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Khader Shameer › Likes
For the Love of Science - http://www.sciencemag.org/cgi...
Khader Shameer and Richard Badge liked this
Which is a better predictor of a student's continued participation in science, facile understanding or personal interest? Hulleman and Harackiewicz (p. 1410) designed an experiment to find out what drives high-school students. First-year high-school students were asked either to write about what they had just learned or about how what they had just learned connected to some facet of their personal lives. Connections of personal relevance were stronger than good grades for predicting interest in further science courses and future science careers. This low-cost intervention seemed to have its largest effect on students who began the class with the least amount of confidence in their abilities.
- Kohl S Gill
from Bookmarklet
Hmm - seems from my own experience that making science personally relevant is a big motivator - mum was a medical lab technician, always enthused about power of diagnostic tests to really help people (this was in the days when the technician took the sample, did the test and delivered the results!)
- Richard Badge
from Nambu
Same here. I think it serves as a constant, daily reminder about science, and it can't help but pique one's interest. On 29 Dec 2009, at 1:38 AM, Richard Badge wrote:
- Kohl S Gill
from email
If anyone at Google is looking for something to open source, the core machine learning infrastructure (like Seti) would be very good for the world.
Meryn Stol, Federico Bolsoman, Mac Sharp and 51 other people liked this
I agree, SETI would be great. But whoa, it would be a huge amount of work to open-source it.
- Daniel Dulitz
Search for Extra-Terrestrial Intelligence?
- Gabe
Har har.... I assume there is ZERO chance of this ever happening.
- Jay
@Jay - I suspect Paul wouldn't ask if he thought there was zero chance. Last time I remember Paul asking for something from Google to be open sourced it was their JS compiler. That took a while, but http://code.google.com/closure...
- Nick Lothian
@Jay: Remember that Paul's referring to (relatively) generic infrastructure here, not search ranking code. But I think Daniel's right that it would be a *lot* of work, since most Google infrastructure is not "productized" and easy to wrap up in a bow for public release. Like any company with a lot of infrastructure, there are a lot of interdependencies that would be difficult to untangle. I think it would probably be better to simply publish papers on how it works, as with GFS, BigTable, etc.
- Joel Webber
Boy, that would be a bold move Paul. Agreed that it would help out many though!
- manielse (Mark Nielsen)
How about just dumping the source to the web without all the dependencies, even if it doesn't even compile? If it looks useful enough there's a good chance someone would adopt it.
- Jim Norris
I suspect you're right about that, Jim. But Google would probably catch more crap about a "throwing it over the wall and letting it stagnate" open-sourcing than it's worth. But maybe I'm just down on it because Google catches crap no matter what these days...
- Joel Webber
It's hard to open source distributed algorithms -- there's no obvious public standard to use, and the reasonable choices (TCP sockets? MPI?) are nothing like Google's internal infrastructure. I think a paper would be more useful than source code, the way MapReduce papers lead to Hadoop. Paul, have you looked at Vowpal Wabbit (http://hunch.net/~vw/)? It has experimental support for cluster parallelism, and I hear good things about it.
- ⓞnor
Well, it doesn't have to be an either/or issue.
- Jim Norris
If the code is too hard to separate from the infrastructure, then maybe a compute service like EC2 that provides an application interface specifically for solving problems with SETI could be good for both the world and good for the Google.
- Bill Strathearn
@Bill: Now *that* sounds like a good idea to me, especially if accompanied by a paper describing the algorithms in use.
- Joel Webber
Although technically really interesting and usefully, I do think that Google will not open source or even give inside information about such a key differentiating technology in the hands of their competitors. But I agree that it would be really great for the world.
- yusuf arslan
I saw mention of JS open sourcing, did you folks see CoffeeScript yet? great stuff from Jashkenas, http://jashkenas.github.com/coffee-...
- Mark Essel
The value of "differentiating technology" is not in novel algorithms, but in the thousands of places where implementations of these algorithms have been fixed and customized and tuned to solve the problem at hand -- which wouldn't have to be described in a whitepaper.
- Tudor Bosman
@Tudor Bosman: I do not agree that the competitive advantage is the knowledge of fine tuning and implementing the algorithms. The concept/design of Google's machine learning infrastructure is very important. Don't get me wrong, I do think that Google SHOULD open source this. But I think they WILL not because of business considerations.
- yusuf arslan
btw, ML+AI papers by Google - http://research.google.com/pubs... - http://research.google.com/pubs...
- Amund Tveit
I think even just a paper would be very useful and fruitful.
- Ruchira S. Datta
Ruchira, do you have particular biological datasets in mind? Are they too large even for a single machine version of Vowpal Wabbit to comfortably cope with (say, several tens or hundreds of billions of labeled instances)?
- Simon
Simon, my comment was just general. Now that you mention it, I could use Vowpal Wabbit on some of my projects, which are not anywhere close to that big. Thanks for the tip!
- Ruchira S. Datta
"The need for opensource in machine learning" http://jmlr.csail.mit.edu/papers... (author affiliations of relevance)
- Amund Tveit
Nature Methods supplement: Next-generation sequencing data analysis - http://www.nature.com/nmeth...
Justin H. Johnson, Nakao M., Khader Shameer and 2 other people liked this
Fwd: Should you be tweeting? - http://www.hubmed.org/display... (via http://friendfeed.com/ff-for-...)
Sandeep Gautam, rowlikeagirl, Kubke and 19 other people liked this
No mention of friendfeed, so what about writing a correspondence piece on this? It could be based on http://ff4s-paper.wikidot.com/start and perhaps also put the recent NIH grant for a "Facebook for Scientists" ( http://ff.im/beKk7 ) in perspective by providing an overview over existing tools along these lines and why they are not widely used.
- Daniel Mietchen
http://www.cell.com/authors... / Correspondence: "The Correspondence format provides our readers with the opportunity to respond to an article in Cell—either a research article or Leading Edge article—that has been published within the last 2 months. Correspondence should be no more than 900 words in length with up to five references and should be of interest to the broad...
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- Daniel Mietchen
Now that sounds like a good idea! I'm all for it - especially mention the gazillion "facbook for scientists" already out there.
- Björn Brembs
I gave it a start at http://etherpad.com/Microbl... - feel free to join in!
- Daniel Mietchen
Added some stuff...
- Björn Brembs
333 words so far, and once the generic FF description and some highlights from the spreadsheet are in, we will be near the limit. So probably no time to dwell on fb4sci, though I would still like to mention the NIH grant in the hope that those people will build on the ideas we lay out.
- Daniel Mietchen
Maybe steer away from a "but we want to talk about friendfeed" towards more "there is a much richer set of tools out there...and here is a good example..."? Might mean the Fb4Sci stuff can get squeezed in?
- Cameron Neylon
I would actually prefer the Fb4Sci stuff in there, and the article would be more balanced if we were to name a few more services that offer microblogging (I listed some in the Organization part of the document). FF can then be described in two sentences as a particularly useful example because it provides hierarchies of threaded conversations in which the most current and the most popular entries compete for the top of attention.
- Daniel Mietchen
Correspondence has to be submitted within two months, so we got four weeks to go if we are to submit something on the matter. Perhaps we can indeed expand this into a general overview on the potential of web 2.0 stuff for science. To this end, I just started a vote on the "open science breakthrough of the year" at http://ff.im/cidKG .
- Daniel Mietchen
thanks guys - a very interesting read (the paper, these responses, the etherpad document). I've added a couple of possibly-relevant points to the etherpad doc. :)
- Allyson Lister
...bumping to remind me to try and do something about this before deadline...
- Cameron Neylon
To those coordinating this: let me know if you need any extra help with anything...
- Allyson Lister
Allyson, help with shortening the FF part and with adding in something on the non-FF alternatives would certainly do something good to push things forward at this stage. Thanks!
- Daniel Mietchen
Edited a bit and tried to merge the new contributions into the draft. The word count for the FF part now stands at ~570 excluding FF real science examples. I still don't see how we can give an overview of more than one of these services and accomplish anything better than a boring enumeration without spirit. On the contrary, people will just get the impression that scientists can't make...
