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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

I just rephrased the critical section (lines 45-47). further brushing welcome. - Daniel Mietchen

That letter looks great! Kudos to all of you! - Kubke

Cameron Neylon to Cameron's feed, scienceapps, The Life Scientists

I'm going to do a round of looking at some of the Science Social Networking sites again. Is anyone active on ResearchGate, Epernicus etc. and interested in testing functionality?

November 20 - Comment - Like - Share

John Delacruz, Jack H. Pincus, Dan Hagon and 24 other people liked this

I'm interested in joining the testing. Need to agree on criteria for comparison before starting, though. - Daniel Mietchen

63 more comments

I'm willing to keep an open mind but so far FF surpasses these in terms of networking and ease of use. But if you want to experiment I have accounts in many of these and I would be willing to try. - Jean-Claude Bradley

I'm really just looking to make sure that things haven't moved on and improved significantly, particularly in the light of the NIH projects. - Cameron Neylon

I tend to migrate to social networking sites based on "pull" - virtually the only time I go on LinkedIn or Facebook is when I get an email alert to something relevant to my interests. I would assume that if there was anything really cool going on in these new sites I would get these alerts generated by actions by you and my other friends. - Jean-Claude Bradley

BTW Cameron - that is one of the issues I'm finding with Wave - I tend not to check it because I don't get alerts that there are updates - is there a way to get an email alert for Wave updates? - Jean-Claude Bradley

Yes, there is an email alerter. I'll add you and it to Wave... - Cameron Neylon

Agreed to the general point though - if there isn't a pull, I'm not going there really. And I think that is a big issue with Wave - people just aren't checking in. - Cameron Neylon

@Jean-Claude I don't think there's currently a way of doing this with the current interface without adding a robot but I saw there's a robot on the Haskell public wave which has similar support http://wave-xmpp.appspot.com/public... - Dan Hagon

I'd be interested in testing (I recently started looking over Epernicus for an article on NGS). Where is the email alerter for Google Wave? Currently, I'm using Waveboard (Mac), which alerts you when there's activity. However, it needs to be running in order to do so. - Walter Jessen

Just added you to a Wave with the email notifier Walter... - Cameron Neylon

New SNS from American Institute of Physics, got email invite today: http://www.aipuniphy.org/ - Andrew Lang

I have accounts on Epernicus, SciLink, Laboratree, and maybe could consider BenchFly a social networking site too, but like JC, I don't go to any sites besides FF and Twitter (and those are typically through 3rd-party apps), not even Facebook or LinkedIn, unless I get some alert. But I would be happy to see if anything's changed in those science-oriented sites I mentioned - Shirley Wu from twhirl

I do get alerts that new people have joined the organic chemistry group in Research Gate but there is no discussion and my questions have not been answered there by anyone so not much motivation to check in. - Jean-Claude Bradley

I have accounts at NN, Epernicus, BioCrowd and SciLink. I have begged for account deletion at the latter for months, to no avail and have not visited most of the others for as long as I can recall. So: active - no, interested - no. It's all FF/Twitter for me. - Neil Saunders

It's alright - this is a benefit of the doubt exercise - making sure that things haven't changed or that we've missed something. My brief look around yesterday suggested that nothing much has but I wanted to make sure I'm not missing something. - Cameron Neylon

What about the criteria for comparison other than some "pull" functionality (which they all seem to have, to different extents)? Does usability boil down to feed import/ export and (hierarchically) threaded conversations ordered by novelty and importance, as at FF? - Daniel Mietchen

When considering the usefulness of the individual platforms, perhaps discipline-specific ones should also be on the list? Besides http://polymathprojects.org/ (maths), these would include, for instance, http://openanthcoop.ning.com/ (anthropology), http://www.apecs.is/ (polar research), or this very life science group at http://friendfeed.com/the-lif.... - Daniel Mietchen

It would be worth doing a compare and contrast - also things like Math Overflow and even some of the chemistry blogs act more like community sites. Seems particularly apposite with respect to Pawel's blog post yesterday about the idea to set up a next generation sequencing community site. - Cameron Neylon

I have a ResearchGate account but don't actively use it. I currently do some FriendFeed, Nature Network (where my blog is hosted) and Google Wave, but mostly Twitter. - Martin Fenner

The last issue (November 23) of the German computer magazine c't has an article on social networking for scientists. They like ResearchGate and Mendeley, but also include ResearcherID, Scholarz (a German network), Nature Network, SciLink and Scientist Solutions: http://www.heise.de/ct... - Martin Fenner

That c't article (which shall come out in some OA fashion soon) may serve as guidance but I found the choice of networks therein rather arbitrary, and the comparison between sites was done on a more general level rather than on the basis of specific criteria. - Daniel Mietchen

The article makes two obvious omissions: a) no mention of CiteULike (or Connotea), b) no mention of the recent $12 Mio social networking NIH grant to U of Florida/Cornell University. There are some more things in it I don't like, so I wrote a letter to c't magazine. - Martin Fenner

Cameron, what criteria were you thinking of using? - Mr. Gunn

Key questions: a) What is the immediate impression on signing up? Is there a pull for people to come back? b) What functionality is being offered? Is it immediately available? How dependent is it on having a network in place? c) Funding model and stability d) User numbers, ideally active users and accounts, but whether we can get those is another question. Those aren't very objective criteria and they are built on my biases but nonetheless - Cameron Neylon

Sorry if this is slightly tangential to the discussion, but I was imagining a new kind of social network for publication of research results here: http://virtualchrisleonard.co.uk/blog... - Chris Leonard

Chris - when you talk about "credit" are you expecting tenure and promotion committees to count it or do you have some other system in mind? If you set something up I have content that might be suitable to play with. As for citability - in our last few papers we have used blog posts and wiki pages as references and have not had any problems with that - so I think the system is quite flexible and can accommodate the types of activities you are proposing. - Jean-Claude Bradley

I think Chris means system credit or karma. The idea as I understand it is somewhere between Friendfeed and Stack Overflow - Cameron Neylon

Thanks Cameron, yes, that's what I meant by 'credit' - however, by quantifying and metricising that credit, there is a possibility that one day tenure and promotion committees may want to use it as another measure of a scientists influence in a field. Apologies to Cameron for hijacking his thread. There is another discussion on this blog post here: http://friendfeed.com/chrisle... - Chris Leonard

That's fine, it's not my thread, it the communities thread :-) Pointers are good, they link up the information. - Cameron Neylon

Blog postings to replace (journal) papers and (in-depth) peer review a luxury that can only be acquired if paid for and to be replaced by blog comments instead? Weakening both readability and certification? That does not sound like a healthy idea. - Wobbler

Wobbler: why should blogs lack any aspect of peer review? the standard of any publication depends on how editorial powers are used - Mike Chelen

...and we already pay for peer review. It just isn't a cost transferred as actual cash. - Cameron Neylon

But blogs do not have any editorial powers? What advantage do blog postings have over (journal) papers? They lack format = lack of consistency = lack of efficiency = lack of scalability. Are you seriously suggesting that blogging/blog posts have the potential to replace journal publishing/ (journal) papers as the primary scholarly communication model/channel? Upgrading the traditional... more... - Wobbler

@Cameron: that's true, but now peer review is at least mandatory for the primary scholarly communication model i.e. scholarly publishing. Replacing that with something else and having peer review only on request/payment is a very different story. - Wobbler

Wobbler - there is a difference between requiring the peer review to be performed before making some information public and allowing it to take place after that. I do not see why the latter option would generally fare worse than the former. In fact, we already practice it here at FF, with numbers of likes and comments roughly indicating the popularity of a topic, while the quality has to be sought in the individual comments (and of course the source item that started the thread). - Daniel Mietchen

