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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-...)

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

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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

Opensource Obscure to Opensource's feed, Second Life

Second Life Wave Users Meet-Up - 11AM SLT Saturday, Dec 19th - New Berlin sim - http://instructionalalchemy.com/blog...

Friday from Bookmarklet - Comment - Like - Share

LiamGunes and Peter Miller liked this

"Who: Second Life developers who are also Google Wave users -- What: Developers Discussion -- Where: Free University of Berlin -- When: 11AM SLT Saturday, Dec 19th -- Why: To discuss the integration of SL applications and XMPP -- SLurl: http://slurl.com/secondl... -- Join programmers and content creators to discuss how wave technology (XMPP) might be integrated with SL applications. What would this look like? How could it improve the SL experience?" - Opensource Obscure from Bookmarklet

If you're using or are interested in Google Wave, a SL in-world group exists: "Wavers in Second Life (Google Wave)" - Opensource Obscure

12 people right now - come here: http://slurl.com/secondl... - Opensource Obscure

Lars Juhl Jensen

Bioinformatics: SNPs while you wait - http://www.nature.com/doifind...

Friday from Google Reader - Comment - Like - Share

Peter Miller and Pierre Lindenbaum 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

Bill Anderson, Nakao M., Konrad Förstner and 15 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

19 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

Graham Steel

Right, It's that time of the month again... Tonight I'll be making 4x chicken tikka garlic garam masala and 4x extra hot chicken balti w/green peppers and cashew nuts.

December 12 - Comment - Like - Share

Peter Miller, Rajarshi Guha and Cameron Neylon liked this

Thinking I best get on with the roast duck which is downstairs. Ought to be writing a talk but struggling to get started... - Cameron Neylon

9 more comments

I need to visit you guys one day - Rajarshi Guha

Life is full of priorities, innit.... Mine now is get the beers in and doing a remix of http://mcblawg.blogspot.com/2009... (can't be arsed blogging it this time) - Graham Steel

Did someone say duck? http://www.youtube.com/watch... <ducks> - Graham Steel

Yum ... Graham, by any chance do you make those in a non-extra hot flavour? - Deepak Singh

That could be arranged, Deepak ;-) I do lower and raise the "heat content" depending on how I'm feeling. Might even DARE to go for a korma/chick-pea batch next time around..... - Graham Steel

Good ... some us can't handle the heat quite as well - Deepak Singh from IM

Rajarshi (and anyone else) You are more than welcome to drop by anytime you're in the area :-) - Cameron Neylon

+++UPDATE+++ 1) As Cam says, drop by anytime.... 2) Having had one of the latter curries for lunch at work today, what I thought was a chunk of red (bell) pepper was a reconstituated whole red hot chilli pepper. A near death experience and I for one am taking Deepak's earlier advice ;-) Unrelated question. Do you remove curry leaves before eating a curry or leave 'em in but not eat, or indeed eat?. I dunno ! - Graham Steel

Graham, I usually leave them in, but don't eat them, but that's me - Deepak Singh

Thanks, Deepak. That is indeed what I did... I'm more attunded to cooking Chinese rather than Indian cuisine so am always grateful for such advice :) - Graham Steel

Lars Juhl Jensen

Kinase mutations in human disease: interpreting genotype–phenotype relationships - http://dx.doi.org/10...

Friday from Google Reader - Comment - Like - Share

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Robin Ashford

Teambuilding in Second Life - http://www.youtube.com/watch...

Thursday from YouTube favorites - Comment - Like - Share

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Hope Leman

Health 2.0, Personal Genomics and Open Science: A Talk with Shirley Wu of 23andMe http://significantscience.com/2009... Thank you, Shirley, for a nice chat!

Thursday from Twitter - Comment - Like - Share

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Björn Brembs

Embedding 3D models of biological specimens in PDF publications - http://www.citeulike.org/user...