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- Björn Brembs
Correction: 660 words... :-)
- Björn Brembs
See also Jean-Claude's stylesheet about FriendFeed + Science ? FFscience: https://spreadsheets.google.com/ccc...
- Pierre Lindenbaum
Thanks, Pierre, was already mentioned. Just added some examples from this spreadsheet. Word count is now at 760. Tasks remaining (if you agree on the general structure): polishing and final, concluding paragraph. Tasks remaining if you don't agree: re-write :-)
- Björn Brembs
have removed a few words, tightened things up. will do more as time permits
- Allyson Lister
Getting there ... >800 words.
- Björn Brembs
953, so some trimming needed. Mentioned the NIH grant in the roundup section. Which references to take?
- Daniel Mietchen
Good job, Daniel! I think the references are fairly clear, most of them are in the text already (i.e., papers from FF). We have until December 30 to get it all finalized, so we have some time, but I'd rather get it there sooner than later. I think a few more runs of polishing and honing and we should get the final author list together and submit. I suggest everybody who wants to be an author leave the URL to their FFfeed at the end, that way readers get an idea of what FF looks like.
- Björn Brembs
What about signing with a group pseudonym (something like D H J Polymath; http://arxiv.org/find... ) and a link to this thread or the etherpad?
- Daniel Mietchen
I have inquired with them whether links count as references.
- Daniel Mietchen
@Daniel as a pseudonym, I suggest to use what Deepak calls the "BioGang" http://openwetware.org/wiki... http://www.linkedin.com/groups...
- Pierre Lindenbaum
What about the title? "Should you be sharing science online?" would be my favourite but it is not reflective of the current emphasis. Any suggestions?
- Daniel Mietchen
Pierre - good one. Perhaps add FF as initials?
- Daniel Mietchen
BTW, the doi does not resolve - anybody has the correct one?
- Björn Brembs
895 words...
- Björn Brembs
I like Clay's idea for a title: "It's not information overflow, it's filter failure " :)
- Allyson Lister
884 words, and a few more slight tweaks. This means we could probably fit an entire sentence about other approaches' existence, if we wanted :)
- Allyson Lister
Björn - http://dx.doi.org/10... .
- Daniel Mietchen
@Allyson: awesome! @daniel, sorry, meant this one: http://dx.doi.org/10...)
- Björn Brembs
Added ref 4: the NAR paper ( http://tinyurl.com/mr5kvm )
- Pierre Lindenbaum
Right now this sentence is a mixture of DOIs & links: which to use? : "Such conference coverage has even received direct (e.g. ISMB09 http://www.iscb.org/ismbecc..., BioSysBio09 http://dx.doi.org/10...) or indirect (e.g. ISMB08) support from the conference organizers, see e.g. http://friendfeed.com/ismbecc... ." We can convert them all to links, & save some of the 5 publications, but all three examples here have papers associated with them (well, ISMB09 paper is accepted)
- Allyson Lister
Ah - actually it looks like the ref we would use for ISMB08 is actually ref 1 - am I correct? There isn't much detail in ref 1 yet. That could solve part of the problem
- Allyson Lister
I'd also like to find that out, but the DOI does not resolve (for me?). Haven't looked at ref1 yet, to determine if it's redundant.
- Björn Brembs
The DOI, if intact, should point to http://genomebiology.com/2009... , which is behind the paywall for me but perhaps Allyson can give us a hint ;-)
- Daniel Mietchen
Sorry - yes, @Daniel, the DOI seems broken, but the genomebiology link is the correct one. If we're limited for references, we could just link to the FF room, which is http://friendfeed.com/biosysb...
- Allyson Lister
We have 5 references and thus I added Allyson's to make it 5 :-)
- Björn Brembs
Question as to whether its advisable to include reference to the RW room. I think someone raised this somewhere but I can't see the discussion now.
- Cameron Neylon
Otherwise made a few very minor changes
- Cameron Neylon
I'm about adding a ref to O'Reilly/"Beautiful Data". The collaboration for this book started here: http://friendfeed.com/fgibson...
- Pierre Lindenbaum
@Cameron - yep, a few of us have brought up that point (me and michael and some others I think in the etherpad doc). I'm happy to go with whatever the owners of the room, or the general consensus, wants :)
- Allyson Lister
Cameron, do you have a reference for the second grant? I am only aware of http://www.labgrab.com/users... .
- Daniel Mietchen
Added mention of polymath project.
- Daniel Mietchen
Found reference mentioning both grants: http://www.nih.gov/news... .
- Daniel Mietchen
RW room discussion is in the header of the document. IMHO there are several crucial reasons for finally going public: it's a grey area probably still fair use; more subscribers mean more access; readers will see the usefulness of this room, even if they don't get any of the other features; the kinds of hoops we have to jump through to get access need to be made public and the room has a significant record now.
- Björn Brembs
I think we need to drop ref 6 since we only have 5 and it's not a journal article, correct?
- Björn Brembs
With Etherpad deleting everything by March 31, we should think of ways to archive existing pads - particularly relevant for this one, as it was meant to be citable. As far as I can tell, none of the currently available options preserves the version history, so if we want to have that, we should do a screencast.
- Daniel Mietchen
Indeed, we need to think of something!
- Björn Brembs
Incidentally, the threat of such services disappearing certainly contributes to the hesitation of people to adopt social networks, and the best ways I see to cope with that problem is to have either open standards on data portability, or - better still - social networks (or at least one of the most suitable ones) that are built entirely open source platforms, with open configuration (and of course data portability too). Any suggestions on whether and how this could fit into the concluding paragraph?
- Daniel Mietchen
Isn't it already in there, sort of? Where we write that these tools are in development and NIH funded?
- Björn Brembs
from iPhone
Haven't seen mention of open source and open standards in the news on these NIH grants, so it may be worth making more clear that this is needed.
- Daniel Mietchen
Interesting turn: Etherpad will remain operative until at least when they release their source code. http://etherpad.com/ep... .
- Daniel Mietchen
Upon feedback from Graham, I took the RW reference out. Still think some mention of Open Source would be good. http://www.nih.gov/news... does not mention it. 816 words.
- Daniel Mietchen
Can we be part of that feedback, please? I find the RW functionality so convincing for non-social web users that I fear the whole article might be wasted, i.e, preaching to the converted, without this component.
- Björn Brembs
It was in a DM that I just forwarded to you (dunno whether that works), and I asked him to comment here too.
- Daniel Mietchen
Did anyone manage to do a screencast? I could try and do that today if its useful? But maybe better to wait until you feel is finished?
- Cameron Neylon
I think we should wait until it's basically submitted.
- Björn Brembs
@Daniel: DM was blocked (private).
- Björn Brembs
Nothing wrong in testing, otherwise I'd also wait till it's submitted. @Björn - sent you screenshot.
- Daniel Mietchen
I'll comment once I get back form work (only have internet access here during lunch hour).
- Graham Steel
Right. 1) Having consulted with Bill, we have (the same) mixed views vis a vis raising the visibility of the RW room. 2) We don't feel that we "own" the room though, it belongs to everyone who uses it. 3) We agree that a poll should be set up for subscribers of the RW room to vote on the issue of whether or not they feel it appropriate to raise visilbility of the room outwith FF. 4) The poll is http://www.micropoll.com/akira... and I'll post a link to it in the RW room shortly.
- Graham Steel
Apart from inclusion of the RW room, the title has not been decided yet. Two suggestions are in there now (I threw away my older one).
- Daniel Mietchen
Also, what about the "like=bookmark" discussion? I would like to see that paragraph go back in.
- Daniel Mietchen
I thought that like=bookmark was clear from the context? If not, then it should be easy to add a sentence to make it explicit.
- Björn Brembs
Björn - see chat bar - Michael was not comfortable with the notion. Any other opinions? Also turned Shirky quote from title to quote and set the title to "Social filtering of scientific information - a view beyond Twitter".
- Daniel Mietchen
Besides, FF search has now been unusably slow for weeks, so I wonder whether we should take this formerly excellent feature off the draft. See also http://ff.im/cO3Jw .