... it isn't a cost transferred BY YOU as actual cash. Yet. It should be, in my not-terribly-humble opinion, however, because the market disconnect in the current system has proven ridiculously unsustainable. Wobbler, some of my blog posts have had more measurable impact than anything I've ever written. Sure, it's a lightning-strike sort of thing, and most of my blog posts languish in... more... - D0r0th34

@Daniel: I'm not talking about post-"publication" peer review. That's still different from random blog commentary on blog posts. There's no evidence that what we're doing here isn't just a "niche" thing that works well because we're a niche. There's certainly no consistency in quality in our blog postings (well, at least not in mine :p ). Not to mention a lack of consistency in... more... - Wobbler

@D0r0th34: No, we should absolutely not ignore lighting strikes. But we should see them as lightning strikes and consider them to be an exception more than a rule and focus our attention on something that provides that level of quality more as a rule than an exception. Blogs as a complement to (journal) papers is great. But once you start to see it as a primary source, a replacement for... more... - Wobbler

We don't know about our OA bets. As for slow-and-steady, a well-run blog isn't? Lightning strikes aside, building a reputation and a readership is hardly an immediate thing. - D0r0th34

@D0r0th34: That's one more reason why blogging as the primary scholarly communication model is a broken idea. "Popularity" and "building a readership" will be important for blogs (and other post publication peer review models) to be visible/significant. But aren't we going after journals for using their JIF to attract peeps to read their stuff? How is "blog (poster) popularity" to get a... more... - Wobbler

I think the most important property of non peer-reviewed scientific communication is that the content be easily indexed and searchable. Relying on comments and rankings can be very misleading indicators for utility in long tail systems. For example we get over 100 searches a day for our solubility data via Google and Wikipedia but we have never had a comment or any type of feedback from the people who searched for and found information. - Jean-Claude Bradley

Shrug. System-gaming goes on everywhere; there are a number of studies of citation-impact gaming, if you look. Also, why is connectivity a bad thing? We are talking about scholarly *communication* after all, right? Restricting "what counts" only to what goes through the baroque serials-publishing process is IMO an extraordinarily blinkered and limiting view of how knowledge really advances. Sure, it's not easy to come up with more inclusive views -- but that doesn't mean it's not worthwhile. - D0r0th34

The problem is that I'm not sure we can talk about "gaming the system" rather than "an intrinsic part of the system that everybody will be forced to play or greatly risk invisibility" when it comes to blogs and other models relying on postpublication "peer review". PLoS ONE is, intentionally or not, already trying to stake their claim on an as large a readership/community as possible.... more... - Wobbler

@D0r0th34: And connectivity can be unfair if your serious/scientific works are getting more attention than others simply because you've managed to draw a bigger crowd through non serious/scientific stuff. On a slightly more personal note: for someone who occasionally complains about the (lack of) readability of (journal) articles, I had expected that you, of all people, would appreciate... more... - Wobbler

I have to say reading down this I am unsure of whether the complaints apply to blogs or journal articles. Consistent structure and copy editing would be nice but it is rare for both blogs and journal articles. Quality is an issue across the board. Going back to peer review - it's only mandatory for the author, refusal rates for reviewers are going through the roof and unless we acknowledge that cost the system will collapse sometime soon. - Cameron Neylon

@Cameron: Consistent structure and copy editing are rare for journal articles? They are? Not entirely sure about copyediting, but surely most, if not all, journal papers have a recognizable structure? And I don't think they're as rare or rarer than for blog postings. I also think the issue is with peer review, and not with the (journal) paper (format). As such, we should find ways to... more... - Wobbler

Of my recent papers, only one received close copy editing by anyone but me. And that was the Nature piece for which to be honest I would have been happier if the editor had got a co-credit. And formats are all over the place - maybe consistent for a single journal but that's not use to me. The costs of both peer review and publication are so high we need to find a way to lower them -... more... - Cameron Neylon

@Cameron: I'm not sure that's a convincing enough argument for me. Maybe your other papers were written clearly enough already? You're a prolific blogger/writer, Cameron. It's not weird to assume that your ability to communicate concepts clearly is higher than the average scholar. Maybe high enough to not warrant copyediting (in a lot of journals)? My impression of journals is that... more... - Wobbler

Well others can pitch in but perhaps a different anecdote. Until I started getting into arguments with Maxine Clarke I didn't even realise that journals might do copy editing. Nature and similar are very different beasts to the average of course. - Cameron Neylon

So, generally speaking, only the high profile/impact journals provide copyediting services? Hmm, that is definitely not what I expected. If you had to estimate the % of journals that provide copyediting services, what % would that be? The (top) 10% of all journals? - Wobbler

I have the same experience as Cameron - the only time my manuscript was copyedited was when I published in Nature - Jean-Claude Bradley

So far as I'm aware, no-one here wants to replace peer-reviewed journals entirely by blogs. Yet that seems to be what you're arguing against, Wobbler. For some functions, journals are a lot better than blogs. But for other functions, blogs are a lot better than journals. At the least, I really can't imagine how, say, DHJ Polymath or Galaxy Zoo or the Open Dinosaur Project or [fill in... more... - Michael Nielsen

Most of this is as a response to an FF comment by Chris Leonard on the 23th of November in this thread, who is arguing for exactly that. - Wobbler

Cameron, any progress on the roundup? Is there any information I can provide from Mendeley? - Mr. Gunn

Right - getting there slowly! Have set up a wiki page (ignore the state of the rest of the site I am working on it!) at http://wiki.cameronneylon.net/index... You should be able to login with openids, any problem give me a yell. I would suggest a week by week schedule to dive into and try and use a specific site, give it a good shot and then report as we go. I... more... - Cameron Neylon

Cameron, what do you mean by "stability" - things like a service being bought/shut down vs. server outages? What about one week to agree on parameters and sites to check? I added data portability. - Daniel Mietchen

I was thinking more of medium to long term financial stability - but technical stability is a good criterion in terms of functionality. Data portability is a good point! - Cameron Neylon

Cameron, I spoke with Drew Endy, Bill Flanagan, and a couple other PIs that use OpenWetWare (Maureen, Pam) last week about the future of OWW. There are two major issues (a) funding and (b) overhauling the platform. I think funding will work out, if we can figure out what is the best way to do (b). Bill and Drew have some good ideas at this point, but in my gut I think we're still not... more... - Steve Koch

I guess my easy question for everyone who's familiar with OWW: Do you think with the resources we have (one full-time excellent lead developer) we can transform OWW into a killer openscience resource for many more people going forward? One thought that keeps coming to me is that something could be (needs to be) done to tap into the energy of the user base. I.e., obsessed students who... more... - Steve Koch

Another thing that keeps coming into my head since the conference call last week: FriendFeed is quite possibly very similar to what many people need for OpenScience. As far as science goes, we generate information from all kinds of different sources (Machine-specific data; gel photos; microsoft word; evernote; scratch paper; blogging; etc.). This needs to be aggregated and shared in a... more... - Steve Koch

Oh, and to clarify a bit: I don't want to replace FriendFeed with OWW. I want to use the FriendFeed model as a starting point for the new OWW. As an OpenScienceAggregator / Networking tool. As others have pointed out, much of the value of friendfeed is that it's not limited to scientists generating data. - Steve Koch

Steve, that's a great way of asking the question. I'd go one step further and say how can we make it the framework in which we can integrate all the other things we do on other services. It's never going to be a no-brainer to move from what you use to something else - there is always the simple problem of the activation barrier to change - its a question of the balance. But my guess is... more... - Cameron Neylon

Cameron, I agree with you exactly: I don't want people to switch, and indeed I want to think "one level above." Do you think there's a real possibility for doing that? - Steve Koch

If we could coordinate a series of activities and get proper funding then yes. Quite a lot of interest in the pieces of this (including the grant I'm currently rushing to finish), Chris's ideas further up this thread, OWW obviously, Mendeley/Citeulike/Zotero. But coordination is the hard bit - and getting agreement that its what enough of us want. Do I think we have a clear idea of what... more... - Cameron Neylon

Should we include some discipline-specific ones or are we going for general-purpose only? - Daniel Mietchen

The Life Scientists: Rajarshi Guha

Does anybody have suggestions for project managment software - ideally, web based, would allow attachment of documents. The primary goal is to track status of screens (so steps like, assay design, optimization, full screen, followup). I don't need a hugely complex framework - but I also want to avoid writing it from scratch if I can.

