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I'm so glad we didn't have to do wood cuts. http://usefulchem.blogspot.com/2009...

Christina Pikas, Dan Hagon, carolh and 5 other people liked this

the next generation will note that they are glad they don't have to extract knowledge from human-only readable documents - Jean-Claude Bradley

+1 Jean-Claude. A few more "information generations" and working scientists will consider our current methods functionally equivalent to woodcuts. I hope. - Bill Hooker

Strictly speaking woodcuts were an extravagance in Newton's time since it was only used for inline figures within the text (itself composed of metal type) so each figure had to be individually, skillfully and laboriously hand-crafted. Also since it was wooden it had an extremely short lifespan compared to the rest of the text block which meant that only short print runs were possible... more... - Dan Hagon

Julian

*boom* *quaaaaaaaaack*

23 hours ago - Comment - Like - Share

Cameron Neylon and D0r0th34 liked this

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-...)

November 10 - Comment - Like - Share

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

113 more comments

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

Hilary

ArXiv to begin asking for voluntary donations: http://arxiv.org/help/support/

Wednesday - Comment - Like - Share

Rafael Sidi, suelibrarian, Claudia Koltzenburg and 5 other people liked this

"Cornell University Library is beginning an effort to expand funding sources for arXiv to ensure its stability and continued development. We intend to establish a collaborative business model that will engage the institutions that benefit most from arXiv — academic institutions, research centers and government labs — by asking them for voluntary contributions. We are working with library and research center directors at the institutions that are the heaviest users of arXiv to refine our plan and to enlist support. We expect to release the plan, with a call for broader engagement and contribution, in early 2010." - Hilary

5 more comments

Doesn't really help the "Green OA is a financially sustainable practice" meme much :( - Wobbler

I wonder if to some extent this is a matter of having to demonstrate profitability rather than sustainability. In most things academic, it isn't enough to show you're breaking even, regardless of what the service might be. - Mickey Schafer

Although in the case of OA services, "breaking even" sounds like a sufficient enough objective IMO. Making profit might eventually stifle collaboration, increase competitiveness and decrease the overall efficiency and effectiveness of scholarly communication. It doesn't help that "sustainability" is probably a weaker incentive than "profitability", though. And that financial sustainability is still a question mark. - Wobbler

I would be SUPER EXTRA interested in the Cornell-library-internal politics behind this one. If I had to venture a guess, with library budgets getting hit bad everywhere, somebody gave arXiv the $400K fisheye. Easy to do, since OA is *still* seen as a non-core library activity. There's also SCOAP to compare it to: "libraries are chipping in for THAT, why not THIS?" - D0r0th34

What chafes my scrote is that $400K is pocket change relative to gummint spending on physics research in total, plus the fact that without arXiv physics will have to go back to the "beg a publisher and wait six months" model of information transfer, likely reducing ROI on that research funding by considerably more than $400K -- and yet, here we are with arXiv needing "donations". The stupid, it burns. - Bill Hooker

lol, Bill, I have several bad jokes about powder, but they don't seem appropriate given the reality here. - Mickey Schafer

Bill Hooker to Bill's feed, Science 2.0

Welcome to Orwik - http://orwik.com/

Wednesday from Bookmarklet - Comment - Like - Share

Borya Shakhnovich, Rafael Sidi, Steve Koch and 10 other people liked this

Platform for ONS? Anyone looked at this? - Bill Hooker from Bookmarklet

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I've not seen it before but I like this form the About page: "Orwik is not Facebook for scientists. Orwik is not about what you’re doing right now. Orwik is not who you know, but what knowledge you want to share with colleagues and with the world." Will take a closer look... - Cameron Neylon

Waiting for an account activation... - Cameron Neylon from twhirl

waiting for an account too - Jean-Claude Bradley

Terms of service clearly state that there are paid accounts, but I find no price list for these plan son the public site. Maybe this is a pet peeve, but it just screams "shady" when you advert for free accounts and hide the fact that there are paid accounts and how much they cost. - delagoya

hopefully the paid accounts are the private ones - I just hope the public information is not behind a username and password - otherwise it won't get indexed - Jean-Claude Bradley

ok reproduced part of a lab notebook page here: https://orwik.com/contrib... - Jean-Claude Bradley

Basically it is a simplified wiki - you can add files or text in sections. Compared to Wikispaces, didn't see a way of comparing versions and didn't see way of making images more than a thumbnail. Also didn't see a way to insert HTML so can't add a sitemeter or embed Youtube videos or Google Spreadsheets, etc. - Jean-Claude Bradley

Abhishek Tiwari

Public PhD defense - http://www.slideshare.net/yannick...