- Daniel Mietchen
Two weeks left to submit. I plan to do it on Sat (Dec 19) around noon UTC. Still to address: RW room and perhaps ephemerality of non-Open Source services like FF. I think I saw somewhere that FF have released (part of) their source code, or plan to do so. Anyone know details?
- Daniel Mietchen
Added "the permanence of services whose source code is not public" as an unresolved issue. brushing welcome. What about the RW room?
- Daniel Mietchen
Also, authors need to identify themselves in the document, or they will be missed. Academic affiliations and FF feeds, please!
- Björn Brembs
Like the current version a lot! Also the source code permanence point was important! We should get it ready, clear authorship and author order. My suggestion is Daniel in front, me in the back and whoever feels should have a place in the middle, but I'm flexible (or does author order matter here at all?). From Bill's argument, we should leave the reference to the RW room in, but I'm also flexible there. If there are no storms of protest now, let's keep it the way it is.
- Björn Brembs
I did some more brushing - 899 words now without the title (spot landing). As for authoring, I would really like to go for a group pseudonym (as explained above), but the submission process will probably ask for the usual contact information (incl. email) anyway. Order does not matter to me. Will check back in about 36h, with the intention to submit.
- Daniel Mietchen
I was only pointing out that if you mention the RW room at all, you might as well name it. The poll stands at 41 votes (~25% representation, but it seems to me that there aren't many more than 41 really active contributors/users). The tally is No - 56%; Yes - 32%; Unsure - 12%. I don't think the piece loses much by deleting the mention of the RW room, and it seems to me that the users prefer to continue to keep quiet for now.
- Bill Hooker
I tend to agree with Bill. It seems to me that mentioning (and in doing so effectively naming) the RW room is not what users (that cared to vote) want FULL STOP
- Jan Wessnitzer
from iPod
(1) The point of the letter is to attract scientists who are not using social media for their work to FF. As far as I can tell, the one single thing that everybody can profit from that doesn't already exist in mailinglists etc. is the sharing of papers. Moreover, this is also the one single aspect that touches every single reader, as nobody has access to all the literature. So while it...
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- Björn Brembs
(2) This has been mentioned before, but I see no reason why one would have any interest other than supporting closed access, in keeping quiet. The purpose of the room clearly is to 'document', so nobody in his/her right mind would think that their actions remain anonymous. This means that everybody participating must have been well aware that one day this documentation will be...
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- Björn Brembs
(3) I have now voted often enough to skew the results to more than 50% 'yes'. Who can verify that this has not occurred before, on the 'no' side?
- Björn Brembs
Bjoern, I do agree with your arguments. W.r.t. (3), I was merely trying to argue that the vote should be respected (if it were representative). Allowing multiple votes clearly screwed that up beyond repair! ;)
- Jan Wessnitzer
BTW, I voted 'yes' and maybe the only way to do this now is to vote openly here in the Forum!
- Jan Wessnitzer
@Bjoern: "I see no reason why one would have any interest other than supporting closed access, in keeping quiet" -- are you going to pay my legal bills for me, if I get sued? That's a completely serious question. I'm one of the heaviest suppliers of papers in the room -- if anyone is targeted, I certainly will be. I have said many times that I don't think I am doing anything wrong OR...
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- Bill Hooker
@Bjoern, cont'd: I see no reason to think that (before you fucked it up :-) ) the vote was not representative, which means that most of the RW room users were less willing than you to take up arms against their closed-access oppressors. Judge that as you will, my friend, but some of us have limited resources. If even one publisher sends even one cease-and-desist letter to FriendFeed we...
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- Bill Hooker
@Bjoern, cont'd: I fucking HATE that I have to make this calculation. I would rather publish and be damned -- if the publishers do send lawyers, mount an international campaign in defense of the room and its users and bring their shitty empire crashing down around their beancounting ears. But I have my newly acquired all-American cowardice to consider: I have no health insurance and my...
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- Bill Hooker
P.S. I do not really think I can be accused of "supporting closed access"... merely of refusing to fight it to -- not my, but my family's -- last drop of cash...
- Bill Hooker
Bjoern, I will add that any librarians in this room (and I am not the only one) may have a professional interest in keeping mum. We are pathologically helpful folk, so it's hard to resist sending papers -- but we also belong to a profession that looks incredibly askance at even a HINT of copyright-related impropriety. Are you willing to lose me my job over this? Like Bill's, completely serious question. Remember also that my job is intimately OA-related.
- D0r0th34
I cannot sit here and say nothing in light of recent input. I'll be brief simply by saying, 'as Bill and D0r0th34 say(s)'. I too am not willing to put my livelyhood on the line over this (single) issue. All my (OA) eggs in one basket re. this one? I think not.
- Graham Steel
Just a couple of points. (1) I'd assumed that most or all contributors voted in good faith, i.e. once, on this issue. (2) Having read through the draft at etherpad, I think it reads as a good summary of the utility of FF, with or without the mention of RW room (which is only one small paragraph). Is this one aspect really so important, really such a major component of the FF science experience? I think our interactions and discussions are much more important and interesting.
- Neil Saunders
IMHO, the 'no' voters here are blowing the matter way out of proportion. I'll try and put it back into proportion, which may or may not work :-)
- Björn Brembs
@Neil: Good point. I think it may not be all that much of FF for us, but for people not using social media for their work, it may well be *the only* useful thing they can see in this article. That's one of the reasons I'm fighting for it to remain in the letter. I agree, for anybody who is already using this technology, the RW room may only be a minor benefit, compared to the rest of the features.
- Björn Brembs
To all those who "are not willing to put their livelihoods on the line": what part of "document" did you not understand when you signed up? Bill used the right description for this kind of behavior: cowardice. But if you really think our little room of 40 scientists with inadequate access to scientific literature will wake a sleeping giant, I have several additional accurate descriptions.
- Björn Brembs
(1) Delusion. If you really think someone like Elsevier is risking their 800 millions annual profit in tax payer money by going after people who can barely support themselves, you must be deluded. The music industry doesn't have any profits left to lose, but publishers do. They wouldn't be making record profits during the worst financial crisis in 80 years if they really were so stupid to go after us.
- Björn Brembs
(2) Stockholm syndrome. How many salaries and healthcare plans could you pay from 800 million each year from Elsevier alone? Basically, these guys take your salary and your healthcare and then hold you ransom to shut up and keep your head down - and in response you have nothing better to do than to defend that behavior and cozy up with your captors? You must be the only ones who can see any shred of sanity in such behavior.
- Björn Brembs
(3) Hypocrisy. Isn't it hypocritical to oppose a regime on the surface but then support it when real action needs to be taken? Isn't it ironic that a German is arguing for and volunteering to putting your actions where your mouth is and Americans are arguing in favor of personal safety long before any hint of a serious threat is even perceivable?
- Björn Brembs
(4) Paranoia. There is no precedence of any publisher going after individuals. Publishers have much more to lose than we. Thus, the only potential threat is purely in your minds. There isn't even the slightest hint of any hazard for any one of us on the horizon, yet you defend yourselves against imaginary future actions of your oppressors. More than any of the above, this paranoia...
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- Björn Brembs
(5) Documentation. This thread, more than any number of exchanged papers documents how bad corporate publishers are for the scientific community. Their stranglehold on the community stifles freedom and liberty, intimidates all community members to the point that they delude themselves, develop paranoia and act hypocritically. I think this thread documents more than anything else in this...
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- Björn Brembs
(6) Anticipatory obedience. It is a well-known consequence of dictatorships around the world that individuals in these dictatorships support the dictator even if there is no explicit force, merely because they imagine some bad consequence for themselves or their family if they wouldn't support the dictator. In Germany, every child is raised with what the term 'anticipatory obedience' means. We are being taught how it works to stop all potential threats to democracy at the roots.
- Björn Brembs
1) Elsevier has lawyers on retainer, sending a take down letter costs them very little and makes a point - compare to RIAA - how many college students did they take to court? they are actually legally in their right so you would lose without even a trial 4) it's not paranoia if they really are after you. There is a precedence - in the OSTP letters someone complained about ACM going after a Taiwanese grad student
- Christina Pikas
Björn, don't take this for more than the friendly advice that it is: I don't think it will win over many people in a debate (or win you many friends) to accuse those who are not willing to publicly encourage illegal activities of suffering from delusions, Stockholm syndrome, hypocrisy, and paranoia.