November 24 - Comment - Like - Share

Jamie McQuay and Daniel Mietchen liked this

Open source is ideal, but I wouldn't ignore commercial either - Rajarshi Guha

15 more comments

BioData maybe? - Alejandro Montenegro

http://biodata.com might do the trick. @rubp says is designed to be lightweight and easy to use, and they have free accounts now, too. - Mr. Gunn

Thanks for the pointer. But I was looking for somethign that I could install locally but accessible by browser for collaborators - Rajarshi Guha

We use Unfuddle in our group. It was designed for software development, but you might be able to get it to do what you want, using tickets and milestones. - Ruchira S. Datta

Pretty happy with Basecamp. Yes, commercial, not open at all, but files can be hosted locally if needed. Main benefit: just about every bench scientists gets it right away, which wasn't the case with other solutions (RT, Bugzilla, ...) - Oliver Hofmann

I tried Trac for a while -http://trac.edgewall.org/, designed for source code but worked (kind of) for other purposes. Not very user- or admin-friendly, though. At the moment, I like the look of Redmine - http://www.redmine.org/, but haven't tried it out. Otherwise, a wiki/CMS? - Neil Saunders

@Oliver, yes, I've been looking at Basecamp and it does look quite good - Rajarshi Guha

@Neil, I've been trying to look at the Redmine demo, but Heroku was down. A wiki/CMS is useful, but the higher priority is the ability to keep track of the state of multiple, simultaneous projects. So the main priority is keeping track of steps/milestones - maybe associating a few docs with a given stage - Rajarshi Guha

Unfuddle allows you to attach files as well. - Ruchira S. Datta

@Ruchira - thanks for the pointer. This looks useful - Rajarshi Guha

Over the last 2 years we are using dotProject in the lab for research project management. It is very effective, simple, free and web based. Please have a look : http://www.dotproject.net/ - Khader Shameer

You might want to skip dotProject... they go 18+ months between minor releases, so getting updates takes forever. web2project is a public fork and we do quarterly releases with functionality and fixes. (core developer here) - Keith Casey

Hi, You should take a look at jtrac which is desinged on springs and it can server the purpose. It is a general issue tracking system but could be customized to your need by editing the lables. It allows attachment of files. I use it for my systems biology software development. It could be as well used for your need.. I guess so. By the way if you are looking at similar but more complex ones -- several commercial options exist JIRA is one among them and you avail academic discounts. hope this helps - pradeep

Keith, Thanks for your tweet about web2project. We have updated dotProject only twice in the last 2 years and it works fine with all the features. - Khader Shameer

@Khader - How is performance for you? We've done enough optimizations in web2project that you should see 50-100x improvement. No, I'm not kidding. Have you done a security audit of the code? The latest round of security patches came from our web2project work but they haven't made all the fixes yet. - Keith Casey

Keith : Thanks for the suggestion, we will try web2project. - Khader Shameer

Deepak Singh

Re: Academic software and infrastructure – AKA more ranting - http://mndoci.com/2009...

November 29 from Disqus - Comment - Like - Share

Jamie McQuay and Mike Chelen liked this

"Open source does not close avenues for commercialization. Most of the current models (and I've worked in those for a long time) do not really work. Well perhaps for a few individuals, but not for the quality of the code and the improvement of science. The reason is that almost none of the software by itself is worth that much in the first place, i.e. unique enough to be absolute must. Bioinformatics has done fine with very little closed source software (in fact, closed source has lost) and the places where money is paid is in areas such as data management, not algorithms. Pharma etc will pay for custom development and would rather be contributors to the open source world. Can you imagine if R were not open source? Would all of you be even talking that much about it? Would it be half as successful and it's actually broadly usable and has a lot of value." - Deepak Singh

'Mummi' Thorisson to 'Mummi''s feed, The Life Scientists

Fwd: The Climate Modeling Leak: Code and Data Generating Published Results Must be Open and Facilitate Reproducibility - http://blog.stodden.net/2009... (via http://friendfeed.com/cameron...)

December 1 - Comment - Like - Share

Steve Koch, Jean-Claude Bradley, Jamie McQuay and 2 other people liked this

Yeah, I think I heard about that. Isn't that what they call science? That whole thing where you observe, guess, experiment, speculate, experment again, until you can reproduce results consistently and then you tell someone else who does the same thing with your data? - Aaron Kendrick

So I've heard! :! - 'Mummi' Thorisson

No. science is where you do what you can get funded which absolutely does not include replication checking or audits. None of which generate nature papers - Cameron Neylon from Android

Bill Hooker to Bill's feed, Science 2.0

Internet Evolution - Mathew Ingram - Social Media Help Generate Science 2.0 - http://www.internetevolution.com/author...

November 30 from Bookmarklet - Comment - Like - Share

Jean-Claude Bradley, Jamie McQuay, Mr. Gunn and Daniel Mietchen liked this

Mentions several of the usual suspects. - Bill Hooker from Bookmarklet

Hilary to Hilary's feed, The Life Scientists, Science 2.0

Communicating Chemistry: http://www.nature.com/nchem... Nature Chemistry 1, 673 - 678 (2009)

November 23 - Comment - Like - Share

Jamie McQuay, Joe, Oliver Schuster and 11 other people liked this

By Theresa Velden and Carl Lagoze: "New web-based models of scholarly communication have made a significant impact in some scientific disciplines, but chemistry is not one of them. What has prevented the widespread adoption of these developments by chemists — and what are the prospects for adoption over time?" - Hilary

10 more comments

With a discussion of the role of open access, data sharing, electronic lab notebooks, preprint servers, and blogs in chemistry communication. - Hilary

I think the latter part of the article by Velden and Lagoze hit the nail on the head albeit sideways. There is a lot of chemistry disciplines and the pharmaceutical and beauty industry would be especially open to espionage. There is also the issues of security with the organic chemistry field as research from that branch could be turned into catastrophic weapons of mass destruction. The... more... - Aaron Kendrick

so given that those fields are only small parts of a decentralized whole, why should they hold the rest of the discipline hostage? - D0r0th34

Aaron: is that scenario realistic? the knowledge and facilities required to make nuclear or biological weapons are considerable. simpler methods such as guns or explosives may still be a more effective and reliable means for violence - Mike Chelen

it is confusing that this article states "Hardly any established scientists maintain a blog" then cites an article http://dx.doi.org/10... which says "they contribute to the current practice and reputation of science as much as, if not more than, any popular scientific work or visual presentation" - how could blogs be so influential with supposedly no participation from established scientists? - Mike Chelen

Full whitepaper here: http://hdl.handle.net/1813... (I would have liked to see this linked to in the article). Also http://ff.im/bU7ae - Hilary

Security of biological weapons is a much more serious issue than for chemicals. Mustard gas is nasty but limited in spread, and most seriously nasty chemicals are natural in origin anyway. On top of that I think its been reasonably well established that security in e.g. cryptography is best served by an open approach. Espionage similarly is a separate issue. What we have at the moment... more... - Cameron Neylon

i definitely don't think the issue is about weapons/weaponization, an undergrad in chemistry (or a high school kid who can read on the internet) should know enough to make some serious bombs. Velden talked about her dissertation research at 4S. It was interesting how the members and PIs of the labs carefully do not reveal details of their work. They've had things scooped by other labs with more money/people so they don't talk about the details at conferences. - Christina Pikas

