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Daniel Mietchen to Daniel's feed, Science 2.0, Science Online, Science in the long run

Fwd: Should you be tweeting? - http://www.hubmed.org/display... (via http://friendfeed.com/ff-for-...)

Noah Gray, Jonathan Eisen, Hope Leman and 22 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

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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... more... - 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... more... - 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... more... - 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... more... - 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... more... - 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... more... - 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... more... - 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... more... - 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... more... - 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... more... - 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;... more... - 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... more... - 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

Got mail from Cell: "Dear Dr. Mietchen, Thank you for your proposal to write a Correspondence for Cell in response to the article on tweeting by Laura Bonetta published in the October 30th 2009 issue of Cell. Your proposal has now been discussed by the Cell editorial team. We think that your proposal would work well as a 500-word online comment. Our new online comments feature enables... more... - Daniel Mietchen

I hadn't even noticed the comment feature before but here are three previous comments on the Bonetta article: http://www.cell.com/comment... . The first one by Jo Badge ( http://friendfeed.com/jobadge ) already tells much of our story, and we could simply build on it. An easy way to comply with the 500-word limit (which is stated as 8000 characters in the guidelines for posting comments) would be to just split it in two. - Daniel Mietchen

Found out why I hadn't seen the comment feature before: The comments are only visible if you access the article directly via cell.com (I usually go there via sciencedirect.com). - Daniel Mietchen

It seems the comments are not indexed by Google - taking the first sentence of Jo's comment as a search string does not yield any results: http://www.google.de/search... . In other... more... - Daniel Mietchen

Asked Cell Press via Twitter: http://ff.im/dC7Na . - Daniel Mietchen

I just tried to add our comment. It was below 8k text chars but contained links, which blew it up to well over 10k, so it was rejected automatically. I thus think it is best to post the stuff jointly on our blogs (using the title "Social filtering of scientific information - a view beyond Twitter") tonight, and I have put the HTML source for that into http://bit.ly/7ejHlJ . - Daniel Mietchen

I'm surprised that the comments aren't indexed, and that does make it much less inviting as a method of replying to the article. - Allyson Lister

Just for completeness: Part of FF has been made open source as Tornado: http://www.techcrunch.com/2009... (via @joergkurtwegner ) - Daniel Mietchen

The Life Scientists: Ruchira S. Datta

A long day of live-blogging the Pacific Symposium on Biocomputing http://friendfeed.com/pacific... Wish you were here!

Wednesday - Comment - Like - Share

Khader Shameer, Duncan Hull, Frank and 4 other people liked this

Ouch. Nice work. Thanks - Pedro Beltrao

Ruchira, great stuff. Thanks a ton - Deepak Singh

Glad you like it. :-) - Ruchira S. Datta

April Buchheit

This video just kicked up Lady GaGa as "pretty good" to "F-ing Awesome" in my book - http://www.youtube.com/watch...

January 1 - Comment - Like - Share

Nick Mutton, Kurt Starnes, Jimminy Fuller and 24 other people liked this

I love how she just kept going with her performance despite the technical difficulties. Just like the song, she just kept dancing and singing and worked the crowd to her advantage. That's talent, imho. - April Buchheit

12 more comments

Heck, yeah. Given all of the lip-syncing pop stars who can't seem to dance and sing at the same time, you forget what it is like to see someone who can actually perform :) - Jennifer Dittrich

"I promised these people a 30 minute set.." love. - Jennifer Dittrich

Yes, in spite of the ridiculous costumes, she does seem pretty talented. - Gabe

Wow. Color me impressed. I'm gonna have to get over myself and check her out. - Derrick

This girl can really sing. Like singer/songwriter credentials. - Eric @ CSTechcast.com

Youtube "stefani germanotta" if you want to see her without the fashion persona. - Cole Jolley

http://www.youtube.com/watch... FFound that while following Cole's advice... judge (?) at the end says "norah jones watch out" or something to that effect - Chris Heath

I'm a metalhead, and a GaGa fan. - Christopher Galtenberg

i'm not really a fan of hers but this (and other things like her NYU years) makes me think a lot more of her than i did previously... now if she would just focus on the music instead of the circus i might become a fan... her pr/marketing people have turned me (and a lot of others) away just because of the spectacle that is her persona... do not want - Chris Heath

but they sure are geniuses for keeping her in the press constantly... i guess - Chris Heath

I agree: fantastic recovery and amazing live singing! - Gordon Herd

God I love her so much. Total fangirl. - EricaJoy

girls with cohones - amelia arapoff

Kevin Z

New blog post at the Online Lab: Redefining Authorship? http://www.zelnio.org/2010...