- Lars Juhl Jensen
Bjorn, you have lost my respect. I am blocking you and leaving this room. My email is findable if you care to apologize.
- D0r0th34
Re-reading my posts from this morning, it seems indeed I may have over-exaggerated my points a bit too far. It was and still is my purpose to rouse people and ruffle some feathers on a topic which to me is the worst side of my job. In my frustration that even people who I thought were on my side don't dare to leave their comfort zone for something I find so important, I may have gone a...
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- Björn Brembs
Hadn't voted earlier, but vote now for the references to RW to be included in the article. (nice commentary/response BTW) . RW room is one great thing that you guys are doing and should be proud of. People like me who have no access to any scientific literature (that OA or PNAS or some other because of my country of origination (india) ) are able to do science because of that support;...
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- Sandeep Gautam
I am basically offline now and thus postpone submission until Dec 22. Hope to be able to comment in more detail tomorrow night.
- Daniel Mietchen
@Bjoern: I do understand your position, and I cannot disagree with a lot of what you say. But this is my point of view when I step back a little. 1) the number of subscribers to the room cannot claim to represent the sceintific community (they may or may not be representative, but the claim cannot be made based on the numbers). Nor do I think it can claim to represent the scientific...
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- Kubke
@Kubke: Indeed, very measured words. Last night I've also come to the conclusion that apparently, the situation is not bad enough, yet, for people to seriously push for change. It first has to become a lot worse, before it will get better, I totally agree.
- Björn Brembs
I just rephrased the critical section (lines 45-47). further brushing welcome.
- Daniel Mietchen
That letter looks great! Kudos to all of you!
- Kubke
Sorry, won't make it today. Next online time scheduled for 27, just in time.
- Daniel Mietchen
Just submitted. Latest version: http://etherpad.com/ep... .
- Daniel Mietchen
@Daniel - thanks for submitting, and for including me :)
- Allyson Lister
Just caught up on the thread as I was on vacation for the past week or so. I'll just say that although I am not a member of the room in question, I am in agreement with those who did not wish its inclusion.
- Allyson Lister
Median age of NIH grantholders - http://dl.dropbox.com/u...
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Bill Anderson, Mr. Gunn, Rafael Sidi and 13 other people liked this
Stunning graph: the median age has increased by nearly half a year per year for the past 35 years.
- Michael Nielsen
I guess librarianship isn't the only field eating its young.
- D0r0th34
It's a horrible graph. If I hadn't heard other facts consistent with this, I'm not sure I'd even believe it. It does suggest that the NIH granting system is badly broken, at least if creating a new generation of researchers is anywhere on their agenda. It also suggests a great topic for a PhD - figuring out a good explanation for what's going on. I imagine someone with an interest in...
more...
- Michael Nielsen
Incidentally, there is more background here, including links to the original data: http://metamodern.com/2009...
- Michael Nielsen
I would like to see this plotted against tenure-track line numbers in the relevant disciplines. I don't necessarily think it'll be a gluelike correlation because NIH research goes on in industry, but it *might* be.
- D0r0th34
If this trend continues, by 2072 the median age will exceed life expectancy in the U.S....
- Adam Ratner
Similar story in Australia. Head here - http://www.arc.gov.au/ncgp... - scroll down to the ECR (early career researchers) section and weep.
- Neil Saunders
Dislike. :-(
- Ruchira S. Datta
Um. I don't know what I'm talking about of course, but if grantholder's keep their grants for more than a year wouldn't you expect to see some increase? Isn't this graph just showing that grantholders tend to get their grants renewed?
- Nick Lothian
in a healthy ecosystem, young people would be filtering in as older people retired. doesn't seem to be happening.
- D0r0th34
actually, now that I think about it, other things to graph against this are time-to-degree and number/length of postdoc positions
- D0r0th34
I've heard the median age of _1st_ NIH grant is an even steeper curve but have not seen data. and who is to say this isn't a healthy system: just miserable for those who can't get grants (raise hand).
- dubbio
Drexler addresses my issue in a follow up comment in the link that Nielsen posted above. Yes, there is a skew in the age of first granting.
- dubbio
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
Developing effective bioinformatics programming skills - http://mndoci.com/2009...
Khader Shameer and Neil Saunders liked this
Thank you for this voicemail transcription, Google Voice:
"Bitkisel diyet", ElijahBailey-Zu of FF <0,, Khader Shameer and 51 other people liked this
Wow. What was the actual message?
- Michael R. Bernstein
I love Google Voice, but the transcription skills are uh lacking
- Bryan R. Adams
Well, in this case the last three quarters is some kind of busy signal, so it's a trick question :-)
- Casey Muller
Hillarious :-)
- Shahaf Abileah
Yeah their transcriptions are atrocious
- LANjackal
I've found them to be just awful or spot-on. Then again, I've seen the same with Gmail's spam filter. Some accounts are terrific at blocking spam and others are pretty bad.
- Kevin Fox
It's fascinating what comes out of statistical learning when something goes wrong. I just got a transcription that said "Hi. See you later." The audio was just a couple of clicks. But those phrases make sense statistically, if you assume the caller must have said *something*. The good news is that it will most likely get a *lot* better over time, as more training data becomes available.
- Joel Webber
Someone forgot the "!" before the isStopWord(...)
- Manas Tungare
Joel: sounds like a pretty accurate translation to me.
- Jim Norris
Secret lover trying to spit it out
- Will Higgins™
"Please take your name off your phone number, my wife went through my messages. I'm in deep doo doo"
- Bryan R. Adams
lol lol lol lol *BREATHE* lol lol LOL LOL
- Kamilah Gill
Don't forget to donate bad voicemail transcriptions: http://googlevoiceblog.blogspot.com/2009... Given that Google Voice respects your privacy, providing voicemails as training data has to be an opt-in decision.
- Matt Cutts
Life Scientists 2009 summary - http://nsaunders.wordpress.com/2009....
Jason Stajich, Yaroslav Nikolaev, Abhishek Tiwari and 19 other people liked this
This blog post is rather rough and ready - a work in progress - but I wanted to push it out before the holidays. Find out which items from this group in 2009 were most discussed (comments/likes)!
- Neil Saunders
hey, good stuff: especially like the healthy diversity concerning the contributors of most commented/liked entries, do you happen to have a little stat on the most frequent contributors in terms of number of entries, likes, comments or all of them?
- Attila Csordas
It's certainly easy to calculate per user contributions using the API data, but I haven't done it. Might be fun, but I'm more interested in what's discussed than who posts. Feel free to adapt my code!
- Neil Saunders
what's the license for the code, and is there a way to download it other that copy+paste? looks cool, thanks for sharing!
- Mike Chelen
Licence is "it's on my blog, you can copy it and do what you want" :-)
- Neil Saunders
ok cool, that means CC-BY-NC-SA?
- Mike Chelen
It means I don't take licencing of my posts very seriously :-) Although now I look closely at my blog, the relevant icon is top-right, just above the search box.
- Neil Saunders
although NC and SA clauses are a bit restrictive, it is fine for the time being. since the code is useful, giving licensing some consideration may be worthwhile :)
- Mike Chelen
If it were actual code for download, I'd think about it more. When it's text on an open, public web page, I just assume people will do with it what they will. Anything goes, except claiming that you wrote it :-)
- Neil Saunders
copyright law prohibits duplication without your consent, regardless of whether it is on a website or in a repository. while some may break these laws, many of us are committed to working within its boundaries through the use of open-source licenses :)
- Mike Chelen
I'm intrigued that things are so spread out - no one person has more than one entry in the top 10 list...good sign of collaborative effort IMO
- Cameron Neylon
Facebook acquired FriendFeed on August 10. Am I right that there is no significant change in number of posts over the year or after the acquisition?
- Martin Fenner
This is really cool Neil. When I saw readI immediately though if this could be done on a rolling monthly basis this could be the new version of BioBlogs. Maybe some sort of simple Sinatra app.