This talk of "dangerous science" is a red herring for a discussion on Open Science. It could leave one not familiar with the chemistry publication process with a very false impression. With very rare exceptions, all the information required to synthesize explosives and other dangerous compounds is already contained in regular research papers. If anything Open Science could make science... more... - Jean-Claude Bradley

Finally got round to reading the Nat Chem article. Can we stop talking about weapons in this thread - totally irrelevant. The article makes some excellent points, particularly in the section "Chemistry distinguished". The "focus on creation" paragraph will irritate many, but there is an element of truth there, as anyone will acknowledge who spends much time reading organic synthesis or catalysis papers. When/where is the second workshop? - Matthew Todd

Mat - if there is any follow-up meeting it will be discussed in the Google group http://groups.google.com/group... - Jean-Claude Bradley

Carey Lumeng to Carey's feed, The Life Scientists, Science 2.0

You know you want it....HP reincarnates calculators on iPhone - CNET Reviews - http://reviews.cnet.com/8301-19... (via http://friendfeed.com/iphone-...)

You know you want it....HP reincarnates calculators on iPhone - CNET Reviews - http://reviews.cnet.com/8301-19512_7-10273119-233.html (via http://ff.im/4tWaK)

June 28 - Comment - Like - Share

Jamie McQuay, 'Mummi' Thorisson, Bruce Keener and 3 other people liked this

Given the UI flexibility of the iPhone, why recreate older, less intuitive HP calculator interfaces? - Steve Levin

2 more comments

@Steve: Nostalgia, I guess. - Christopher Granade

This would probably work better with a Bold and the clickable screen. I do miss the feel and thunk of pressing the keys on that thing. - Carey Lumeng

Older?...yes. Less intuitive? You've obviously never used the HP-12c. It has the best interface around for time value of money (TVM) calculations. Also, if you can't wrap your head around RPN logic, you could always turn that feature off. Best of all, with an app like this I can leave my HP-12c at home. - Edwin Webster

Mike Chelen to Mike's feed, Science 2.0, Cloud Computing

Fwd: ArXiv in the Cloud Coming? - http://scienceblogs.com/pontiff... (via http://friendfeed.com/xixidu...)

October 24 - Comment - Like - Share

Deepak Singh, Jamie McQuay and Claudia Koltzenburg liked this

one cool thing about having entire article collections on remote and local mirrors is that custom analysis and search methods can be more readily applied - Mike Chelen

Deepak Singh to Deepak's feed, Science 2.0

Fwd: Any Science 2.0 people who are also Wikipedians? Notability of Timo Hannay being debated. Please chime in! http://en.wikipedia.org/wiki... (via http://friendfeed.com/boudicc...)

September 23 - Comment - Like - Share

joergkurtwegner, Lisa Green, Richard Akerman and 4 other people liked this

They actually really want to downscale WP... Wikipedia-- - Egon Willighagen

8 more comments

If they keep this up there will be nothing about the web on Wikipedia - Cameron Neylon from fftogo

Done. I also added the reference to PhDComics in the article. - Pierre Lindenbaum

@Pierre, please check the comic ID... - Egon Willighagen

Joi Ito is adding material.... the article looks pretty good already to me. Added a "Keep" on the deletion page. - Michael Nielsen

@Egon thanks, fixed - Pierre Lindenbaum

I can understand WP doesn't want to have an article on every John Smith in the world, but these endless notability battles are tedious. If you present at one conference are you notable? If you get one interview? "regarded as an important figure by peers" is not exactly a quantitative metric. Timo has a demonstrable body of work in many venues; that should be enough for notability. I was... more... - Richard Akerman

Just weighed in, it will certainly be kept. - Berci Mesko, MD

Yay - just noted that the wiki entry on Timo is no longer being considered for deletion http://en.wikipedia.org/wiki... Common sense prevailed..... - Graham Steel

w00t - Deepak Singh

Cameron Neylon

Feature requirement for "Friendfeed for scientists": citeable comments...

May 11 - Comment - Like - Share

Claudia Koltzenburg, Benjamin Tseng, Björn Brembs and 22 other people liked this

URIs to the FriendFeed entries seem stable now, so, you know, if instead of recreating FriendFeed for scientists, the scientists come to FF, there's always that. - Chris Lasher

14 more comments

I've no interest in recreating it if we don't have to. But I think a URI for comments is definitely a must have for the modern social aggregation site :-) - Cameron Neylon

We're very interested in hearing how various groups of people use FriendFeed (or what unique features they would like in order to use it effectively). Please post in the FriendFeed Feedback room (http://friendfeed.com/friendf...) or let us know by email (feedback@friendfeed.com). - Tudor Bosman

Remember you can use claimid as well to keep track of your FF contributions - Jan Aerts

+1 citeable comments. Skinning would be nice; stats would be useful for some people; really really want the "related entries" function to work properly again. - Bill Hooker

Idea: rather than individually posting suggestions to the room or address Tudor gave us upthread, how about a new room: Suggestions For FriendFeed From The Life Scientists? We can use the room to co-ordinate ideas and pass them on when they're ripe. Would that be useful, or am I on crack here? - Bill Hooker

Agree that it would be useful to track specifically suggestions from the Life Scientists group; either as a thread (this one?) or a new room. - Neil Saunders

Easier to find a room than a thread when you think of something and want to make a note. - Bill Hooker

I think a room makes sense. - Steve Koch

Great Idea, Bill, but how to we make sure that our less frequent pre-digested ideas don't get lost in the churn of hundreds of "thinking while they type" posts in the feedback room? - Mr. Gunn

Don't use the room, use the email address? Maybe even co-ordinate and have multiple signatures on each "digest from the Life Scientists" email. - Bill Hooker

Maybe once the pre-digested idea has been posted to the official FF Feedback room, a link to that thread could be posted to the "Suggestions for FF from Scientists" room, and we could all 'like' up the thread in the offical room. Question is .. are there enough of us to ensure the pre-digested ideas don't get lost in the noise with this approach ? - Andrew Perry

I just started http://friendfeed.com/ff-for-... to give this approach a try. - Daniel Mietchen

check out friendfeedCommentAnchor http://friendfeed.com/friendf... - Mike Chelen

Mike - thanks for picking that up - will look closer later. - Cameron Neylon

Cameron: sure, it works as bookmarklet or userscript, to generate links such as http://friendfeed.com/cameron... its mentioned in list at http://friendfeed.com/fftools... - Mike Chelen

Cameron Neylon

Why don’t scientists share data? - http://duncan.hull.name/2009...

September 10 from Google Reader - Comment - Like - Share

Slavomira Vladimirova, Claudia Koltzenburg and Jamie McQuay liked this

Mike Chelen to Mike's feed, Ruby for Bioinformatics, Visualization

rubygems now has plugins! - Polishing Ruby - http://blog.zenspider.com/2009...

September 11 from Bookmarklet - Comment - Like - Share

Abhishek Tiwari, Jamie McQuay and Deepak Singh liked this

NextBio to The Life Scientists, Science 2.0

Onconome sues researchers for contributing fraudulent data to their database http://www.genomeweb.com/biotech...

September 9 - Comment - Like - Share

Jamie McQuay, Khader Shameer, Abhishek Tiwari and Cameron Neylon liked this

Woah - now that's a sanction for scientific fraud... - Cameron Neylon

I wonder if any of the grad students or postdocs were tempted to blow the whistle. It seems like it went on for years, there must have been several people who were aware of the deceit. Lisa - NextBio

Science Online London: Martin Fenner

List of blog posts about Science Online London now at 41. Happy reading and commenting, and let me know if I missed any: http://network.nature.com/people...