January 2 from Twitter - Comment - Like - Share

Bora Zivkovic, Bill Hooker, Cameron Neylon and Jonathan Eisen liked this

No easy ways out! No incentives to cheat the system! Problem is: publishers will not cut the branch they're sitting on and only few professors can be bothered. - Björn Brembs from iPhone

So it comes down to "Meh, suck it up kid like I did"? I reject indifference! lol - Kevin Z from twhirl

Well, the first step towards change is clear: getting rid of commercial publishers... - Björn Brembs

Jason Stajich

Covariation of Branch Lengths in Phylogenies of Functionally Related Genes - http://www.citeulike.org/user...

December 31 from CiteULike: stajich's library - Comment - Like - Share

Paul Gardner, Jonathan Eisen and Leonardo Martins liked this

Steve Mount

The Tool-Builders - http://www.genomeweb.com/blog...

December 31 from The Daily Scan from GenomeWeb - Comment - Like - Share

Jonathan Eisen liked this

Jason Stajich

Happy holidays microbial art - http://fungalgenomes.org/blog...

December 30 from The Hyphal Tip - Comment - Like - Share

Jonathan Eisen and Mark A Jensen liked this

Graham Steel

Should Copyright of Academic Works Be Abolished? http://papers.ssrn.com/sol3...

Should copyright of academic works be abolished -... 580 KB

December 28 - Comment - Like - Share

suelibrarian, Steve Koch, OpenSci Info and 14 other people liked this

"Abstract: The conventional rationale for copyright of written works, that copyright is needed to foster their creation, is seemingly of limited applicability to the academic domain. For in a world without copyright of academic writing, academics would still benefit from publishing in the major way that they do now, namely, from gaining scholarly esteem. Yet publishers would presumably have to impose fees on authors, because publishers would no longer be able to profit from reader charges. If these author publication fees would actually be borne by academics, their incentives to publish would be reduced. But if the publication fees would usually be paid by universities or grantors, the motive of academics to publish would be unlikely to decrease (and could actually increase) – suggesting that ending academic copyright would be socially desirable in view of the broad benefits of a copyright-free world. If so, the demise of academic copyright should probably be achieved by a change in... more... - Graham Steel

17 more comments

As much as I am pro-OA, it should be used because it is beneficial to the author as a decision. Using the force of law seems mighty excessive. - Jean-Claude Bradley

I disagree Jean-Claude -- the people who pay for the research (i.e., taxpayers) should have some role in deciding how things are published, whether or not authors like it - if someone does not like government funding related rules, they can get funding elsewhere and publish however they want - Jonathan Eisen

I've only skimmed thru this one, so far. From the conclusion, "I have endeavored here to examine the effects of eliminating copyright of academic works and the factors determining whether that change would be socially desirable. On the basis of a number of empirical judgments – notably, that universities and grantors would tend to subsidize publication fees – I suggested that ending... more... - Graham Steel

In the US, the explicit purpose of copyright is "to promote the progress of science and the useful arts." Insofar as copyright gets in the way of that, *even if it helps authors*, it should be abolished. So saith US law! Granted, we haven't kept sight of that lofty goal, but... - D0r0th34

Dorothea - of course funding bodies can impose any rules they wish and making work resulting from funding OA makes a lot of sense. I read it as the abolishing of all academic copyright. - Jean-Claude Bradley

I'm not talking about the US as a funding body. I'm talking about the US Constitution and its clearly-stated reason for copyright! Copyright was not invented as an author gravy train. Copyright was not invented as a credit mechanism. Copyright was invented *to promote the progress of science and the useful arts*. Again, insofar as it is hindering that mission, it SHOULD be abolished, NO... more... - D0r0th34

For the record, I spotted this via this tweet from CharlesWBaileyJr to the #oatp http://twitter.com/oatp... - Graham Steel

Well Dorothea I guess we do disagree in the end then :) I think there are too many interested parties that will object to abolishing copyright and it is not a fight that can be won directly. What I do think is possible is convincing individual authors that it is in their best interest to choose OA. Publishers will feel increasing pressure going forward from that - in addition to any funding agency requirements. - Jean-Claude Bradley