- Michael Barton
Sample sinatra app on Github and hosted on Heroku :)?
- Deepak Singh
Neil, I agree w/ you: most commented/liked entries are more interesting than the list of most frequent contributors (although that is interesting nevertheless)
- Attila Csordas
I like the idea of automated monthly analysis as a web app! Tricky bit will be fetching only new entries and not missing any, but once a db structure is in place, shouldn't be too hard. I'll give that some serious thought.
- Neil Saunders
Prediction for 2010: FriendFeed is going to see a resurgence.
ravi karandeekar, Adrian, Flavio and 80 other people liked this
What's the rationale?
- Pavan
Really?!
- Michael Liss
I think this prediction's outcome might fall into the hands of Facebook. We'll see what they do with the property this year.
- Andrew Dobrow
Funny that this comes from Twitter. =D
- Junebug (aka Sarah Jill)
ROFL.
- Derrick
So is RSS if we're going to follow Robert's logic.
- Jimminy Fuller
HOW TO SPOT COMMENT BAIT IN 100 EASY STEPS — STEP 1: DID IT COME FROM ROBERT SCOBLE? STEPS 2-100: REPEAT STEP 1.
- Akiva Moskovitz
already happening, yo
- Josh Haley
it started surging (again) after ppl let the knowledge of fb purchase fall into the bits of history pages
- chaz2b
Lets cross our fingers
- polou/indigo_bow
This is SO an experiment on Scoble's part.
- Jeremy (on vacation)
WTF is FriendFeed?
- David Cohn
Rational, Twitter usage is flattening, people are finally figuring out that Twitter sucks for having a conversation. People though Friendfeed was hard to use, try having to install several software 'crutches' to be able to use Twitter productively without even half the functionality as Freindfeed.
- Jeff P. Henderson
if you say so...
- MobilAdam
Either this is tounge in cheek or Robert really hasn't gotten over our breakup... Robert, I hope we can still be friends but we have to move on and grow... FriendFeed will always love you, but we need some 'us' time to find out who 'we' are... *cues The Bodygaurd soundtrack*... *walks out into the rain, adjusts collar, walks off down the road*... *fade to black, credits*
- Johnny Worthington
from iPhone
LOL Johnny!
- Jeff P. Henderson
Best Christmas present ever!
- Jemm
Comment bait. Even Robert can't generate interest these days.
- Russellreno
I agree. Friendfeed is for those who need more from a 2d interface. Until there spatial interface is there, Friendfeed is on top of the pyramid (especially when one knows how to use it best).
- Kirill Bolgarov
Up
- Luca Perugini
from iPhone
*slow-mo head shake*
- Micah Wittman
from iPhone
Too funny! Johnny and Akiva -- you guys crack me up.
- Mathew A. Koeneker
I would agree with a few here and say that FriendFeed is already resurging, Robert. #friendfeed
- Kol Tregaskes
AMEN!
- zʍıɔ
The stats don't agree though: http://thenextweb.com/2009...
- Kol Tregaskes
it's like drunk dialing an ex-girlfriend...
- Aron Michalski
from BuddyFeed
i guess so too..
- Daniele - Viralavatar
so too :)
- ★ Soner Gönül
Agreed wholeheartedly Robert
- Roberto Bonini
Akiva: lol, Kol: that article only looks at unique visitors, and doesn't consider user hours.
- Mike Chelen
:) @ Aron - sums it up perfectly...
- 1x29
Lets hope so ... Miss some of my old peeps :)
- Charlie Anzman
I'm surprised Robert made this statement but I find it very interesting in the change of view and wonder what has changed his mind or if he knows more info.
- manielse (Mark Nielsen)
The unpredictably erratic Scobot is at it again...
- Ciro
Well, after glancing at his Twitter timeline, he's just making a bunch of joke predictions. I'd like to think that there's some truth in this one though...
- manielse (Mark Nielsen)
Sniffs... Do you smell that? It's what we used to call a troll. Robert is getting dangerously close to becoming irrelevent.
- Jason Williams
from iPhone
Robert is waiting until 2010 to respond to this thread. :)
- Louis Gray
I told you so
- Jesse Stay
Kol: the *stat* doesn't agree (note the singular)
- Jesse Stay
Well, since I'm ready organizing the elections for the best Dutch blogs I can say the resurgence already started last week. ;-)
- Ton Zijp
Kol: Here are many more stats that imply the contrary: http://staynalive.com/article...
- Jesse Stay
Excellent idea.
- Richard A.
from FreshFeed
Scoble - I disagree ONLY because I think that FriendFeed activity is already migrating to Facebook via deeper integration over there but I'm wiling to hear you out (as are the other 40+ people commenting here). Do share why you think this is true?
- Aaron Strout
I wrote this tweet for Twitter, not for FriendFeed. But nice to see you all! :-)
- Robert Scoble
Jason: I'm definitely irrelevant if the people calling me irrelevant don't even have 1,000 subscribers. Sigh.
- Robert Scoble
I actually see FriendFeed growing instead of slowing and there will also be new enhancements. A testing ground for Facebook. Just to expand, Robert's still the man!
- amarquart
Akiva wins the internets with this mathematical formula for spotting comment bait.
- Nicholas Kreidberg
You think we're fighting, I think we're finally talking! -all in one page
- Tim Jones
Funny, when I write, I write for everyone, everywhere
- Johnny Worthington
Beat ya to it Robert: http://friendfeed.com/jhuebel... And the resurgence is already happening.
- Jason Huebel
@Jason Williams, wow that's the pot calling the kettle black, doncha think? Robert's not a troll.
- Jason Huebel
@Kol, somebody mentioned that those stats often only consider US visitors (why that would be, I don't know). FF's non-US contingent has grown tremendously, so that graph may not show the whole picture.
- Jason Huebel
Akiva wins the thread.
- Mark Davidson
from BuddyFeed
let's hope so - I love the darn thing
- Arthur Coleman
I'm finding that FriendFeed is fiendishly sticky. On Twitter lists do help, they make twitter better and all but but but-but I think a lot of users are getting more sophisticated in their web usage faster than Twitter can evolve their tech. Louis Grey recently postulated that even if there is no interaction on FriendFeed it makes complete sense to stay riding this horse. That got me...
more...
- JSLeFanu
Dude..... I totally hope you're right, but not too sure about this! LOL Explain your rationale please :)
- Susan Beebe
i agree with the original prediction. by the way, what's a resurgence? is it different than insurgents? :-)
- Morgan Haley
Morgan - the insurgents never left ... ;-p
- Robyn Hawk
Jason, OK. Good. :-)
- Kol Tregaskes
I'll stay one faithful user, for those "outside the US" stats. Still feature plenty, still enjoyable. Still effective. Thanks for rallying the troops again Robert. Bring the hopes, and forget the ropes! 8)
- ElijahBailey-Zu of FF <0,
like Elijah
- maxilprof
I like this whole thread. ++Akiva, Johnny, JSLeFanu, Jason Heubel, Mike Chelen . . . Robert, Twitter may have geeks and famous people, but you can actually do things here. Oh, wait - I'm not here. I'm in a widget on a blog in someone's Posterous whom I don't even know, that I'm searching through to find FF peeps to subscribe to over here. Now, that's just mind-blowing!
- MaryB, BrandingBroadOfFF
Filling in the evolutionary blanks, genome by genome - http://bytesizebio.net/index...
Jason Stajich, Mickey Kosloff, Khader Shameer and 2 other people liked this
The realtime connection from Twitter to FriendFeed is back! (thanks to Twitter's "birddog" api)
Nicholas James, Garin Kilpatrick, (1)Bebekvegebelik and 151 other people liked this
Awesome news!
- Jorge Escobar
Very good!
- Kurt Starnes
Sweetness!
- Alex Scrivener
34 secs flat for my latest tweet. Thanks Paul and team for this!
- Jorge Escobar
wow, that makes actually want to use Twitter. I may just go tweet something.
- Mike Nencetti
It should be even faster than that Jorge, but our systems are getting near their limit. I hope to have it down to 1 sec sometime next month.