Wednesday from CiteULike: brembs's library - Comment - Like - Share

Dan Hagon, Kubke, Mike Chelen and 5 other people liked this

Microscopy Research and Technique, Vol. 71, No. 11. (2008), pp. 778-786. By providing two examples, the option for embedding 3D models in electronic versions of life science publications is presented. These examples, presumably representing the first such models published, are developmental stages of an evertebrate (Patella caerulea, Mollusca) and a vertebrate species (Psetta maxima, Teleostei) obtained from histological section series reconstruction processed with the software package Amira. These surface rendering models are particularly suitable for a PDF file because they can easily be transformed to a file format required and components may be conveniently combined and hierarchically arranged. All methodological steps starting from specimen preparation until embedding of resulting models in PDF files with emphasis on conversion of Amira data to the appropriate 3D file format are explained. Usability of 3D models in PDF documents is exemplified and advantages over 2D illustrations... - Björn Brembs

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Awesome 3D models, rotatable, zoomable, everything within a PDF with no extra plug-ins! Amazing! - Björn Brembs

I think they should have mentioned some Open Source alternatives to Amira/Adobe, my favourites being http://rsbweb.nih.gov/ij/ and http://www.ctan.org/tex-arc... . For the fossil part, see also http://www.virtualpalaeo.org/ (summary in http://newsletter.palass-pubs.org/pdf... ). - Daniel Mietchen

+1 Björn - this is a most impressive piece of work !! @Daniel, I'll check those links out tomorrow. - Graham Steel

Now I need to find out how to get the 3D model of our experimental setup into our PDFs! - Björn Brembs

Daniel: how is imagej used to embed 3d models? - Mike Chelen

imagej produces the 3D models, animate the embedding. - Daniel Mietchen

That is a great link Bjorn. My student has been producing similar models of brain/brain regions that are extremely useful since one can rotate the brain, remove regions, or "slice" it at different angles (great when trying to interpret histology and also to calculate stereotaxic approaches for electrophysiology). But it never occured to me he could publish the dynamic pdf. - Kubke

Does anyone know if Osirix can do the pdf trick? http://www.osirix-viewer.com/index... - Kubke

Opensource Obscure

#Twitter feature request: "Let this user DM me even if I'm not following her" option. /cc @twitter

Wednesday from Twitter - Comment - Like - Share

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Opensource Obscure

@yourtechsupport I use Grid URL Persister by @lkalif to update my http scripts: http://gridurl.appspot.com #secondlife #LSL

Wednesday from Twitter - Comment - Like - Share

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Andrew Su to Andrew's feed, The Life Scientists

I'm getting frequent 503 errors on NCBI's eutils (retrieving PubMed entries). Anyone else notice that? Or am I getting throttled because I'm missing some usage limits?

Tuesday - Comment - Like - Share

Mike Chelen and Peter Miller liked this

There are some usage limits, how hard are you hitting the server? - Paulo Nuin

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in my few automated runs, I've put in at least sleep(1), now sleep(5). But I'm getting it just from debugging my web app too (i.e., hitting refresh after a code change). Seems to have gotten worse later in the day... - Andrew Su

I've seen various errors using NCBI in the last couple of days (e.g. 404s and 502s using GEOquery via R). It seems better at certain times of day. Suspect general flakiness in their servers. - Neil Saunders

bummer, now I can barely get a good request to come back.... e.g., http://eutils.ncbi.nlm.nih.gov/entrez... must be all those Australians waking up and hitting NCBI... - Andrew Su

Sometimes they also block your IP for some amount of time if you tried to access their servers constantly. - Paulo Nuin

I've not been hitting the server hard - this has been happening on my first GEOquery call of the day, but then working a few minutes later. - Neil Saunders

any note on where I can find their usage guidelines? this search (http://www.google.com/search...) and variants didn't turn anything up... - Andrew Su

This is quite old but you get some ideas http://osdir.com/ml... - Paulo Nuin

Very helpful, thanks... Interesting though, since I'm running my stuff through Google App Engine, have I effectively blocked all other GAE users too? (Or, perhaps there are other eutils-consuming services there and we are collectively getting blocked...) - Andrew Su