We don't disagree on the objections that would pour forth, Jean-Claude. I just wish this country would wake up to the Constitutionally-established purpose of copyright and go "hey, wait a minute here..." I also wish I could agree that convincing individual authors was in the cards. I think that's pretty much hopeless without reform-from-within efforts like Shieber at Harvard forcing a mass decision. - D0r0th34

Speaking of objections: http://host.madison.com/ct... *eyeroll* - D0r0th34

Stimulating thread, folks. I've alerted the author. Why not ! - Graham Steel

But isn't OA a form of copyright? The complete absence of copyright is public domain - in this case how can we enforce author attribution or sharing conditions (so that the work isn't changed without explicitly saying so)? - Leonardo Martins

(just to contextualize my previous comment since I pressed "return" too soon ;) For me it's obvious that the current implementation of copyright is simply wrong, but whenever I read "abolition of copyright" I fear for what would replace it (and my conclusion is that it would be another copyright). I must say that I haven't read the article so I might be beating a dead horse... - Leonardo Martins

Wouldn't abolition of copyright destroy Creative Commons licensing? For Gold OA, "author retains copyright" is functionally equivalent to "there is no such thing as copyright anymore", but for Green OA, abolition of copyright would mean that ALL journals were instantly 100% Green-compatible. Big Pig Publishing would have to find some way to prevent authors' self-archiving that didn't... more... - Bill Hooker

Forgot to note: did not read OP. Apologies if I got any stupid on anyone; it washes off, I promise. - Bill Hooker

Ah, but Bill, a license is between licensor and licensee. So Big-Pig Publisher can say "Author, you will not self-archive!" in a license, but that agreement is *not* binding on me as librarian. ;) If Big-Pig Publisher wants a license binding on the institutions, it'll have to go up against University Legals all over the country, and it ain't gonna win. - D0r0th34

But don't libraries typically have licenses with the BPPs as well? What's to stop 'em slipping in the relevant terms there? Universities don't exactly have a stellar track record when it comes to standing up to the BPPs, and I bet there are plenty of idiot beancounters who would jump at the chance to sign away their library's archiving rights in return for a 1% cut on this year's subscriptions. :-( - Bill Hooker

Take copyright out of the picture, and why are libraries negotiating with the big-pigs at all? Anyway, this also can be finessed, at some places at least. Frex, our land-grant university has certain licensing provisions we simply cannot accept -- we're legally forbidden to. Publishers try it; library negotiators stalwartly strike out the illegal stuff. And SOME libraries are pretty mean negotiators. ;) MPOW has a pretty good rep, as a matter of fact. - D0r0th34

Paul Buchheit

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.

December 22 - Comment - Like - Share

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

19 more comments

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

Martin Fenner

Why I like science blogging? Because I can read blog posts like this one http://phylogenomics.blogspot.com/2009...

December 26 from Twitter - Comment - Like - Share

Benjamin Tseng, Jonathan Eisen, Graham Steel and joergkurtwegner liked this

Leonardo Martins

just by following @hyphaltip and @phylogenomics I have the whole Tree Of Life covered. Apart from a small branch maybe.

December 24 from Twitter - Comment - Like - Share

Jonathan Eisen and Jason Stajich liked this

=) at least the mainly unseen part! - Jason Stajich

Martin Fenner

What is the scientific paper? 4: Access - http://www.cotch.net/blog...

December 24 from Bookmarklet - Comment - Like - Share

Bill Hooker, Rafael Sidi, Jonathan Eisen and Cameron Neylon liked this

"So I told m'colleague to explain to her author that unless she deposits her genome sequences, the last three years of her professional life will ultimately have been wasted. An average paper in a high-volume mid-tier journal that will be glanced at by a few colleagues when published. Another bullet point on a CV. They will never further science beyond that." - Martin Fenner

Adam Ratner

Totally cool. A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea. http://www.nature.com/nature...

December 23 from Twitter - Comment - Like - Share

Jonathan Eisen liked this

Tim O'Reilly

Amazing tale of threat responses in plants: Sorry, Vegans: Brussels Sprouts Like to Live, Too http://www.nytimes.com/2009...

December 23 from Twitter - Comment - Like - Share

Jonathan Eisen liked this

Ruchira S. Datta to Ruchira's feed, The Life Scientists

NIH to crack down on conflicts of interest among its grantees http://www.the-scientist.com/blog...