- Paul Buchheit
Thank god!
- Miguel Caetano
@Paul, believe me, 34 secs is a charm compared to what we had before!
- Jorge Escobar
Great news!
- Rasmus Lauridsen
Is the birddog api open to all developers, or is it only to you guys?
- Jorge Escobar
Jorge, everyone can access the streaming api, but you need an agreement to follow a large number of ids. See http://apiwiki.twitter.com/Streami...
- Paul Buchheit
Thanks Paul.
- Roberto Bonini
that cool. Thanks Paul
- Peter Dawson
Yay! That's fantastic! I was getting really bored of manually refreshing it every time I tweeted. Especially from my phone. :)
- Jandy, ConcertMaven of FF
Does this mean that Scoble can get smarter on FriendFeed again?
- Crutis
NICE!
- Jason Huebel
Thanks Paul, nice work :)
- LANjackal
wow no posts on the majors yet - usually within mere moments of an announcement we'd have posts.
- Allen Stern
Thank God.
- Ahmet Alp Balkan
cool!
- barbarars
What was the problem?
- Ozkan Altuner
Now....if you could just get rid of the @ replies again. I would be very happy.
- Chris Nixon
relief ! :)
- asli subasi
You are still working on Frienfeed (: how nice !
- Murat Can Demir
whoa, it took less than a minute. i accdently tested it but it's great :) thnx
- asli subasi
awesome, keep it up guys, i knew you would not let us down
- Iggy Mwangi
Great news, love the efforts still put in to FF.I use Google Reader to share into FF (PubSubHubBub) then FF to Twitter (now Real-Time). The URL shortener is great (ff.im), and so FF is central to my social lifestream. I don't care what Scoble says, FF is technically better and feature-rich.
- Keith Rowland
P.S. Conversations are still better here than on GReader, and you just can't have one on Twitter.
- Keith Rowland
You didn't break the FF Facebook app while you were at it, did you? It hasn't worked since.
- Tim Tyler
Oh, awesome!!! 12 seconds :) I can finally go back to Twitter (...okay no I can't I've turned into a Friendfeed junkie..) but prior it took hours upon hours for me to see a feed. Dumb I am, I never suspected a problem LMAO.
- H0llywoodWh0re
Thank you!
- Micah Wittman
Awesome news :)
- guruvan (Rob Nelson)
eyvallah hacı
- Mücahit Yılmaz
Cool. Haven't tried it but yay!
- 'Like' robot (frɐnc)
Yippee! I love real time
- Sandra Large
Paul ?? Twitter updates facebook status and then facebook creates a new feed here on friendfeed. So we have same entries both from twitter and facebook on friendfeed. Could you guys please work on how we can avoid duplicate entries? Thank you. ( If there's already a way to avoid this, pls let me know)
- Murat Can Demir
Cool, thanks, Paul! :-) RT Twitter updates have been missed. :-)
- Kol Tregaskes
And just as I say that, I see my tweets are not coming into FF in real-time. :-(
- Kol Tregaskes
Kol. I just tweeted and it was here before I could get out of Tweetie and launch Safari... It's working :)
- Johnny Worthington
from iPhone
awesome.; thank you a lot..
- Jaap Willem
Nice! Thank U Paul :)
- zʍıɔ
:)
- ★ Soner Gönül
Oh, so nice to have that back again.
- Hutch Carpenter
Johnny, cool. Just me then. It's still slow. Maybe it's FriendFeed then?
- Kol Tregaskes
It truncates retweets, even in the middle of a link...
- Raphael, Raphael
seems that there are only 140chars allowed for a tweet (on FF) and the new twitter retweets are being translated on the way through to old RT @name style - thus are too long.
- guruvan (Rob Nelson)
New figtree is out: FigTree v1.3 is now available for download from the website:
http://tree.bio.ed.ac.uk/softwar...
Khader Shameer and Mike Chelen liked this
The Top 20 Films Of The Decade As Decided By 40,000+ Flickchart Fans | Flickchart: The Blog - http://blog.flickchart.com/index...
 |
Flickchart, Nathan Chase, Khader Shameer and 3 other people liked this
"Since our public launch in September, we’ve grown to well over 40,000 users, and garnered a total of more than 60 million rankings. As we approach the close of the year, and the start of a new decade, we thought we might take a moment to showcase the Top 20 films that our users have deemed to be considered the best-of-the-best from 2000-2009. So without further adieu, here are the best ranked films on Flickchart of the decade:"... - post your comments here to have them appear on the Flickchart: http://friendfeed.com/flickch...
- Kol Tregaskes
from Bookmarklet
LOVE children of men
- Terry O'Fee
The book is great too.
- Kol Tregaskes
Just got my head around the R plyr package (for "reshaping" data). Very, very useful.
Justin H. Johnson, Brad Chapman, Abhishek Tiwari and 2 other people liked this
Bit old but I made a screencast a while ago - http://www.youtube.com/watch...
- Michael Barton
Thanks - you should do more of those screencasts, nice intro.
- Neil Saunders
Thanks also but I don't think they were getting watched very much and each took a fair amount of effort to make.
- Michael Barton
Yeah, these things are a lot of work. Perhaps you can find sponsors and launch "This Week in R" ;-)
- Neil Saunders
Ah ha! Excellent idea :)
- Michael Barton
Build Statistical Graphics Online With ggplot2 - http://flowingdata.com/2009...
Abhishek Tiwari, Khader Shameer and Greg Tyrelle liked this
Far from ready for the prime time, would be nice to see the code.
- Neil Saunders
@Neil I think the ggplot website has some nice examples.
- Michael Barton
It does; I was thinking more of the code behind Jeroen Ooms web application.
- Neil Saunders
Ah sorry, I should have read the article more closely - I see what you were referring too.
- Michael Barton
PLoS Medicine: A New Year's Wish List for Authors, Reviewers, Readers—and Ourselves - http://www.plosmedicine.org/article...
Khader Shameer, Steve Koch and Graham Steel liked this
Ask TLS: is non-access to published literature a problem for those who have reviewed manuscripts? It never occurred to me until I had to review something, wanted to check a few references, and found them behind a pay-wall...
Khader Shameer, Steve Koch, Hope Leman and Cameron Neylon liked this
Is there a precedent for the journal reviewing a manuscript paying for reviewers to access subscription-only articles at other journals, or, heaven forbid, for reviewers to pay for access themselves? Or is it that reviewers check references so rarely that it just isn't an issue? When they do happen to come across one they don't have access to, do they just go "meh" and move on?
- Shirley Wu
Also, I suspect that since many reviewers are well-ensconced in the cozy surroundings of their institutional subscriptions, this occurs much much much less often for them than it would for a reviewer like me, who is not in academia...
- Shirley Wu
Despite my academia-level access, I frequently find myself unable to read references I want while reviewing. If they are essential to my understanding or my argument, I post to the RW room; if that fails I note in my review that I think [cite] is important but I was unable to access it. I suspect that most reviewers go with "meh" though...
- Bill Hooker
Thanks, Bill, those are good alternatives to going "meh" ;).
- Shirley Wu
from twhirl
JMB give 30 day access to a large range of literature to their referees via a temporary account on Scopus.
- Iddo Friedberg
from Android
Kudos to JMB -- I'm surprised, because that is tacit acknowledgement that there's an access problem, which is something that most publishers deny.
- Bill Hooker
Reviewing for cross disciplinary journals can require access to many different journals. As Bill H notes, academia access is no guarantee of access.
- Bill Anderson
from twhirl
Though it involves paying $$ -- Deep Dyve is what I've been recommending to health providers not associated with academic institutions. At $19.99/mo for unlimited access, it's not a bad price, though the site's received some negative reviews for its search engine. I haven't given it a try, though, so don't know how specific one needs to be to get to a precise article. This testing is on the list for the new year!
- Mickey Schafer
Just for fun, I ran "autism prosody" at Deep Dyve, and although the citation count was absurdly high, the first dozen or so articles are the same ones that come up in gopubmed or novoseek. A few articles were freely available.