Even manual queries (through links provided by HubMed rss feeds) have been causing errors about half of the time for the past few days for me. - Daniel Mietchen

you may want to subscribe to utilities-announce@ncbi.nlm.nih.gov and check out http://www.ncbi.nlm.nih.gov/mailman... - Mark A Jensen

Thanks Mark, good idea. (But now having done it, why does NCBI restrict viewing of the archives to only subscribers? Especially when there are only 3-4 email per year? grumble grumble...) Anyway, it did help highlight this section (http://eutils.ncbi.nlm.nih.gov/entrez...), which says "Run retrieval scripts on weekends or between 9 pm and 5 am Eastern Time weekdays for any series of more than 100 requests..." - Andrew Su

(solidarity with your grumble-grumble!) - Mark A Jensen

fyi, I emailed their help desk last night, they replied today that they were "having issues" yesterday that was probably the root cause. Sure enough, things are running much smoother today... - Andrew Su

Frank

Journal 'OMICS' recommends MIBBI - http://www.biosharing.org/2009...

Wednesday from Google Reader - Comment - Like - Share

Peter Miller liked this

...but the doi in the snippet doesn't resolve...? Oh the irony :-) - Cameron Neylon

Opensource Obscure

Do you want people to make photos&movies in your SL region? Add it to Machinima Friendly Sims http://wiki.secondlife.com/wiki... - or tell me & I'll do it

Wednesday from Twitter - Comment - Like - Share

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Cameron Neylon

Video Friday: Science 2.0: The Design Science of Collaboration - http://www.elementlist.com/element...

Wednesday from Google Reader - Comment - Like - Share

Jan Schmirmund, Peter Miller, Michael R. Bernstein and 3 other people liked this

From about 0:35:00 onwards discussion of "Trajectory of Participation" and "de-lurking". The novice begins through "Legitimate peripheral participation" and eventually becomes a leader. Trifurcation: 1% of the people do 20-30% of the effort with a very long tail. - Dan Hagon

Opensource Obscure to Opensource's feed, 2024

Future Interfaces: Gestures, Light and the BiDi Screen - http://www.readwriteweb.com/readwri...

Wednesday from Bookmarklet - Comment - Like - Share

Peter Miller liked this

"MIT's bi-directional display interface (BiDi) screen is capable of capturing both touch and off-screen gestures through the use of embedded optical sensors" - Opensource Obscure from Bookmarklet

According to the project team, "The BiDi Screen uses a sensor layer, separated a small distance from a normal LCD display. A mask image is then displayed on the LCD. When the bare sensor layer views the world through the mask, information about the distance to objects in front of the screen can be captured and decoded by a computer." - Opensource Obscure

Jon Udell

Computational Thinking - http://www.slideshare.net/judell...

Wednesday from delicious - Comment - Like - Share

Peter Miller, Cameron Neylon and Deepak Singh liked this

Presentation at UCEA 2009 - Jon Udell

Daniel Lemire

versioned web-based text documents (via @hjarche) - http://writeboard.com/

Tuesday from delicious - Comment - Like - Share

Peter Miller and Claudia Koltzenburg liked this

Seems to provide RSS feeds for notification of changes in the document - a feature long requested for Etherpad. - Daniel Mietchen

Robin Ashford

Prediction (a first)-Seth Godin's free ebook "What Matters Now" http://sethgodin.typepad.com/seths_b... will become twitter trending topic

Tuesday from Twitter - Comment - Like - Share

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Andrew Lang

Google Wave notifier extension for Google Chrome browser: http://download.cnet.com/Google-...