December 22 - Comment - Like - Share

Jonathan Eisen and Steve Koch liked this

Tim O'Reilly

Love Eliot Spitzer's idea that AIG emails should be released to the public to "open source" investigation http://www.nytimes.com/2009... #gov20

December 20 from Twitter - Comment - Like - Share

Iggy Mwangi, etag, A.T. and 15 other people liked this

How does a modern lynch mob advance justice? - Nathan Wenzel from iPhone

5 more comments

More Greek Chorus than lynch mob. - Todd Hoff

Something like the Enron e-mail archive would be interesting, to understand what people were thinking. http://www.enronexplorer.com/ etc. - Ho John Lee

I guess calling it a mob or a Greek Chorus would depend on whether or not you're on the same side as the mob- err... Greek Chorus - Nathan Wenzel from iPhone

I would love to hear the logic that reduces the two to being equal. But my guess is logic and unreason are the same depending on which side you are on so question answered. - Todd Hoff

Hey we bailed them out, so I guess we can now peek into the emails, we own the company - Shakeel Mahate

open source is probably the most democratical way of justice, at least the most transparent one - A.T.

Maxine

Author reports negative Amazon reviewers of her book to the FBI - hope doesn't translate to scientific open peer review http://www.guardian.co.uk/books...

December 22 from Twitter - Comment - Like - Share

Jonathan Eisen liked this

Kevin Z

RT @p_binfield: #PLoS ONE review of 2009 - an amazing year packed full of new developments! http://everyone.plos.org/2009...

December 22 from Twitter - Comment - Like - Share

Jonathan Eisen liked this

Steve Koch

Invited to be a PLoS ONE Academic Editor; stoked!

December 21 - Comment - Like - Share

Jason Winget, Anna Croft, Cameron Neylon and 13 other people liked this

Welcome aboard! - Adam Ratner

Congrats! - Mickey Schafer

Thanks! I'm reading through some of the guidelines for editors and learning a lot. One good thing is that I learned that post-publication comments by the academic editor of the paper is encouraged. I wasn't sure of this, because for the papers I've read on PLoS, I don't think I've ever seen this. - Steve Koch

Michael Barton

Deciding what genomes to sequence - http://www.michaelbarton.me.uk/2009...

December 22 from michael barton - Comment - Like - Share

Jonathan Eisen liked this

Tim O'Reilly

Watch bacteria turn tiny gears: http://radar.oreilly.com/2009... Awesome taste of the nano future.

December 21 from Twitter - Comment - Like - Share

Kubke and Jonathan Eisen liked this

Mike Chelen to Mike's feed, Article-level metrics, OpenSci Info, Science Commons, Bibman2

Open-Access-Statistics project DINI - Deutsche Initiative für Netzwerkinformation - http://www.dini.de/projekt...

November 29 from Bookmarklet - Comment - Like - Share

netpiano, Hilary, Mr. Gunn and 7 other people liked this

"Scientific Publications cover a wide variety of publishers, hosts, business models, usage models, publication stages, logical and technical presentation. Therefore it is important to learn which portions of the publication space can be and which agents want to be included in the sampling. For those willing to participate only two aspects are relevant: 1. What data needs to be gathered? 2. How can it be transferred to the statistics provider? Open-Access-Statistics (OA-S) is a joint project adressing these questions. Starting in July 2008 an infrastructure for the standardised accumulation of heterogenous web log data with an emphasis on institutional repositories will be built. In tight cooperation with the Network of Open Access Repositories (OA-N) various added value services will be made available to users." - Mike Chelen from Bookmarklet

5 more comments

WONDERFUL. We have needed this a long time. - D0r0th34

What D said. - Bill Hooker

Only took about 15 mins to complete the questionnaire - Graham Steel

Won't load for me at the moment. - Bill Hooker

Completed the questionnaire, provided links to things like http://dataportability.org, OpenID, friendfeed, etc. Have to say, though, that some of the questions were worded somewhat unclearly. - Mr. Gunn

D0r0th34: thrilled to see existing and ongoing exploration of the topic, which is a natural extension for scholarly repositories and a crucial goal for ongoing curation. now reading one of the linked papers, "Open Access Statistics: an examination how to generate interoperable usage information from distributed open access services" (Herb, Ulrich '09) http://www.dini.de/fileadm... - Mike Chelen

Neil Saunders

Has our quest for completeness made things too complicated? - http://nsaunders.wordpress.com/2009...