August 25 - Comment - Like - Share

Jan Schmirmund, Jamie McQuay, Victor / Mendeley Team and 5 other people liked this

Oh. Thanks! - Heather

3 more comments

http://scienceoftheinvisible.b... - AJCann

see Dave Munger's http://ff.im/7bgKy - Duncan Hull

Brian Kelly http://ff.im/7aP0H - Duncan Hull

I've added these blog posts about Science Online London (and a few more). - Martin Fenner

Kendra <3 Three Lions to Kendra's feed, LSW, Science 2.0

I'm in a meeting where we want to use Zotero to collect citations, but then something (Drupal?) to display them on the web in an easy to search format. Think Reference Manager, only with the files attached and open source. Are we crazy?

July 31 - Comment - Like - Share

Jamie McQuay, Mitchell J Stanton-Cook, marlene and 3 other people liked this

Why not use Zotero 2.0 for that? Or use CiteULike or Mendeley. - Martin Fenner

7 more comments

They want these documents to be freely available on the web for people who aren't using Zotero. (The guy in charge loves EndNote and refuses to switch.) The end product should be a simple web database with some advanced search feature and citation exporting. I'm not sure Mendeley can do that? - Kendra <3 Three Lions

maybe use the Zotero plugin Zotz http://simile.mit.edu/wiki... to export to Exhibit then integrate with http://drupal.org/project... maybe? - Mike Chelen

Have a closer look at CiteULike. - Martin Fenner from iPhone

bibapp? http://bibapp.org/ - D0r0th34

You could use the biblio Drupal plugin and write some custom code to integrate it with Zotero. Otherwise it might be possible to write some code to integrate a webapp like Aigaion or refbase with Zotero. - Matt Leifer

BTW, it is not clear from the post whether you are happy to use hosted services or whether you prefer to host your own database on your own servers. I was assuming the latter because you mentioned Drupal, but others who mentioned CiteULike and Mendeley are assuming the former. - Matt Leifer

What did you end up doing? - Kristin Partlo

For my study, I am using CiteULike to store the pdfs of articles, then I have an RSS feed of a particular tag pulling titles/links of these into a badge on the sidebar of my Drupal installation where I am keeping my notes. Is simple once set up and very easy to do if you have Drupal already. You could easily import from Zotero to CiteULike regularly - Kathryn says love n peace

Michael Nielsen to Michael's feed, Science 2.0

Facebook Acquires FriendFeed - http://www.techcrunch.com/2009...

August 10 from Bookmarklet - Comment - Like - Share

Philip Lei, Joe, Lisa Green and 7 other people liked this

I'm delighted for the FriendFeed founders, but am not sure what this will mean for the continuation of FriendFeed as a platform, and the continuation of rooms like the Science 2.0 room. There's a lot of overlap with Facebook. - Michael Nielsen

17 more comments

It means the end of the way we (the science 2.0 community) use FriendFeed. I can't imagine that we will move our activities in their current form over to Facebook. - Neil Saunders

The reason for using Friendfeed instead of Facebook for groups like this one is that the features are so much better. If those capabilities are brought to Facebook, what reason would their be against migrating to that platform? - Mike Chelen

Mike - privacy concerns, terms of service concerns, endless requests to use stupid applications and the slow, buggy interface all come to mind :-) - Neil Saunders

Don't be shy, Neil. - Michael Nielsen

Neil: user interface is indeed one of FF's biggest advantages over FB and other sites. if the FF team is able to bring this standout feature to FB then it will represent a huge improvement in usability. that is a big "if" though - Mike Chelen from IM

I am taking a "let's see what happens" approach, but definitely integrated into FB as is would not be something I'd like - Deepak Singh

Ah, that's a pity. The move doesn't seem well received by the FF community, which says something about FB. Maybe something could be built on top of google's wave. - Alexei from Nambu

I don't want to be one of those conservative "I don't embrace change" types -- but I am also very worried. Facebook has a different vibe/purpose then Friendfeed (not to mention privacy concerns/stupid applications/advertising), and I would prefer to keep my two account-worlds separate (I have been keeping my Facebook profile private); Mike Chelen, I do hope that you're right, that all... more... - Benjamin Tseng

I second the motion to move rooms such as this one over to a wave-based thingamajig.... - Wladimir Labeikovsky

might we test that on shareflow? prob is of course that only 5 Flows are supported by the free version... but perhaps it would be good if some "beta-testers" would look around on that platform. We might formulate ideas how to organize all later on wave. - Phil

What I like about both Friendfeed and Twitter, is that you can follow people because you find them interesting. Facebook is more about being friends. - Jo Vermeulen

Let's wait for Google Wave. - Enrico Guarnera

Benjamin: the characterization as a talent acquisition provides some hope in that expertise is more meaningful than a particular piece of software. if this means that the ff staff has a wider, more significant effect on users through fb - Mike Chelen

Jo: yeah that is a problem with facebook's friend model. there is sort of a workaround with fan pages, however it is currently far less intuitive than on twitter or friendfeed. will facebook improve the flexibility of their model, with friendfeed team's help? - Mike Chelen

ReComment from Abhishek's post: Oh noes. How long before you need a Facebook account to log in to FriendFeed? I don't intend to sign up to those intrusive spammers any time soon. Where's the 'Dislike' button? - Andrew Clegg

First Newsgator abandons its online users to GReader, now FF team hands over to Facebook. I cannot imagine the discussions I very much enjoy on FF being as fluid and fast in FB. - Polly Potter

I know someone who built a framework that could become a FF replacement with just a little bit of modification. I told him about the sentiment among the science folks here and he was interested. I will let you know if he agrees to do the modifications. Please keep commenting on what a FF replacement should (and should not) feel like. - Lisa Green

I've been holed up in the lab and off friendfeed for about a month now, and so I'm probably looking at this acquisition from a different perspective than I would have a couple months ago. But when I first heard the news I wasn't worried. How was FF going to survive without a sale anyway? Maybe Facebook will decide to keep the FF platform, but actually try to make money from it. Is there... more... - Steve Koch

Shirley Wu

Overheard regarding papers published in PLoS ONE - "it was rejected somewhere else", "The bar is 'not crackpot'", "people publish in CNS because that's where the attention is, I don't know anyone who reads PLoS ONE", "The reputation of the journal is a good way to filter out noise". Is there truth to these claims? Discuss.

July 30 - Comment - Like - Share

Cesar Sanchez, 'Mummi' Thorisson, Mike Chelen and 19 other people liked this

Almost all papers, in all journals, have been rejected from somewhere else. Our bar is "is it science, is it conducted properly, is it reported properly, and do the conclusions follow the data etc" - the bar is not "is it sexy, or impactful, or a major advance". At the same time, we are not CNS - as we are not selective. CNS combined publish just 5,000 articles a year between them but... more... - Peter Binfield

40 more comments

Peter, I certainly don't disagree with what you're saying and think PLoS ONE is valuable and innovative. But I was wondering if these negative judgments are pervasive (FF/twitter is a bit of an echo chamber and the real world can be a shock sometimes) and if so how to change them. There are those who argue that CNS has high precision even if they miss some good papers and so it's more... more... - Shirley Wu

The problem with echo chambers is that the Internet echoes forever; and forever is a long time. We just need to push out as much positive info as possible to try to combat any negative comments which may have been made rashly, or in error, but which get re-referenced for eternity. Our article-level metrics program will presumably show people whether any given paper in PLoS ONE is 'high'... more... - Peter Binfield

There's this thing known as FUD. Happens when someone sees their status eroding. The whole PLoS articles are not as good is just that, FUD - Deepak Singh