Tuesday - Comment - Like - Share

Jean-Claude Bradley, Peter Miller, Neil Saunders and Cameron Neylon liked this

Here too: https://chrome.google.com/extensi... - Andrew Lang

Seems to work, more or less. Probably useful to have a notifier - there's not much else directing my attention to the wave client just now :-) - Neil Saunders

Robin Ashford

8 of 10 students want universities to revamp traditional learning environments (& use virtual worlds) http://sphauth.asiaone.com/amserve...

December 15 from Twitter - Comment - Like - Share

Peter Miller liked this

Lars Juhl Jensen

The sequence and de novo assembly of the giant panda genome - http://www.nature.com/nature...

Tuesday from Google Reader - Comment - Like - Share

Peter Miller liked this

Cameron Neylon

In which priorities clash - http://network.nature.com/people...

December 15 from Google Reader - Comment - Like - Share

Matthew Todd, Peter Miller, Steve Koch and Björn Brembs liked this

Good post on the asymmetry of risk and reward for the researcher vs the PI in making things open. - Cameron Neylon

Michael Nielsen

The Great Beyond: Flu database row escalates - http://blogs.nature.com/news...

December 14 from delicious - Comment - Like - Share

Peter Miller liked this

Remarkable wrangling over databases containing genetic information about influenza. - Michael Nielsen

I'm on a panel with Ilaria Capua in a few weeks time. This could make it rather interesting... - Cameron Neylon

Michael Barton to Michael's feed, Ruby for Bioinformatics, The Life Scientists

Are there any existing solutions for creating a generic DNA sequence database with a website front end? - http://stackoverflow.com/questio...

December 11 - Comment - Like - Share

Mike Chelen, Endre Sebestyen, george and 7 other people liked this

I was thinking of creating my own as a Ruby on Rails engine to hook into the lab's existing site. I don't want to reinvent the wheel though. - Michael Barton

9 more comments

instead of implementing your blast search on the server side, why about creating a web services to search and retrieve the sequences and then, people can submit it to whatever they want (taverna...) - Pierre Lindenbaum

Like create a web service, then wrap the webservice API in a website front end? - Michael Barton

Your web site would propose a set of web services: just like the NCBI (e-utils). Then people do whatever they want with your data. But you can also write with some interactive HTML forms. I like this idea of "generic DNA sequence database". - Pierre Lindenbaum

That's a good idea. It's what Neil was talking about on his blog this morning, about having a good API to bioinformatics web services. - Michael Barton

BioMart? - Paulo Nuin

I like the idea of a simple, generic database with web front-end that supports storing structured data, versioning it, searching it, and plugging in analysis tools (which might run local or remote via whatever API). - Eric Jain

Eric ... wouldn't we all. Doesn't happen too often though - Deepak Singh

@Paulo BioMart looks like a good option. GMOD was suggested in the answers on stack overflow. I think these would both have good APIs. - Michael Barton

There's several GMOD components which may help here, lots of wheels so probably no need to reinvent any. See overview at http://gmod.org/wiki/Overview, more specifically a couple of relevant bits are Tripal (Drupal front end to a Chado db http://gmod.org/wiki/Tripal), and GMODweb (http://gmod.org/wiki/GMODWeb) - 'Mummi' Thorisson

we had started on a similar venture way back and using the Gmod tools and a rails frontend. http://rubyforge.org/project... - george

AJCann to AJCann's feed, Future of Education

Classroom rewards 'do not work work' - http://www.telegraph.co.uk/educati...

November 13 from Bookmarklet - Comment - Like - Share

Jo Young, Peter Miller, beatrice cherry and 2 other people liked this

Reward schemes reduce intrinsic motivation. - AJCann from Bookmarklet

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Curious -- how many children are born with "intrinsic" motivation? Or is this something that is environmental? - Mickey Schafer

Intrinsic versus extrinsic. - AJCann

yes, learning can be both intrinsically and extrinsically motivated--and I believe this is true for everyone with variation depending on what has to be learned. But I've also encountered the terms as personality dimensions, and it isn't clear in the article which one was being used. - Mickey Schafer