December 1 from What You're Doing Is Rather... - Comment - Like - Share

Marcos de Carvalho, Brad Chapman, Michael Nielsen and 31 other people liked this

Neil, great post. And you're right, we do make things too complicated sometimes, but do we do that at the level at which we ask questions, or at the software implementation level? My take is the latter, cause you need to ask questions the way you want to, but that doesn't mean what makes it all come together has to be one complex mess - Deepak Singh

42 more comments

Glad you like it. One of those that bubbled up out of frustration at inability to achieve! I feel that science is the business of turning complex (real-world) things into simple models - and that we've moved away from that idea. - Neil Saunders

I'm a sucker for this kind of ambitious thinking. Go Neil! - Bill Hooker

I think it's a good sign that things like this are now obvious. Things start out as a complex mess of disconnected things, overlapping complicated ways of connecting them are devised, then it becomes obvious what the simpler thing to do is. - Mr. Gunn

Great ! But aren't you re-inventing something like RDF Neil ? feature/probe/value is nothing but a RDF statement... - Pierre Lindenbaum

No, I don't want to reinvent anything. If RDF will work for me, I'll use it. I'll also use SQL, NoSQL, key-value pairs, document-oriented or whatever it takes. I just think that trying to integrate data by combining other peoples large, complex representations is not working. We need to simplify the whole business. - Neil Saunders

I think there is a middle road here - we need high level generic descriptions like what Neil is proposing (and like my "We have stuff, we do stuff to it, which makes stuff"), but also a way of pointing to more sophisticated information that might be useful in specific contexts. I think we can have the best of both worlds as long as the data representation is separated from the metadata and the organization of each can be described in a machine readable (and agreed!) form - Cameron Neylon

I'm too old school, leaving comments on blogs... who does that any more. I’m sure you’re aware that you’ve just described a model using *triples*. Which means you could start storing these kinds of simple relationships in a triple store like virtuoso etc. As you say, you don't have to reinvent anything, just simplify the use (conventions) of existing approaches (e.g. RDF). I would like... more... - Greg Tyrelle

@Greg about the web interface, one cool interface for adding RDF statements/triples is freebase/Acre: http://www.freebase.com/apps/ - Pierre Lindenbaum

I like blog comments :-) Yes, my example looks like RDF triples. No, that was not really my intention. Let's ask these questions: (1) what data relationships would make sense to a biologist? (2) what are the commonalities in the data, which a biologist may not have considered at an abstract level? As I wrote in the post, many datasets that look different are really different ways of looking at the same thing. - Neil Saunders

The joys of data modelling :-) For (1): I'm afraid asking for a definition of some data relationships is building an(other?)) ontology. - Pierre Lindenbaum

Let's put it another way. What we have, presently, are quite complete, often large and complex, but useful and usable descriptions of individual experiment types. "Integration" essentially means "parse them individually and mash-up the results". That's what makes it difficult. Perhaps we need an "ontology of integration" :-) But let's keep it really, really minimal. - Neil Saunders

I actually think you will struggle to find data commonalities across bioscience. Even the simple proposal of target, measurement, value could break down in many cases e.g. we tried ages ago to get some intensity data from a bunch of microarray experiments and we gave up because we couldn't get across what we needed. What are you really measuring? Does it mean the same thing to different... more... - Cameron Neylon

I think there's a good case for storing, in the first instance, raw values. Figure out how to process them later (that's statistics). Focus on trends (up, down, stayed the same). Focus on well-defined variables that do mean the same to everyone (intensity, in theory = amount of transcript, regardless of the very real difficulties). And I think more experiments fall into... more... - Neil Saunders

@Pierre freebase is exactly what I had in mind, however the web client (the best part) is not open. @Neil Store the data first, ask questions later. Nice. One of my hopes for semantic web technology was that is could be come a universal mashup system (RDF+ontologies+triplestores). But you start down that path, and you suddenly realise that the semweb is asking you to get your data... more... - Greg Tyrelle

But for me your example of a gel isn't raw data. The raw data is the image. Which might have several targets or assays on it. Up/down stayed the same is only really of interest in particular types of science. And I challenge you to find any well defined variables :-) Intensity to me is a measure of optical density but questions of background, object size, masking, averaging algorithm... more... - Cameron Neylon from twhirl

