk/pmr...
Bloody genius OA 'comic strip' sketch !!!!!!!!! http://dl.dropbox.com/u... - Graham Steel
Awesome!! - Björn Brembs
Amira
"I'm sorry, but we can't send a search and rescue team into Plato's cave..." http://xkcd.com/876/
Plato's cave.jpg
Deep. - SteVe C
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