Tuesday from Slideshows for Tag:... - Comment - Like - Share

joergkurtwegner, Steve Koch, Deepak Singh and 6 other people liked this

It's almost too nice to be a thesis defense! - Benjamin Tseng

Laurent Keller: great work and apparently also great lab! - Björn Brembs

is there supposed to be audio? - Jean-Claude Bradley

Jonathan Eisen

Knight Science Journalism Tracker: includes discussion of @NYtimes article by @carlzimmer on our new paper - http://ksjtracker.mit.edu/2009...

Tuesday from Bookmarklet - Comment - Like - Share

Cameron Neylon liked this

Chris Miller to Chris's feed, The Life Scientists

Does anyone else find it odd that "Nature Methods" doesn't actually print the methods section of their articles? It's only available online. Whaaa?

Tuesday - Comment - Like - Share

Mickey Kosloff, Benjamin Tseng, Christopher Harris and 2 other people liked this

Yup, 'Nature Methods' has the methods only as supplement. How absurd is that? http://friendfeed.com/the-lif... - Björn Brembs

Haha - I even "liked" that post the first time around, before completely forgetting it. - Chris Miller

Neil Saunders

Every time you open a sequence file in Word, a bioinformatician cries out in pain - http://rrresearch.blogspot.com/2009...

December 24 from Twitter - Comment - Like - Share

Mike Chelen, Peter Miller, Chris Miller and 5 other people liked this

The original has dying angels... I wonder about the death rate cause scientists are so bloody sloppy... - Egon Willighagen

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That is... if we were more accurate, would science have progressed further, finding earlier and better cures? - Egon Willighagen

Maybe not, but we might avoid spending money on useless things. - Paulo Nuin

sometimes when computers contain only basic software suites, it is easier to use whatever is available - Mike Chelen

Dan Hagon

Exploring the possibility of re-implementing my Google Wave ChemGadget with TwirlyMol

December 20 - Comment - Like - Share

Cameron Neylon liked this

This is way easier for TwirlyMol than ChemDoodle Web Components because there is a clear seperation between the 3D rotation matrix and the atom coordinates. In the former case these two only get multiplied just before the canvas gets redrawn whereas in the latter case the original coordinates are destroyed as soon as the user rotates the molecule since they get replaced with the newly multiplied version - thus rendering the code, as-is, unusable for my purpose. Great example of how design decisions can have a fundamental effect on subsequent re-usability. - Dan Hagon

Dan, thanks for the comments, we will have this addressed for ChemDoodle Web Components in the future. For now, can you just save a copy of the molecule with the original coordinates for whatever purposes you need, then it doesn't matter what happens to the molecule object that is rendered? - Kevin Theisen

Neil Saunders

The worst scientific idea of the decade: vaccines cause autism - http://genome.fieldofscience.com/2009...

Monday from Google Reader - Comment - Like - Share

Steve Koch, Anders Norgaard, Info Glutton and 5 other people liked this

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

The Life Scientists: Hope Leman

Hi, all. I want to urge everyone to add to the public comments here: Policy Forum on Public Access to Federally Funded Research: Features and Technology http://blog.ostp.gov/2009... It is an unprecedented opportunity for the Open Science community to help influence the course of public policy on matters you all care about and are eloquent and incisive...

Monday - Comment - Like - Share

Anders Norgaard, Kubke, Björn Brembs and 5 other people liked this

Bora Zivkovic

ScienceOnline09 - an interview with @CameronNeylon: http://scienceblogs.com/clock... #scio10

Monday from Twitter - Comment - Like - Share

Jean-Claude Bradley, Cameron Neylon, Martin Fenner and Rafael Sidi liked this

Next Generation Science

Focusing on Science via FriendFeed [NGS] - http://www.nextgenerationscience.com/next-ge...