But agree with what you and Greg are saying, first thing get the data somewhere, with allt the metadata you can automatically collect. Then worry about capturing more metadata as people do stuff with the data. Writing this grant proposal right at the moment. - Cameron Neylon from twhirl

And in microarrays, "raw" data is the image of the slide. But aside from a cursory inspection to ensure that it isn't complete rubbish, nobody much cares about that. I'd argue that there's a point in the preprocessing at which a numerical value emerges which could be called "useful" and which encapsulates the object being measured. It needs more work (e.g. normalization) to get information from it, but it's the "value" in feature/reporter/value. - Neil Saunders

To me this about finding something a bit like an upper ontology that describes the general category that objects (targets, assay, value, inputs, outputs, data, process, sample) fall into. That lets you do the general integration, and the more detailed local data structures become more useful as you can agree more and more on what details are important. So I absolutely agree with what... more... - Cameron Neylon

Heh heh It was exactly that image that we did care about - which was the problem :-) I will admit to being an edge case, but in some ways we're all edge cases, they're just different edges... - Cameron Neylon

Neil, may I link to this FF thread from Book of Trogool? - D0r0th34

It's in a rough state but - http://dl.dropbox.com/u... - Cameron Neylon

:-) Sure, different questions, different "levels" of data. I guess my angle is more a statistical one: how do I compare (seemingly) quite different datasets - what numbers can I extract and crunch? Less interested in the capture and description of data at every stage in the process. - Neil Saunders

Dorothea, sure, not a problem. - Neil Saunders

"This is a gel", "this is a sample",.... AFAIK all those kinds of statements are part of the OBI ontology: http://obi-ontology.org/page... e.g. "Agarose Gel" http://bioportal.bioontology.org/ajax_co... - Pierre Lindenbaum

Sure, and those are very complete descriptions of experimental components. But what I want is: "I saw A on my gel, B in my LC/MS, C on my expression array and D on my SNP array and when I plug all that into some Bayesian predictor, it says cancer" :-) - Neil Saunders

Ontologies are not the issue, it's more low level than that. I also work with microarrays, proteomics, metabolomics, and numerous physiological data sets. To keep all the data in one place I use a relational database, in this case postgresql because I like to store raw intensity values in array datatypes, along with pylons based web interfaces to display various views of the data to my... more... - Greg Tyrelle

My argument would be that the reason you're less productive is not because of the RDF and ontologies per se, but because the ontologies aren't really built for what we want to do. They're for describing certain types of outcomes, not for integrating data in a discovery phase. But Neil's (entity, probe, value) is still an ontology of sorts. It is just a higher level one. My belief is... more... - Cameron Neylon

But keep the discussion going - this is exactly the problem that e.g the SAGE project will have - http://sagebase.org - and as a notional member of the data working group I could do with all the ideas and help that's out there... - Cameron Neylon

We are thinking too much in terms of data representation here. In the end what you are looking at is a data warehousing problem. You have different front end systems and you want to be able to pull data in for offline processing into a warehouse. That's pretty much what you do at any company doing a lot of analytics/business intelligence. Different types of data being collected in... more... - Deepak Singh

This reminds me of the type of approach we were considering a while back - with a focus on each observable event during an experiment. http://usefulchem.blogspot.com/2008... - Jean-Claude Bradley

Neil, I was under the impression that normalization across arrays and labs wasn't actually a solved problem, yet. Surely that would have to come first before stripping things down to just assay-key-value? - Mr. Gunn

Normalization ... aaargh! Most definitely not a solved problem - Rajarshi Guha

Normalizing within your own experiments is hard enough, never mind across unrelated datasets. It's something we have to solve though, to make the most of public data. - Neil Saunders

Neil, you may be intersted in looking at the Ontology-Based eXtensible Data Model (OBX) that was developed by Richard Scheuermann's group at UT Southwestern. It is being used for the ImmPort database (www.immport.org) The OBX model utilizes the BFO / OBI ontology as guides in creating a data model that is robust to new datatypes. You can see a presentation about it here:... more... - Burke Squires

Thanks Burke. ImmPort looks very impressive, I must say. - Neil Saunders

This reminds me of what the TCGA is starting to do, by defining "data levels". For microarray data, Level 1 might be the raw images, Level 2, the intensity calls, Level 3, the normalized intensities, and Level 4 information on whether it's up or down regulated across multiple samples. For people like me, doing integrative analyses, it's easy to focus just on the higher level data and... more... - Chris Miller

which is exactly why you need separation of the layers and tools to bring data together for the downstream stuff - Deepak Singh from IM