Indeed, it may be fear, uncertainty, doubt. It may also be lack of information and hard data. We are going to fix the latter. Certainly, people are voting with their feet - we have 37,000 published authors in under 3 years, and people are publishing with us in ever increasing numbers (http://poeticeconomics.blogspot.com/2009... ) - Peter Binfield

"it was rejected somewhere else" - perhaps. This is hard to tease out, but I have a feeling that most of the manuscripts that come to PLoS ONE have never been submitted elsewhere - Bora Zivkovic

"The bar is 'not crackpot' - good bar, IMHO. Why is any other bar necessary? Think. Really. - Bora Zivkovic

"people publish in CNS because that's where the attention is, I don't know anyone who reads PLoS ONE" - who still reads journals? Srsly? Don't people search online for papers they are interested in? Do physicists read biology papers when their copy of Nature arrives? No, they read Nature for "news and views". - Bora Zivkovic

"The reputation of the journal is a good way to filter out noise" - perhaps a century ago when every scientist could read every scientific paper and understand it, and every scientist was a 'Victorian scholar' who felt the need to keep up with ALL of science. Today, you read papers in your narrow field - you find them online. News from other sciences you can find in pop-sci magazines, on blogs, etc. - Bora Zivkovic

@Bora, I think there are still a fair number of people who don't search for papers necessarily, but browse TOCs, and so only browse the journals they're familiar with. During the discussion, someone asked, baffled, "but there are already so many papers [without PLoS ONE publishing so many more], how would people find ones of interest to them??" - Shirley Wu

A related discussion - based on a correspondence in Nature by a proponent of the views Shirley cites - is at http://ff.im/4GWlM . - Daniel Mietchen

@Shirley - although ToCs are certainly an important discovery tool, any publisher will tell you that the vast majority of their usage comes in from Google (who then read an article, and leave again to run another search) - Peter Binfield

@Peter, that would make sense, but I'm wondering if that necessarily translates into Google being the majority of people's preferred method for finding papers. At least the impression I got from folks in my lab was "so many papers, so little time" and so they're skeptical of anything that adds to the glut of papers without clearly adding value. They might agree on the principle that... more... - Shirley Wu

They also think, "if [a peer reviewer] didn't make a value judgment on whether this paper is significant, why should I waste time reading it?" - Shirley Wu

"I'm wondering if that necessarily translates into Google being the majority of people's preferred method for finding papers" - Good point. I guess you would want to measure time spent on page by people who come via the 2 (or more) routes to see how targeted their interest was - Peter Binfield

@Shirley - Then they are admitting that they would prefer one (or perhaps 2 or 3) other people to decide what is important for them, and so decide on their behalf what they should be reading. Doesnt sound like a very informed way to filter imho... - Peter Binfield

@Peter, more that a million people access papers through google 25% of the time will mean that publishers see google as a huge source of traffic, but doesn't mean that people think of google as their preferred method to find _NEW_ papers. - Shirley Wu

@Peter, well, it's using expert opinion. We all use it to some extent in areas we're not familiar with. If people aren't that internet savvy or aren't that organized, they depend on other people or name-brand journals to bring things to their attention. Also, commenting on papers hasn't really taken off yet - just a matter of time, probably - but it just means that the post-peer review process hasn't really proven its value yet. - Shirley Wu

"but it just means that the post-peer review process hasn't really proven its value yet." - indeed, and we DONT view our efforts as post-pub peer review. We view it as a new way to do post-pub evaluation / filtering / discovery. - Peter Binfield

Oh, the other thing that someone mentioned was "comments are valuable" - meaning "why would I give away my intellectual capital?" People are willing to share their comments with their labs or close colleagues, but not to the public or to the general scientific community. Is this just another mindset we combat with positivity and action? How to combat the vicious cycle of "no comments, so no value", "no value, so i won't comment"? - Shirley Wu

"Is this just another mindset we combat with positivity and action?" - I would say we combat it by showing them the power of being open about these things. For example, social bookmarking only works when everyone shares their bookmarks - in this example there is a clear benefit to both contribute and use. If people realised that by leaving comments they would be advancing science;... more... - Peter Binfield

@Daniel, ah yes, I remember that thread now. Unfortunately I think many scientists are similar in mindset to the letter writer. They don't know about or understand new ways of receiving content, which might seem strange to those of us here, but there are many more people out there than are in here. - Shirley Wu

Also, you could use the same argument about peer review: "My time and thoughts are valuable, why should I do peer review". Apparently academia feel that the quid pro quo works in that situation at least (and that is done anonymously!) - Peter Binfield

@Peter, true, though I think some of that is tied to the reputation of the journal again - being a reviewer for Nature > reviewer for PLoS ONE (in their eyes), editors know them, they can talk about it and gain status. They get tangible and subtle career boosts. Whereas commenting on papers online and publishing in PLoS ONE doesn't get someone tenure (yet). "It would be very brave and... more... - Shirley Wu

Peter - given the problems that journals have finding suitable reviewers, I would hesitate a bit calling that a working system. - Daniel Mietchen

@Daniel :) - Peter Binfield

Another link that may be useful reposting here: Pubfeed at http://pubfeed.cs.toronto.edu/ basically allows you to treat the whole web of scholarly articles like a TOC alert (just a bit more customizable) and pipe that into your preferred feed reader. - Daniel Mietchen

@Shirley - please dont forget that there are 25,000 journals in the world and millions of papers published per year. CNS is just 3 titles, and if you lump together all similar titles (highly exclusive, professional editors, well known brands, conferring 'bragging rights' on anyone who works with them) then you are still talking about just a handful of the titles, with a small percentage of the content. We need a system that works for everyone, not just a small sub-set - Peter Binfield

@Peter, oh, I'm well aware, just parlaying bits of an impromptu debate I had earlier today with people who don't see the value of venues like PLoS ONE. These are all arguments they make, and while I don't agree with them, it is tough to convince people - Shirley Wu

You could try asking them exactly how many downloads their last paper in a 'high impact' journal got... - Peter Binfield

Fair enough, but you know, I really don't think they think about that. They think "what will be in my CV?" and they think any journal that is somewhat competitive [includes other PLoS journals, BMC journals, etc] looks better than one that accepts anything that's methodologically sound. Again, not my view, but perhaps one that is held by many. Do people list # of downloads on their CV for publications? - Shirley Wu

They dont, because they dont have the data. However, people do list if their paper was rated by F1000; or if BMC designated it a 'highly accessed' article. So I think they will start to say "this paper was downloaded 5000 times in the first 3 months which put it in the top x% of all PLoS ONE articles, the top y% of all PLoS articles, and the top z% of ALL articles" (when the rest of the world starts quoting this data) - Peter Binfield

Ironic isn't it; it's not a battle with the publishers, but with other scientists! I overheard a conversation yesterday concerning choice of bioinformatics journals. It centered entirely around impact factors and at one stage someone said "I think BMC Bioinformatics is online *only*" - as though that were a bad thing. - Neil Saunders

And it's clear that anyone who mentions "filtering noise" simply is not using the web effectively. Presumably their web use is limited to search, after which they print PDFs and go away. Concepts that seem simple to us - RSS, feed readers - are unknown to them. - Neil Saunders

I think of it as trying to set up a social experiment. If I'm right and a more cooperative model can produce better science than the current hypercompetitive structure, then over the next decade or so, facility with new methods and metrics that center on Open practices will provide a competitive edge for some researchers, and unwillingness to change will put others at a disadvantage. We... more... - Bill Hooker

Good thoughts Bill. It's not enough to say "this way is better" just because we believe it to be. We have to demonstrate that it's better - or find out that it isn't. - Neil Saunders