December 26 from Next Generation Science - Comment - Like - Share

Jean-Claude Bradley, Steve Koch, Graham Steel and Cameron Neylon liked this

Michael Nielsen

Installing Etherpad | Pauleira! - http://pauleira.com/13...

December 24 from delicious - Comment - Like - Share

Dan Hagon, Cameron Neylon, Tom Morris and 2 other people liked this

Duncan Hull to Duncan's feed, The Life Scientists, Semantic Web for Health Care and Life Sciences IG

The Semantic Biochemical Journal experiment « O'Really? - http://duncan.hull.name/2009...

December 10 from Bookmarklet - Comment - Like - Share

Mickey Schafer, Hope Leman, joergkurtwegner and 19 other people liked this

"There is an interesting review [1] (and special issue) in the Biochemical Journal today, published by Portland Press Ltd. It provides (quote) “a whirlwind tour of recent projects to transform scholarly publishing paradigms, culminating in Utopia (http://www.getutopia.com) and the Semantic Biochemical Journal experiment”. Here is a quick outline of the publishing projects the review describes and discusses: Blogs for biomedical science Biomedical Ontologies – OBO etc Project Prospect and the Royal Society of Chemistry The Chemspider Journal of Chemistry The FEBS Letters experiment PubMedCentral and BioLit [2] Public Library of Science (PLoS) Neglected Tropical Diseases (NTD) [3] The Elsevier Grand Challenge [4] Liquid Publications The PDF debate: Is PDF a hamburger? Or can we build more useful applications on top of it? The Semantic Biochemical Journal project with Utopia Documents [5] The review asks what advances these projects have made and what obstacles to progress still exist.... more... - Duncan Hull from Bookmarklet

22 more comments

Am I missing something here? I only seem to see a few popups when mousing over references? - Cameron Neylon

Interesting though getting started wasn't entirely transparent. Figs are interactive (pink background and menu) so, for example, data from Fig 9 can be replotted. Tended to spawn popups at an alarming rate. Fig. 13e appeared unable to load into popup. - Peter Miller

@Cameron, you need to download the Utopia client to get the full effect http://www.getutopia.com the animations are embedded in the PDFs and viewable within the client. It's not a browser based thing (yet). - Duncan Hull

Done that, looking at both the paper online in enhanced version and pdf I'm not seeing any visual cues or anything that take me anywhere much. Do I need to have the utopia client running as well? Ok you need to open the pdf in Utopia. That's really not immediately obvious I have to say, particularly with the "enhanced online version" getting billing front and centre. Ok I could have read the instructions but its only the mention that Utopia is a "pdf reader" that tells you what to do. Could be clearer. - Cameron Neylon

Have to say that the idea of a semantically enhanced pdf I have to download and open up in a particular viewer seems to be somewhat missing the point :-) - Cameron Neylon

Also seems odd that the enhanced online version doesn't at least include the links that are in the enhanced pdf - Cameron Neylon

@Cameron I see your point, I'd like to see a more web friendly version but there are some limits to what you can do in a web browser (especially when it comes to sequence alignment and molecular visualisation) - Duncan Hull

Yes, and that is all fair enough - you need to start somewhere but you'd think the links could be translated across pretty easily (e.g. Caspase-3 in paper 1, fig-1 legend is linked in the PDF to a wikipedia entry, why not in the online version?). Bring on HTML5 is what I say :-) - Cameron Neylon

@Cameron ... and yes, its an "experiment" too (normaly caveats apply!). The thing to look for is the little Utopia Documents icon embedded in the text once you've opened up an article (e.g. the review) in Utopia documents. Thanks for the rapid feedback... - Duncan Hull

Yep, found it eventually. I'd suggest changing the instructions to be much more explicit. i.e. Download Utopia, then download pdf, then open in Utopia. Most people will have pdfs set to autoload in something else so its not an obvious path - particularly to people used to plugins and overlays. Heh, next quetions can I leave a comment on the journal article to suggest this....mmmm.....that would be a "no" then... ;-) - Cameron Neylon

Dear Santa, Please can you provide Utopia for Ubuntu/Debian/Linux. Thanks :) - Allyson Lister

I just skimmed it initially - didn't note the requirement for this odd piece of software. Puts paid to it for me, I'm afraid. - Neil Saunders

From Philip McDermott: "ubuntu version in the works but just slightly delayed for launch. I'd have thought it'll be available next week sometime" - Allyson Lister