Yesterday, I overhead a very interesting conversation during which a school counselor was advising a parent with a failing child to remove all things of value to the girl and make her earn it back by achieving passing grades. This included _everything_ the girl liked from clothes and shoes to electronics to time with friends. She quipped after that she frequently has to teach parents how to be parents since today's generation was ill-informed. I found her horrifying. - Mickey Schafer

@Mickey: that sounds like a recipe for leaving home at 16 and never going back to me. Horrifying indeed. - Bill Hooker

There is some truth to this - when I have students play games for prizes, the reward (usually a chemistry book) is not the central motivation but it does make it more fun for the very best students to compete a bit. Similarly, with our ONSChallenge where students do labwork, the cash prize is small enough to not be the primary motivation but again it makes things more interesting. - Jean-Claude Bradley

Jean-Claude, I agree that external motivation is quite useful. Nor does it have to be a big deal! I have premed students who once commented with enthusiasm that they would like get smiley stickers on their papers -- I was amazed. Didn't invest in stickers, but have thought about why this would be the case. In writing, the work is very personal and I get to see so many different sorts of... more... - Mickey Schafer

I also suspect we over-romanticize the intrinsic nature of learning in children. Yes, they do like learning, and they are curious, and the natural process of hypothesizing and testing that occurs can be rewarding (to a normal child). But this isn't the same process being used in school. And getting a kid to study for something like a spelling test in the first grade has very little to... more... - Mickey Schafer

Mickey good points. I experimented with different rewards and didn't find that much difference between a $5 reward and a video ipod - there is a type of student that responds to this type of competition so why not make their experience more enjoyable even if not all students respond? - Jean-Claude Bradley

Doesn't this relate to Dan Pink's TED talk where tasks requiring significant thought were indeed adversely affected by a reward system? - Peter Miller

That's a good point, Peter. And it gets at a real conflict in public education. Tasks that require significant thought are often intrinsically rewarding; James Paul Gee makes this point about computer games that are really quite complex, require hours of play to finish, and which kids readily engage in. In the public sphere, especially a test-driven one like the U.S., such tasks don't... more... - Mickey Schafer

People, remember that we need to be attracting more people to the benefits and rewards of making the effort of deep thinking and problem solving. We could and should considering using a reward system to draw young people (and by 'young', I mean from pre-school to college) into situations where they need to challenge themselves by thinking deeply. When they are at that place, we can... more... - Jason Miller

Very interesting point, Jason, but figuring out how to draw a young child into complex activity, especially in a public school setting, is damned difficult. My kids are in a science/tech magnet precisely b/c the educational tasks are deeper and often collaborative. This particular program also screens more for motivation to learn than sheer "IQ" -- the academic requirements for selection are "B" grades and above, but the clincher is whether the kid wants to work. - Mickey Schafer

And while I agree that drawing a greater population in is really important, my observations after a year of volunteering is an unpleasant truth: kids are not equally talented. They are not all cut out for complex work whether b/c of personality or ability. I would argue that bribing the talented is a crucial undertaking since many of those will not pursue careers in STEM b/c those jobs... more... - Mickey Schafer

Mickey - I agree with what you're saying. One think I'm sensitive to (and it sounds like you are, too) is where and how we look for talent. If we're looking for talent in white-bread communities, then we're doing something wrong. If we're looking for talent in _all_ communities, especially in those that have historically been underrepresented in STEM, then we're doing something right. This will bring new challenges and frustrations, but that is a Good Thing. Don't you think? - Jason Miller

Absolutely -- I spend summers working with under-represented populations and have been puzzling for years about how to get these students more connected to all the possibilities out there. The difficulty that most vexes me, and which I've never found/read/overheard a way to counter is the cultural differences. And this isn't just about color: it's more a factor of education and SES. As... more... - Mickey Schafer

Cameron Neylon

What should social software for science look like? - http://blog.openwetware.org/science...