Neil, I think you have just explained why tab-delimited files are often more useful than complex XML representations of the same data ;-) - Lars Juhl Jensen

Tab-delimitted files would be grrrreat for me in my lab. If any of the rest of you would like to share our data, however, then you're completely screwed. Is the problem not that we're all duplicating each other's work by writing the same kind of parsers for the same kind of data? Proteomics (for example) has a standard (http://www.ebi.ac.uk/pride/). Is it really so hard to use / develop the community-based tools that are being generated around this standard?!? - Neil Swainston

Well, the ratio of usable tools to schemas/ontologies is a whole other debate :-) But sure, in principle the tools are there - for individual types of data. What I highlight in the post is the difficulty of genuine data integration, as opposed to the current "write a parser for everything and mash it up" approach. - Neil Saunders

#1 rule of data integration - if a format exists, it will be used - Deepak Singh

...and if it doesn't exist there is a 70% chance someone will create it :-) - Cameron Neylon

Chris M makes an important point wrt data levels, analogous to trace archives vs sequence dbs. Extending the sequence analogy, obsoleting levels will become important (it will rapidly become cheaper to resequence rather than store sequence). - Chris Cotsapas

Deepak Singh

Secrecy in science is a corrosive force - http://news.ycombinator.com/item...

November 29 from Backtype - Comment - Like - Share

Yaroslav Nikolaev, Konrad Förstner, Leonardo Martins and 4 other people liked this

"Number of efforts across the board, including chemistry and biology. The extreme side of the "open science" world is Open Notebook Science http://en.wikipedia.org/wiki... In general you are required to put enough into the methods section of a paper to be able to reproduce the results, but as the computational side gets more and more complex and supplementary data sets get bigger and more complicated, the need to make the raw data and (if possible) code available for people to reproduce the results becomes almost a necessity. A number of folks are thinking along the publishing side as well. Theres PLoS One (http://plosone.org) and Cell has been doing some very interesting prototyping on the "paper of the future". People have already mentioned JoVE and OpenWetWare. It will happen, but it's going to take a few years. Too many years of established practice." - Deepak Singh

Another point in the discussion: "Perhaps, in the case of data-intensive work, grants should be given in pairs: one research team gets paid to collect the data, and another team gets paid to analyze it." ( http://news.ycombinator.com/item... ) - definitely yes, though two teams may not be sufficient, so the allocation procedure should be flexible. Fundscience have stated that they plan something like this, but they still haven't started out yet. - Daniel Mietchen

Daniel - I can't see that working very well - most scientists I know want to analyze their own data at least to the extent that they are capable - let alone permit others to do so. An exception to that is where core competences of collaborators don't overlap. But I do see a future like that when machines publicly report their experimental results - Jean-Claude Bradley

Bora Zivkovic

Another post on distributed science v. open source science. http://scienceblogs.com/commonk... by @wilbanks #scibling

November 5 from Twitter - Comment - Like - Share

Jonathan Eisen and Mike Chelen liked this

open source principles are at the heart of distributed science because the focus is to increase common knowledge - Mike Chelen

Christina Pikas

Are chemists really grinches? - http://scienceblogs.com/christi...

November 28 from Christina's LIS Rant - Comment - Like - Share

Duncan Hull, Jonathan Eisen, Matthew Todd and 6 other people liked this

dang. beat me to it. :) oh, well, something for the next tidbits post - D0r0th34

14 more comments

When I first read the post title, my eyes actually say, "Are chemists really grouches?" Then I clicked on "like" but that may be due in part to local conditions. - John Dupuis

If ACS would modify its policy and accept pre-prints (or at the very least allow self-archiving) I think that would make a big difference. - Jean-Claude Bradley

... and the cynical part of me says that allowing self-archiving doesn't make a damn bit of difference in the absence of a well-used disciplinary repository, so I really can't imagine why ACS doesn't - D0r0th34

Yes other publishers have come to the conclusion that allowing self-archiving makes sense. - Jean-Claude Bradley

Your final point - will there be two tracks is already happening. Chemistry informatics is dominated in the mainstream by the needs of biological scientists, not chemists. Lots of good cheminformatics being done but most of it is ignored by mainstream chemists - but bioinformaticians and biological scientists expect access to that kind of information so it is being built for their (our) needs. - Cameron Neylon