The idea of a specialized PDF reader for this means it's just a proof of concept at this stage. I'll mention it to the Mendeley people and see if they might like to incorporate some of this into their internal PDF reader. - Mr. Gunn

@Mr. Gunn thanks... - Duncan Hull

@Mr. Gunn thanks. Be interesting so know what they think of it, feel free to put them in touch with us :o) - Philip McDermott

I think that the initial confusion of PPLs website has confused a lot of web-oriented users. Try grabbing the app, the paper, and working through it, and you should get a feel for what we're trying to do. We're not saying web-based is bad, it's just that this is a little different. - Philip McDermott

@Philip see also commentary here http://digitalcuration.blogspot.com/2009... - Duncan Hull

As I understand it the PDF reader software is just an initial client for the backend which lets you annotate whatever - and from where all the annotations are fetched. If (when?) it gets opened up you could extend the existing client to read other files, write your own client, write a Firefox plugin, whatever... - Euan

@Euan yes that's right (and you put it much better than me). As for opening it up, you'd have to ask the Utopia team... it would make a lot of sense. - Duncan Hull

I like the concept of the Utopia reader. But the integration of references could have been done better. Why not use DOIs instead of linking to a Google Scholar search? - Martin Fenner

Dear Santa, like @Allyson I really hope your reindeer's can still pull the Linux version, too. - joergkurtwegner

Besides, how does it compare to the interactive ICM in PLoS ? http://ff.im/acHs9 - joergkurtwegner

Martin Fenner

Somehow missed that. RT @gbilder: Yay!! Official site for new Author Identity initiative (ORCID) is up. http://science.thomsonreuters.com/orcid... #orcid

December 26 from Twitter - Comment - Like - Share

Yaroslav Nikolaev, suelibrarian, Richard Akerman and 2 other people liked this

How can regular scientists participate in the ORCID initiative? Cameron had created a "Unique Identifiers for Researchers" LinkedIn group. Should the discussion happen there? - Martin Fenner

3 more comments

mmm that's still the thomson-reuters branded site. Would be much happier if this had its own domain name. Not that its a major problem but it shows a disturbing lack of awareness of some of the issues people have around identifiers... - Cameron Neylon

http://www.orcid.org exists, but currently still redirects to the Thomson Reuters site. - Martin Fenner

Yep and that's almost precisely my concern - redirects don't look good. Redirects to an organization that many people would feel uncomfortable with controlling their identity looks a lot worse. I like a lot of what they've done with ResearcherID but no way is my identity as a researcher going to sit on TR servers. - Cameron Neylon

@Cameron... I agree that the system must be open, with the option of alternative providers... - Egon Willighagen

Deepak Singh

Peer to Patent Australia recruits volunteer prior art searchers - http://radar.oreilly.com/2009...

December 24 from Google Reader - Comment - Like - Share

Bill Hooker and Cameron Neylon liked this

Rafael Sidi

"The Internet devalues everything it touches."http://www.siliconvalleywatcher.com/mt...

December 24 - Comment - Like - Share

Steve Koch and Cameron Neylon liked this

Jonathan Eisen

Story Behind the Nature Paper on 'A phylogeny driven genomic encyclopedia of bacteria & archaea' #genomics #evolution - http://phylogenomics.blogspot.com/2009...

December 24 from The Tree of Life - Comment - Like - Share

rowlikeagirl, Björn Brembs, Martin Fenner and 2 other people liked this

The Life Scientists: Jon

The Impactometer™ - http://www.lrb.co.uk/blog...

December 24 - Comment - Like - Share

Mickey Schafer, Dave Lunt, Björn Brembs and Cameron Neylon liked this

6. On startup the Impactometer™ will consequently first calculate its own Impact™. Our engineers estimate the Research Impact Projection for the Impactometer™ will be in the order of 14.93 gigapacts™.[2] - Jon

Rajarshi Guha

UPDATED: Copernicus Grades Cameron On The Science of AVATAR!! - http://www.aintitcool.com/node...

December 24 from Bookmarklet - Comment - Like - Share

Cameron Neylon liked this

Matthew Todd to Matthew's feed, Organic Chemists

Harsh Reaction to Chemistry Claims Cast Doubt on Reactome Paper : ScienceInsider - http://blogs.sciencemag.org/science...