- Mickey Schafer
I recently ran into this in a serious way reviewing facility proposals for a well known synchrotron. Some stuff out of my field and I really just wanted to check whether what was being proposed was novel. But I had no way to do that because I couldn't access the relevant literature.
- Cameron Neylon
Putting in author's name in the advanced filter worked to pull up a single article. It appears that it has to be last name, first name/initial, though there are no immediate instructions for that. In any case, may work for fast retrieval of an individual item for the purposes of checking sources (as opposed to downloading them). Don't know if they have a library or folder system which would be particularly useful for organizations.
- Mickey Schafer
Deep Dyve does have a bookmarking function -- didn't see that until I went to the sign up page. I realize this is not ideal OA by any means, but again, for non-academic practitioners, having a "rental" service is a good solution with significant cost savings compared to individual subscriptions to something like MD Consult.
- Mickey Schafer
see also: http://omicsomics.blogspot.com/2009... - pq: "I've been frustrated on more than one occasion whilst reviewing a paper that I couldn't access their supplementary data, and have certainly encountered this as a reader as well. I've sometimes meekly protested as a reviewer; in the future I resolve to consider this automatic grounds for "needs major revision"." via: http://friendfeed.com/mndoci...
- Bill Hooker
Paper access for a reviewer is indeed a problem! I have to admit, I often just go 'meh' and do a second-rate job, simply to save time. Which is just one of many reasons why for me the status quo of scientific publishing is the worst part of my job.
- Björn Brembs
from iPhone
Meh myself. By the time I put the paperwork in for interlibrary loan, it is activated, payment from my grant is approved, and the rest of the madness the deadline for the review would be way past gone.
- Kubke
Nice, I didn't notice the discussion here had expanded until Bill reshared. @Iddo, does JMB automatically provide instructions for the temporary Scopus account or do they wait for the reviewer to come to them with the problem? Still although there are workarounds like this, a lot of these solutions probably don't work too well with the modus operandi of most scientists... namely,...
more...
- Shirley Wu
SSP (shameless self-promotion): Your full-service NCBI blast+ 2.2.22 Perl wrapper is now available from BioPerl : many details at http://www.bioperl.org/wiki... ; send me the bugs...
Mike Chelen, Khader Shameer and Mickey Schafer liked this
Wordle for "The 2010 Nucleic Acids Research Database Issue" (Titles minus 'Database') - http://www.wordle.net/gallery...
Khader Shameer, Björn Brembs, Neil Saunders and Duncan Hull liked this
"update" looks very popular :-)
- Duncan Hull
And I doubt these updates will have to do anything with APIs... where's RDF in that wordle?!?!
- Egon Willighagen
Egon, It was just made with the titles of the articles. Anyway, the word "RDF" doesn't appear in the abstracts
- Pierre Lindenbaum
Poll: Do you publish in the NAR database issue, and do you read what others publish there? - http://larsjuhljensen.wordpress.com/2009...
Peter Miller, Attila Csordas, Khader Shameer and 4 other people liked this
Publish - no. Read - Yes
- Deepak Singh
Publish - no; read -- well, I skim it every year. More often I use the summary info to gauge how the datapile is growing.
- Bill Hooker
I read it every year in growing amazement; how can so many databases be sustained? I guess the answer is they can't. There does however seem to be a low dropout rate over the years... but I realise I've not yet read this years' issue, so maybe that tells a different story.
- Chris Rusbridge
Publish - yes (thanks to Andrew Su). Read : only the "big" ones (NCBI, etc... )
- Pierre Lindenbaum
it's not something I sit down and read cover-to-cover, but google searches often take me there on a semi-frequent basis for tools that sound relevant to my needs...
- Andrew Su
Chris, I doubt many can be sustained over a period and that's a big problem with how we fund infrastructure.
- Deepak Singh
I think I disagree a bit with Deepak on this point. I agree that many can't be sustained, but I don't think that's a problem at all. IMHO, put the tool out there, publicize it as widely as you can (and the NAR DB issue creates a great baseline playing field), and let's see how well it's used. Then it's up to the funding agencies to evaluate usage/impact (which understood, isn't an easy thing), and fund the best ones.
- Andrew Su
Andrew, that's fine, but the way we fund infrastructure is broken cause we don't appreciate it. Nothing wrong with doing something, but even if useful, there is no guarantee it's going to be funded appropriately (the correct kinds of resources).
- Deepak Singh
Plus, I think half these databases exist just for the goal of paper generation. Maybe I am being too cynical but if not half, some non-insignificant number
- Deepak Singh
Publish - not yet. Read - selected articles.
- Ruchira S. Datta
Deepak, definitely agree with your second comment...
- Andrew Su
Deepak, I also completely agree with your second comment.
- Lars Juhl Jensen
I have mixed feelings about the database + web issues. It's exactly the type of content that I think is unsuited to journal article format. The resources themselves should be valued, rather than their dry, dull, traditional and rapidly-obsolete descriptions. On the other hand, in a world where merit is measured by publication, how else are bioinformaticians to gain attention? :-) If you can get it together once a year, it amounts to a free publication opportunity.
- Neil Saunders
Indeed Neil. I think that there is no doubt that the NAR database issue fulfills a need. However, the problem is in my opinion that this need exists in the first place. If you have made a good database or web resource, you should get credit for that without necessarily publishing a paper about it.
- Lars Juhl Jensen
Free Online Course from O'Reilly - Learn to Build iPhone Apps- HTML, CSS, Javascript http://training.oreilly.com/iphonew... /via @jeda21
Khader Shameer liked this
Google Fusion Tables API Is Now Live http://code.google.com/apis...
winckel, Jérôme Flipo, Salvatore Loguercio and 11 other people liked this
"Google Fusion Tables is a free service for sharing and visualizing data online. It allows you to upload and share data, merge data from multiple tables into interesting derived tables, and see the most up-to-date data from all sources. The Google Fusion Tables API enables programmatic access to Google Fusion Tables content. It is an extension of Google's existing structured data capabilities for developers."
- Ruchira S. Datta
Hi Ruchira, as always your posts have been informative. Thanks
- pradeep
Thanks pradeep.
- Ruchira S. Datta
Anyone have any advice on the usefulness of Fusion tables vs Google spreadsheets vs. other online data sharing tools? This got me excited to create a list of all the factors that increase and/or decrease neurogenesis, modify new neuron physiology etc etc as a resource for scientists in my field, since the literature is getting pretty hard to sort through. I started by downloading Pubmed...
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- Jason Snyder
New article on NCBI BlastPlus :Abstract | BLAST+: architecture and applications http://www.biomedcentral.com/1471-21...
Mike Chelen, Khader Shameer, Abhishek Tiwari and Deepak Singh liked this
Any useful biology sites you commonly view on your mobile device? Specifically interested in ones that have a dedicated mobile interface...
rowlikeagirl, Khader Shameer, Andrew Perry and 3 other people liked this
"The Life Scientists" group on Friendfeed :)
- Andrew Perry
+1 Andrew!
- Björn Brembs
Well that's a given... ;) Any others that you use? If not, any that you'd _like_ to use? For example, I've wanted to use NCBI resources in a seminar/meeting before, but the interface right now is pretty poor on my blackberry.
- Andrew Su
Andrew, you need a phone with a proper browser :) http://flashingneurons.deepaks...
- Deepak Singh
Enjoying my new nook.
winckel, Khader Shameer, Jeremy (on vacation) and 13 other people liked this
Also deriving a great deal of satisfaction from removing the air bubbles from under the protective film, probably because it's hard work.
- Ruchira S. Datta
Your hands-on review to counter Pogue's is pretty important to me, thanks.
- Daniel Dulitz
How does it feel to read PDFs of papers on it? Is the size and clarity good enough?
- Karthik Raman
Haven't done that yet, though I've downloaded epubs from the 19-th century from Google Books. (There are a few OCR errors, but this is otherwise very nice.)
- Ruchira S. Datta
Just tried reading a PDF of a paper. The text is much more pleasant to read than on the Macbook Air, but there are too many snafus associated with reformatting the PDF (in two column format) to fit the form factor of the nook, so I probably won't be doing this. I expect the Que would be better for that sort of thing.