December 9 from Science in the open - Comment - Like - Share

Ruchira S. Datta, Meryn Stol, suelibrarian and 32 other people liked this

FF doesn't meet all your requirements but it does seem to work well compared to the specialized services - at least in some fields - Jean-Claude Bradley

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Well I guess that's not surprising given my biases - at some level I'm more interested in what people think I've missed than my own predjudices though. FWIW I think a clever combination of DropBox, FriendFeed and some of the elements from StackOverflow, with perhaps a bit of the coordination ability of posterous would go very close to the mark. Still need better network and filter management tools though - somehow they need more configurability but less configuration... - Cameron Neylon

OpenWetWare is looking to make a major overhaul in the next couple months, and has a bit over 1 year of funding left. I feel like this is an opportunity to at least try to do some of the things that most people think are necessary for SS4S. Not perfect, but better so that we'd have a better idea of what is really needed. I think the time frame (now; already funded) makes "not perfect" a... more... - Steve Koch

I really like what you said in point 10. It's something that I've seen far too many scientists being cavalier about. Federation, open protocols and specifications, along with open source, are very important to science. - Christopher Granade

Might be worth seeing how far sourceforge meets your criteria. Certainly it's totally based around objects, i.e. software projects, and there are lots of high quality open source science projects whose code is hosted there. Although it has community/social networking tools I've personally never really used these and most visits I've had to sf have either been fleeting (to download... more... - Dan Hagon

Steve, absolutely we need to keep evolving with the resources available. OWW is a great place to do that. - Cameron Neylon

Dan, there was a conversation around using Github in a similar way some months ago and I think these things have a lot of potential as a back end. I think federation is important enough that you'd want to use a DVCS rather than SVN as a back end though. - Cameron Neylon

Sourceforge has several DVCS options in addition to svn these days. Although github is great I would be wary of anything that requires scientists to learn the intricacies of git. hg and bzr are much more friendly to non-developer types that don't need the full flexibility of git. I've had some success using them to collaboratively author LaTeX documents. - Matt Leifer

Matt, ok, I'm behind the times (nothing new there!). The intracies are less of an issue as this would only be a back end. No SS4S that any significant proportion of scientists use is going to look _anything_ like a code repository. To start with your average scientist is never going to touch a command line. If you're dealing in Latex you're already talking about a minority I'm afraid.... more... - Cameron Neylon

There are several wikis that use DVCS as a backend. This could be a starting point for developing the type of thing you are interested in. - Matt Leifer

LaTeX isn't the minority in whole areas of math, CS, physics....I guess that brings up the same old complaint: "science" is defined as all biomed, all the time. I'll try to come up with some more substantive comments though - Christina Pikas

Christina, didn't mean to say it should be excluded just that a non-command line system is non-negotiable so most online VCS aren't going to be good enough as a front end. Support for Word, Excel, video, images, XML and Latex are all non-negotiable characteristics of any such system. - Cameron Neylon

Matt, not sure that a wiki is the right starting point - the document model doesn't seem right to me, although I'm way behind on the most recent developments in Wikis so I may be out of date on that as well. What is in my head is a DVCS back end with APIs providing access from e.g document authoring systems, databases, publishers, whatever. A feed system that looks a bit like friendfeed... more... - Cameron Neylon

I wasn't suggesting actually using one of the wikis, just that they have already done a reasonable job of abstracting the version control functionality (in fact, some of them support more than on DVCS in this way) so there may be some things in the codebase that are useful. It is also an example of taking a command-line DVCS and giving it a more user friendly interface. In addition, if... more... - Matt Leifer

Ah good to know - which do you think are the best examples of these wikis? I should take a look. In any case at this stage I'm just throwing ideas out. Have no resource to actually a build anything at moment. - Cameron Neylon

Is there actually a need for social software for scientists? Or should scientists use and customize the existing social networking tools (FriendFeed, Facebook, LinkedIn, etc.)? - Martin Fenner

I'm beginning to think the main issue will be that business models for consumers services are incompatible with what researchers need. So yes, customise might be better than build but if we have to go down that route we may as well have a good idea of whats required. One person's customisation is another person's build. - Cameron Neylon