December 24 from Bookmarklet - Comment - Like - Share

Jean-Claude Bradley, Steve Koch, Neil Saunders and Cameron Neylon liked this

Issues with peer review here, but it sounds like open data might have helped. "In private chats and online postings, chemists began expressing skepticism about the reactome array as soon as the article describing it was published, noting several significant errors in the initial figure depicting its creation. Some also questioned how a relatively unknown group could have synthesized so many complex compounds. The dismay grew when supplementary online material providing further information on the synthesized compounds wasn’t available as soon as promised. “We failed to put it in on time. The data is quite voluminous,” says co-corresponding author Peter Golyshin of Bangor University in Wales, a microbiologist whose team provided bacterial samples analyzed by Ferrer’s lab." - Matthew Todd from Bookmarklet

Maybe we should do a round-up of high profile peer review "failures" from this year? Between this, hydride oxidation and the withdrawn crystal structures its not been a good year really... - Cameron Neylon

Yes, on that note see http://www.coronene.com/blog... - Matthew Todd

Matthew Todd

Official Google Blog: The meaning of open - http://googleblog.blogspot.com/2009...

December 24 from Bookmarklet - Comment - Like - Share

Cameron Neylon liked this

File under "must read later unless Cameron does first." - Matthew Todd from Bookmarklet

I'm reading it - not sure how soon I'll have something useful to add though - brain has gone into terminal end of year decline... - Cameron Neylon

Ok. Brief response - a lot of it is motherhood and apple pie and it would be nice to see a clearer line drawn between where they take the decision not to open source but if that is really the tenor of inside communications and Googlers take this kind of thing seriously (and the contacts I have had with various people within Google all suggest that this is the case) then it is very... more... - Cameron Neylon

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

Andrew Su

Abstract on the Gene Wiki was just accepted for an oral presentation at AMIA Summit on Translational Bioinformatics in March -- http://summit2010.amia.org/

December 23 - Comment - Like - Share

Cameron Neylon and Deepak Singh liked this

The Life Scientists: Neil Saunders

Life Scientists 2009 summary - http://nsaunders.wordpress.com/2009....

December 23 - Comment - Like - Share

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

14 more comments

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

Mickey Schafer to Mickey's feed, Science 2.0

Question about CC declaration and reader-experience -- I originally placed the CC declaration in footer, but realized reader would have to scroll to see it...

December 22 - Comment - Like - Share

Mike Chelen, Cameron Neylon, Itachi and OpenSci Info liked this

Is it better to have it part of side nav bar, then? Is there an etiquette for this? Thanks for help! - Mickey Schafer

5 more comments

Well, WordPress templates normally put it in the footer--so as a reader (and editor who frequently reuses posts with CC permissions), I'm used to looking there first. But that's just me. - Walt Crawford

Thanks, Walt! My current compromise is to have it both ways -- the CC image is part of 3 images stacked in the left side bar in a section headed "Attribution Info" (includes univ, academic unit, then CC) -- the sentence declaration is in the footer. - Mickey Schafer

Okay, another question -- does the CC declaration on the web page cover everything -- text, html, CSS -- or does each component have to be covered separately? My guess is that someone might want to use the text or web page wholesale...can't imagine that the CSS would be that big of a deal, but I'm curious... - Mickey Schafer

think it is taken to mean original content, to which the author would hold the copyright. most websites and blogs use platforms like wordpress whose code is released under its own license, while a selected license would apply to user-generated material - Mike Chelen

IANAL but if someone took any part of your site and used it reasonably under the terms of the licence I think you'd struggle to make any claim against them unless you were very clear and very explicit about where it didn't apply. I try to make mine as prominent as possible to people can find it easily. - Cameron Neylon

What Cam said -- I put my CCZero with my pic, email, RSS and "about" links at the top (right), which is where I'm used to looking for that kind of info on a blog. I also try to make sure all of that is visible without scrolling when the page first loads. - Bill Hooker

Vanessa Fox

This is awesome. RT @brady: Just found someone to help with Ignite Antartica! Looks like we'll have Global Ignite Week on 7 continents.

December 23 from Twitter - Comment - Like - Share

Cameron Neylon, Micah Wittman and Deepak Singh liked this

Cameron Neylon › Likes