- Ruchira S. Datta
I am waiting for Que since last year.
- ashish
Thanks a lot for the update!
- Karthik Raman
That's a shame. Some ebook reader should try to get some special formatting hooks into LaTeX. :)
- Ryan Moulton
In case of a large amount of Ebook , I worry about eyestrain.It's good to read about time gap, I think.
- Ami Iida
Ami, I've read plenty of e-books on computer screens and the eyestrain with e-ink is much less, as the display is not backlit.
- Ruchira S. Datta
Second what Ruchira said about eye strain. You can read an e-ink based device for hours
- Deepak Singh
I mostly want one to carry/read articles (PDF) but I haven't decided on one. I could go for the DX if the price drops a bit.
- Pedro Beltrao
I agree with Pedro -- if the DX weren't so expensive I would have one already. I have a 2-hour commute and a huge stack of literature to read, and the DX would make it very easy to put the two together.
- Bill Hooker
Pedro the kindle2 does native PDF now (or so I think)
- Deepak Singh
from iPhone
Will the Kindle2 display pdf files that contains graphs and illustration in "proper" manner? I had one but returned it because it could not display pdf files properly. I am waiting for Ebook reader that would do that. kindle Dx does that but I am waiting for Que and other ebook readers so that I can compare and buy the one that suits my need. Also, I would love to have functionality of having to print straight to ebook reader using wifi or even USB will work.
- ashish
within limits. One of my friends has his entire library on his Kindle. The new firmware is the same as the DX to the best of my knowledge.
- Deepak Singh
from IM
To be fair, I had Kindle2 before the firmware update for pdf was pushed. I am compelled to try it again but probably wait for reasons mentioned before.
- ashish
Not a bad idea. The scientific capable reader is still a bit away
- Deepak Singh
There is a website that will convert any pdf on the web to be viewed an an ebook on the Stanza iPhone app http://epub2go.com/
- Christian Burns
I am waiting for the ebook reader that syncs with Papers in with the same ease an ipods syncs with iTunes. Oh Apple, where is your ebook reader?
- Matt Leifer
and you haven't put in line ordinary book...
- A.T.
25K$ anyone for some text mining? | InnoCentive - Challenge Overview - https://gw.innocentive.com/ar...
Khader Shameer liked this
"Gathering sequence information from biological publications is a tedious activity if done manually. The Seeker would like Solvers to develop a means of doing this by using publicly available software and a bit of additional ingenuity. Preexisting solutions that fulfill the criteria well would also be considered by the Seeker."
- François Dongier
from Bookmarklet
I just saw this - sounds really interesting, but I'm always daunted by the prize money.
- Mr. Gunn
Right, I think the worries expressed in another thread (http://ff.im/cpbmx) a couple weeks ago are still valid here. Eric Jain: "I'd be concerned that they end up amending the original specs repeatedly after seeing your submission (a typical problem with up-front specs)". Deepak Singh; "I wonder if anyone on this list has actually used Innocentive." How does it work? If you answer that you are interested in the challenge, do you get really precise specs?
- François Dongier
"InnoCentive will notify you within a commercially reasonable period of time after termination of the Exclusivity Period [90 days] whether a Seeker accepts your Proposal and wishes to exercise an Option ("Acceptance")...Upon Acceptance of your Proposal by a Seeker and payment of an Award to you (see Section 5, "Payments"), you hereby assign and convey to InnoCentive all rights, title,...
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- Ruchira S. Datta
"During the term of this Agreement and at all times thereafter, you shall not disclose to any third party nor use for any purpose other than for the performance of this Agreement, any Confidential Information (as defined below) without the express written consent of the owner of the Confidential Information. ... During any Exclusivity Period and after Acceptance and exercise of an Option relating to a InnoCentive Challenge, any Work Product or Proposal relating to said InnoCentive Challenge. "
- Ruchira S. Datta
If a proposal of mine is really good (which is presumably why they would accept it), I don't think $25K would be enough to never work on or talk about it again. My freedom to work on my own ideas and share them with the wider world is very important to me.
- Ruchira S. Datta
I'm not that concerned about transfer of intellectual property of the solution from solver to seeker. I think that's pretty natural and common practice. I'm more concerned about spending a month on a problem to then find out that my solution is not quite acceptable, even if it meets the specs ;-)
- François Dongier
"Q: What if a Solver tells us something that we already know? A: You are not obligated to pay an Award to acquire IP that you are already aware of. Much like the terms of a standard non-disclosure agreement, you would be exempted if you can reasonably demonstrate that you were aware of the IP through independent means. Not only that, your Challenge statement can specifically request...
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- François Dongier
Francois, it's common practice in companies. The company is paying you for that period of time. Here, you may or may not get paid (as you noted). Also, note that I currently don't work for a company, and this is one of the reasons.
- Ruchira S. Datta
Ruchira, I'm also exploring this from a freelance perspective.
- François Dongier
Gene and protein annotation: it’s worse than you thought #bioinformatics - http://bytesizebio.net/index...
Andrew Perry, Nakao M., Shirley Wu and 19 other people liked this
I was thinking "nah, it's probably about as bad as I thought" - but you're right!
- Neil Saunders
Error level (near 0%) for SwissProt looks interesting. People of protein-protein interaction data claim 2-9% error rate on manually curated sets, and the same level I would expect from SP. Some things are better than I thought ;).
- Pawel Szczesny
Not too bad, but I think its even worse than they do. And evidence codes won't fix this. Manual curation and standards for automatic annotation are in dire need of a revolution, and even if we get that it'll still take years to fix.
- Paul J. Davis
@Paul How would you revolutionise it if all the data is still contained in the relatively unnaccessible journal article?
- Frank
Trust Pawel to see the half full (or 60% full) part of the glass. I agree with Frank though: it is not feasible to go through NR and fix the annotations manually. We just have to accept that NR, TrEMBL and KEGG are (mostly) over-annotating, and remember that when we rely on them when delving into the protein family level.
- Iddo Friedberg
Thanks Iddo. I lost count of how many times annotation errors came up in my discussion with experimentalists who lack experience with such databases. (Not surprisingly, they usually think these errors are negligible, especially when it comes to THEIR proteins.) Now I'll just send them a link to your post...
- Mickey Kosloff
Fwd: dear lazyweb, which (preferably biomed-heavy) pop science magazine would you recommend for an 18 year old? (via http://friendfeed.com/psique...)
Christopher Harris, Khader Shameer and Mike Chelen liked this
scientific american, popular science, nature, science, and new scientist are interesting and rigorous
- Mike Chelen
+ GEO and parts of Resonance (mostly physical and chemistry related articles) http://www.ias.ac.in/resonan...
- Khader Shameer
If it's just for light reading and raising interest, http://seedmagazine.com/ is not a bad choice either
- Oliver Hofmann
Science: The looming crisis in human genetics | The Economist - http://www.economist.com/display...
Alexey, Pavlo Zahozhenko, Björn Brembs and 25 other people liked this
"Human geneticists have reached a private crisis of conscience, and it will become public knowledge in 2010. The crisis has depressing health implications and alarming political ones. In a nutshell: the new genetics will reveal much less than hoped about how to cure disease, and much more than feared about human evolution and inequality, including genetic differences between classes, ethnicities and races."
- Itachi
from Bookmarklet
we'll know more than before - surely a good thing.......
- winckel
For a different perspective, see the Nature article "Let's celebrate human genetic diversity" http://ff.im/9PbOx
- Ruchira S. Datta
Uh-Oh...
- Christopher Harley
See rebuttal by Luke Jostins at The Sanger Institute "The Economist has a rather distressingly bad article by the evolutionary psychologist Geoffrey Miller, about the supposed general failure in human disease genetics over the last 5 years...." http://www.genetic-inference.co.uk/blog...
- Duncan Hull
Thanks Duncan.
- Itachi
my opinion sides heavily towards nurture (upbringing, environment) versus nature (heritable traits) in human behavior
- Mike Chelen
Certainly, one could never use knowledge of how drugs work differently in different genetic backgrounds to help cure disease, right?
- Mr. Gunn
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