I'd be curious what you think of HubZero, Cameron. - D0r0th34

Depends a bit on server setup. For Mercurial I like Hatta, but it requires persistent python processes, i.e. no good for most shared hosts that only allow CGI. There is a list of RCS backed wikis here: http://hatta.sheep.art.pl/Similar projects - Matt Leifer

Cameron, I love and absolutely agree with the necessity of "scientific objects". If you lack those, then (as Martin points out) just use the general purpose sites. In that principle, I think there are some viable networks -- DVCS systems around scientific code, Mendeley around scientific publications, (eventually our BioGPS around genes). But I think we should be developing specific networks appealing to specific groups of researchers, rather than trying to serve the needs of all scientists... - Andrew Su

Andrew agreed, but if these are federated then they can all still talk to each other. I'm thinking more framework than site or single service. Ideally all of these things can be plugged in or wired up together...my concern with general purpose sites is primarily that they don't provide the level of trust and stability that we would expect for "research enterprise" - Cameron Neylon

Just one comment. There are protocols out there that allow different social networks to talk to each other. There are protocols out there that allow web resources to talk to each other. It's not really that hard if everyone supports some basic standards. RESTful API's, OAuth, OpeniD/Facebook Connect/Friend Connect, etc. IMO what's more important is that any sites we design have the... more... - Deepak Singh

@D only really had a chance to have a quick look. First impressions are that it is very slick but looks as though everything has to be on the inside - I don't see much mention of pulling stuff in and out. The multimedia talks are nice but why not pull them in from e.g. slideshare to pick an example. - Cameron Neylon

completely agreed, federation through standards... - Andrew Su

Twitter is far from perfect, but look at the infrastructure that has evolved around it e.g. 3rd party apps, services). You don't get that kind of traction around a social networking site just for scientists. Imagine what email or the WWW would look like if there were separate versions just for scientists. - Martin Fenner from iPhone

Absolutely but that actually means we can build something better, and as long as it hooks into Twitter (RSS/OAuth...Deepak's list basically) we get all the benefits and all of the functionality we want - as well as a way of drawing people in. Assuming this framework is any good of course. Imagine PubMed if it had been built for the consumer web (actually maybe not such a good example... more... - Cameron Neylon

Sort of responding to Deepak a few comments earlier. Something like a social network is useful for at least one reason: recruiting scientists who aren't ready for open science, or cannot communicate openly for one reason or another. So, a reasonably secure way of making data private and shared with a limited network is a good thing, I think. I think ultimately that will lead to much more open science (my own lab started out with a private wiki before doing ONS)... - Steve Koch

Steve, but does it have to be a social network per se, or a site for say sequencing geeks (I am looking at you SeqAnswers) with the appropriate features built in. Social networks don't have to be all in the open. Facebook is a social network. 90% of my communication on there is private and you should see how much of my Twitter usage is DM's - Deepak Singh

Deepak, I think I was just using terminology incorrectly. I was assuming Facebook = social networking. - Steve Koch

Jean-Claude Bradley

Project H.M., Phase I - http://scienceblogs.com/neuroph...

December 13 from Google Reader - Comment - Like - Share

Peter Miller and Daniel Mietchen liked this

It is ironic how the whole brain of a human being is made public - "like Google Earth for the brain" but making the NMR spectrum of a routine compound open data is controversial - Jean-Claude Bradley

Steve Koch

Steven J. Koch - http://www.scribd.com/doc...

December 13 from Scribd Feed for sjkoch4914 - Comment - Like - Share

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Cameron Neylon

December 12 from Flickr favorites - Comment - Like - Share

Peter Miller, Jo Young and Daniel Mietchen liked this

That Hype Cycle slide is great. - Chris Lasher

I'm thinking I'll use this one instead though: http://geekandpoke.typepad.com/geekand... - Cameron Neylon

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