And isn't that the scientific way? - Deepak Singh from IM

"I think there are still a fair number of people who don't search for papers necessarily, but browse TOCs" Could it be that those are the people publishing in CNS and miss the most important papers for their work? http://bjoern.brembs.net/comment... It's only one example, as anecdotal as it gets, but it shows two things: 1. CNS 'quality' is merely correlational and highly noisy.... more... - Björn Brembs

My environment is rather positive about PLoS ONE. We all know about the difference between relevance and quality. While many PLoS ONE papers might not be of widespread interest, the review process is of comparable quality or better to smaller conferences and e.g. high volume BMC journals. Other journals have severe issues with reviewer quality these days, and it seems to become worse. - Roland Krause

I'm still wondering about the degree of scalability of post-publication (significance) peer review systems. Is it really realistic to think that once (all) journals go OA and implement such a system that the entire scientific community will benefit? Assuming that it's "fair" for all journals to get equal amount of attention from "scholarly feedback communities", how can we encourage... more... - Wobbler

I agree with Bill Hooker's statement just above. Those who echo Shirley's original quote will be at a disadvantage, which means better odds for the Shirley's of the research world. - Jason Hoyt

I often say something along the lines of what Bill said. The environment is changing. To succeed in the new environment, one has to change not just one's publishing habits, but also rethink how to do research and how to write it. Thus, people who think about it early on will be able to gain advantage over people who are still stuck in the old ways of doing things. As the new environment... more... - Bora Zivkovic

Pawel Szczesny

Visual CV attempt - http://www.flickr.com/photos...

November 17, 2008 from Flickr - Comment - Like - Share

Peter Murray, ''a_a@FF'', Deepak Singh and 16 other people liked this

Feedback request. I try to make a visual overview of my experience so far and my future plans. Any comments regarding both, visual side and scientific/career side really appreciated. - Pawel Szczesny

13 more comments

One quick suggestion: increase the font size and color differences. It might emphasize your primary interests a bit more. - tim from Alert Thingy

Thanks Timothy. That's a good suggestion. I work on another version that would incorporate some more details on the past projects, but so far it's even less readable than this one. - Pawel Szczesny

I really like the concept of this. I take it the colors correspond to particular positions you held? Have you tried using a color gradient for the categories (photography, science, programming, ...) and different fonts to distinguish each job/educational position? - Chris Lasher

Thanks Chris, that's a great suggestion! Having a "now" line makes current color code a little redundant. - Pawel Szczesny

Good idea. How would you show projects that are still on? Maybe you can change the text direction? - Marcin

Most people with color deficient vision (like mine) will not be able to tell your red from your green (I can't). Also it seems a little odd that there is only one thing in the photography category (a hobby?) and so the columns do not really line up. Maybe a third color for non-work-related? And seconding Chris' idea to use fonts to distinguish where you learned/worked on each item in the list. - Bill Hooker

@Bill Did you notice Pawel plots the words according to two axes: skillset along the X-axis, and time of gaining that experience along the Y-axis? I missed this at first and was wondering about the Photo category, too, but then I realized how "scientific animations" and "molecular visualizations" spanned both Science and Photography, and hence, they're in between them on the X-axis. That's neat, because you can see that Pawel's interest in visual things started off in night photography... - Chris Lasher

...and when combined with his exposure to science led him to do, say, visualization of biological networks. Really cool concept. Also, good call about reds and greens. - Chris Lasher

Marcin, things still going are around the "now" line (dashed line in the middle). I don't think exact start/end does matter, it's more about how things circulate in time. Bill, Chris explained already what is the idea behind three "columns" and placing things. In the first approximation phrases were connected (and it was easier to get the idea about various inspirations), but I removed them for the clarity. Colors will be changed. - Pawel Szczesny

Thank you all for comments. Updated version with more explanations and feedback request is here: http://freelancingscience.com/2008... - Pawel Szczesny

Can you describe the method and source data used? It is informative and looks nice :) - Mike Chelen

Mike, it was a manual work done in Inkscape. I work on something similar done in Processing, but it's still at a draft stage. - Pawel Szczesny

That would cool to see, definitely more challenges though. Thanks - Mike Chelen

it's a great idea, it looks great, and it's a great way to have a quick overview of your competences! congrats! - Adrien Joly

SciBarCamp: Kirsten Sanford

OMG! This barcamp was so AWESOME! (I know that was very valleygirl, but I can't help it when I'm excited.)

July 9 - Comment - Like - Share

Naomi Most, Bosco Ho, Jim Hardy and 9 other people liked this

and thanks to the organizers :) - Pedro Beltrao

2 more comments

Definitely worth the pacific ocean crossing. Thanks to all session leaders, organisers and great crowd! - Kubke

Ditto, enjoyed it loads. Thanks to the organisers - Duncan Hull

The attendees make these conferences work :-) - Jamie McQuay

Ariel Waldman

July 10 from Flickr favorites - Comment - Like - Share

Jim Hardy, Cameron Neylon, Jamie McQuay and Andrew Lang liked this

SciBarCamp: Martin Fenner

SciBar Camp: Keynote by Sean Mooney; Biomedical Research in the Age of Cyberinfrastructure

July 8 - Comment - Like - Share

Jason Stajich, Allyson Lister, Frank Norman and 6 other people liked this

Keynote at an unconference is difficult, an untalk? Will take about why he thinks scientists don't use the internet. - Martin Fenner

93 more comments

hi martin :) - Pedro Beltrao

Is all the discussion on Twitter? - Martin Fenner

seems to be quite a lot over there at #scbPA but we know where the quality is... - Cameron Neylon

Scientists are certainly all connected: email, manuscripts and news on the internet - Martin Fenner

but integration a problem, dissemination of data is a challenge - Cameron Neylon

Most of the tools that his group builds are web-based - Martin Fenner

For the majority of scientists, there is no interest in using tools like Twitter or Facebook. - Martin Fenner

streaming video at http://bit.ly/uTeV4 - not from me at the moment - Cameron Neylon

His groups built a biorepository inventory management software, community portal software, bioinformatic analysis tools (often web-based). - Martin Fenner

need to get lots of citations of tools to keep getting funding - Cameron Neylon

Individual tools are not in a vacuum, they should be connected together as cyperinfrastructure. - Martin Fenner

lots of web based tools but individual tools are not in a vacuum. The collection of resources is key and how to combine them together - Cameron Neylon

nasa space programme as an analogy for building an integrated cyberinfrastructure - Cameron Neylon

each part can be tightly specificed for e.g. shuttle but harder to push that kind of integration specification for funded research projects - Cameron Neylon

Difference in space program: NASA clearly says what they want, different in bioinformatic tools. - Martin Fenner

Examples of integration (cyberinfrastructure) tools, CaBIG, NCBI, BIRN, homw-grown... - Martin Fenner

talking about different big programs like https://cabig.nci.nih.gov/ and http://www.nbirn.net/ - Pedro Beltrao

Administrattors always want "big picture", e.g. asset management, researchers want data analysis. This leads to two kinds of projects. - Martin Fenner

researchers totally focussed on specific problems. Administrators have other concerns, want "asset management" - Cameron Neylon

the informatician is a sad clown - Duncan Hull

scientists mistake todays needs for tomorrows neeeds - Duncan Hull

administrators often misjudge their needs for scientist's needs. Scientists often mistake today's need for tomorrow's needs - Cameron Neylon

NIH has 27 institutes, they all have their own approach to informatics. - Martin Fenner

Traditional approach: domain specific coordination - Martin Fenner

traditional approach is to build a specific system or portal for a consortium of researchers - Cameron Neylon

NIH puts out RFA request for applications - Duncan Hull

e.g pharmgkb http://www.pharmgkb.org/ and COBRA breast cancer http://www.pharmgkb.org/views... - Duncan Hull

data sharing is one of the key values of big collaborative projects like PGRN but details are horrific, complex workflows - Duncan Hull