"self-archiving doesn't make a damn bit of difference in the absence of a well-used disciplinary repository" or a standard metadata format to enable indexing of distributed self-archived papers. The actual content doesn't all have to be under one roof if it can be searched in a uniform fashion. - Mr. Gunn

Do people think it's true that Chemistry stands out in this regard? Of being more closed than the other disciplines? - Matthew Todd

@Matthew - yep.that's the point. people use examples from HEP or bioinformatics or other fields and then try to find the analog in chemistry. Chemistry is more closed than other disciplines, in general. I would say that there are parts of chemical physics that act like chemistry and there are probably parts of chemistry that are more in the biomed area.... but in general. - Christina Pikas

well, chemistry isn't as bad as some of the humanities. :) OTOH, it doesn't labor under the serious privacy/confidentiality requirements of some of the social sciences, so it has fewer excuses. Mr. Gunn, the point I was making was socio-cultural: NO discipline has embraced institutional repositories. As far as widespread OA is concerned, IRs are a non-issue. So ACS could relax its strictures on self-archiving and practically nothing would happen. - D0r0th34

I wonder how much of the socio-cultural aspect has to do with the commercial aspects of chemical information. In HEP and astronomy and math, and such, there isn't near as much of a problem with sharing info. Sure, researchers still do not want to be scooped, but the main societies are not out there to make a "profit" like the ACS and the CAS. Anybody see research that pinpoints the problem? - Joe

Not really, no. I've seen that connection asserted as a fact in various reports, but that's all. It's certainly intuitive enough... but then again, there's the counterexample of genomics, where there's a huge $$$ interest but it was overcome anyway. - D0r0th34

it's easy (I often do it) to consider ACS as this external factor that is evil and comes in and prevents change. It is a society, however, so to some extent its development is in response to the needs of the members. With that said, I think that the policies of ACS DO prevent some chemists from being more open. In HEP and Astro there are some key journals published by Elsevier and Springer - for profit organizations. - Christina Pikas

there are 2 parts to the industrial/commercial bit: 1) are the products of the science commercializable - will they make a company money, can they be applied and 2) is the funding coming from industry or are the researchers doing the work in industry such that a) no sponsor requirement to share b) disincentives to share c) actively prevented from sharing except in obfuscatory patent applications - Christina Pikas

Christina, an additional blog post to that effect would be an excellent addition to the discourse, I'm thinking. - D0r0th34

which part - the society bit or the commercial bit? - Christina Pikas

Maxine

Very nice round-up of (mainly) science related podcasts recommended by my esteemed colleague Chris Surridge http://network.nature.com/people...

November 29 from Twitter - Comment - Like - Share

Daniel Mietchen, Jonathan Eisen and Graham Steel liked this

A very nice round-up indeed.... - Graham Steel

Roderic Page

Is there a role for community annotation in biodiversity? - http://biodiversity.stackexchange.com/questio...

November 24 from User roderic page -... - Comment - Like - Share

Bill Anderson and Jonathan Eisen liked this

One way to tackle the task of editing and annotating data is to involve the wider community. Examples include Google Image Labeler http://images.google.com/imagela..., or even tools such as ReCAPTCHA http://recaptcha.net/. Such approaches don't seem to have been applied on any scale to biodiversity data. Is our community capable of supporting such tools? What are the possible applications? For instance, this forum has already had questions about the identity of an organism. Is this something that could be crowd-sourced? - Roderic Page

Funny, I was just preparing a blog on different crowdsourcing science projects that I had come across, wondering whether there would be a way to get the crowd to convert jpeg/PDFs of phylogenies into something more useful. - Joseph Hughes

Cool, let me know when you've posted your thoughts! - Roderic Page

Graham Steel

Open Science: Good for Research, Good for Researchers? - http://www.youtube.com/watch...

November 22 from YouTube favorites - Comment - Like - Share

Jan Schmirmund, Khalid Mirza, Cameron Neylon and 7 other people liked this

Hadn't seen this before. Featuring Bora Zivkovic, Jean-Claude Bradley and Barry Canton (OWW). - Graham Steel

nice find Graham! I had not seen the YouTube version - Jean-Claude Bradley

Bora Zivkovic

ScienceOnline2010 - Program highlights 3 - http://scienceblogs.com/clock...

November 21 from A Blog Around The Clock - Comment - Like - Share

Jonathan Eisen liked this

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