Data sharing was key to PGRN's value - but not the last place the data might go - Cameron Neylon

horribly complicated workflow with lots of different research foci - Cameron Neylon

i guess this approach creates isolated domain knowledge that is hard to integrate with other domain specific projects - Pedro Beltrao

Need to collect disparate data to pull everything together and then push on to the mandated site - Cameron Neylon

Management needs: secure platform, database eneabled - Martin Fenner

This is just like being at ISMB :-) - Duncan Hull

Question: are researchers actually using the web-based tools to collect data? - Martin Fenner

every lab does things differently - Duncan Hull

a successful workflow in one lab is disastrous in another - Duncan Hull

and every lab is probably doing something different to the workflow they say they are using... - Cameron Neylon

Tools are too specific, don't generalise - Duncan Hull

but if you designed better to start with (but need heavy resourcing to do this) then it might be - Cameron Neylon

CaTissue is great tool for tissue sampling, was built from the beginning to work for many different situations. - Martin Fenner

technology moves faster than scientists do, things become obsolete very quickly, e.g. sequencing - Duncan Hull

Current challenges: connect to bigger projects, next generatin suequencing, etc. - Martin Fenner

e.g. national center for biomedical computing http://www.ncbcs.org - Duncan Hull

Mark Musen has one, Russ Altman has another - Duncan Hull

NCBIO Bioportal - Duncan Hull

http://bioportal.bioontology.org/ - Duncan Hull

3 simple tools, integrated ontologies, automated annotation and links to resources - Duncan Hull

pedro asks a good question - is there any mandate for annotation or tagging? Answer from Sean: No, there is money available to support but no compulsion - Cameron Neylon

BIRN biomedical informatics research network http://www.nbirn.net/ - Duncan Hull

Clinical and Translational Sciences Award Informatics will be big - Duncan Hull

Big mover in the next 10 years: funding for translational research centers (CTSA). - Martin Fenner

mandates for CTSAs to work together but no idea how that is going to happen in practice - Cameron Neylon

Indiana CTSI hub http://www.indianactsi.org/ - Duncan Hull

Administrators bite off more than they can chew - Duncan Hull

Purdue has nice web based collaboration plaforms called hubs, e.g. http://nanohub.org/ - Duncan Hull

More than 70,000 users, people actually use it! - Duncan Hull

All PHP and CMS - Duncan Hull

Ask for a laundry list of informatics functionality. Sean "do you know how much this is going to cost" Admin: "No, how much do you need" Sean: "Well all of the money available..." - Cameron Neylon

ability to embed applications in a virtual machine in the web portal. - Cameron Neylon

People rarely find each other through social networks, they just use it to spy on their rivals - Duncan Hull

hub doesn't directly integrate scientific data or handle group collaboration - Cameron Neylon

personal information actually put into their hub implementation by administrative assistants - Cameron Neylon

integration across CTSA informatics projects is not happening, everyone is trying to do everything themselves - Cameron Neylon

scilink, laboratree, labmeeting, researchgate, biomedexperts, scivee, nature network, openwetware - Duncan Hull

And now, the Web2 bit! - Cameron Neylon

lots of web 2.0, hugely popular (really?) - Duncan Hull

this area is of very high interest to the NIH, how do you discover resources that are available to you? - Duncan Hull

popular with adminstrators and funders I think - possibly developers, less so with scientists... - Cameron Neylon

NIH has started to put more grant money into social networking tools, e.g. with the CTSAs mentioned above. - Martin Fenner

don't focus on communities, focus on projects - Duncan Hull

e.g. confluence, sharepoint are extensible tools - Duncan Hull

microsoft booo! - Duncan Hull

but sharepoint very popular in government - never really understood why I have to admit - Cameron Neylon

http://laboratree.org/pages... - Pedro Beltrao

uses OpenSocial - Duncan Hull

first use case: creation of collaborative documents - Duncan Hull

Challenges faced in Mooney lab: Creation of collaborative documents: manuscripts, proposals, management of datasets, discussion. - Martin Fenner

1200 users for laboratree.org - Duncan Hull

Laboratre solves problems in Mooney lab. - Martin Fenner

Applications can be embedded in Laboratree using OpenSocial. - Martin Fenner

Lessons #1 web portals are under used - Duncan Hull

Web portals for science suffer from under-use. - Martin Fenner

Lessons #2 Killer app is "have to use" not "like to use" - Duncan Hull

Successful tools are simple. - Martin Fenner

Start with an existing community. - Martin Fenner

Lessons #3 "if you build it they won't come" so start with an existing community - Duncan Hull

Discussion: Open Science is important, but is a long way to go (publishing as example). - Martin Fenner

Discussion: will HTML be used instead of .pdf or .doc? Is a paradigm shift, particular difficult in clinical medicine. - Martin Fenner

One reason to use OpenSocial for Laboratree is the hope that people would build applications that can easily be reused. - Martin Fenner

Discussion: a lot of our data from a years ago is probably no longer relevant to what we do today. - Martin Fenner

Darn, would have loved to be at this session. Some day I will actually make it to one of these - Deepak Singh

I posted the keynote as a video in three parts on my blog: http://bit.ly/2G0DE - Naomi Most

Thanks Martin, Pedro, Cameron, Duncan, and Naomi! With so many notes and videos, it is almost like being there :) - Mike Chelen

The Life Scientists: Jack H. Pincus

What do you think of web-based research collaboration tools such as: 2Collab; MyNetResearch; Laboratree; MyExperiment; LabMeeting; and BIOCORE? Are they useful tools for internal and distance collaborations? What features would nake them more attractive?

April 28 - Comment - Like - Share

Andrés David Aparicio, Véronique Rabuteau, Richard Klancer and 23 other people liked this

Hi Jack! I wrote a longish post about this some time back. Blog post here:http://synthesis.williamgunn.org/2009... I now use Mendeley (http://bit.ly/181tmi) to collect and share papers. An RSS feed for new entries and a recommendation engine would make it a lot better for my purposes. - Mr. Gunn

37 more comments

Thanks for your comment. The tools that I listed are not social tools although they have some of the same features. They are designed to facilitate collaborative research projects. They allow colaboration on grants and manuscripts, messaging, and organizing into groups and projects. Some incolude workflows, project management, and data analysis tools. The closest non-science analogy is... more... - Jack H. Pincus

IMO collaborative workspaces are very important. That said, I am not sure we've managed to create one that really works specifically on the scientific side any better than MindTouch or Sharepoint (which I loathe having had to use it) - Deepak Singh

Deepak, what would make science collaborative workspaces more useful than MindTouch or Sharepoint? - Jack H. Pincus

Ideally I like the idea of using existing platforms and building on top of those with plugins and services. A science native one would have to be very specific to some particular workflows and optimized for that. Not sure how you'd make any money on that though - Deepak Singh

I guess that depends on whether a science-native collaboration platform is intended for public or private collaboration. You could make public collaboration free, and charge premium accounts for the ability to host private workspaces on the public service, or you could sell service and support for privately-deployed instances. There could be some interesting wrinkles depending on whether the platform supports public-public, public-private, or private-private federation between instances. - Michael R. Bernstein

Michael, Mendeley has discussed doing exactly that. I think the form the private instances would take is that of a local install of the web component, so there would be no private-public issues there, as nothing would leave the local network. - Mr. Gunn

The thing is, isolated behind-the-firewall deployments are not very interesting or useful (though they can certainly be very lucrative for vendors) except in the largest organizations. Think of it in this light: How useful (and used) would a corporate email system that only allowed messages between addresses within the corporate domain? Email succeeded because it was a *federated*... more... - Michael R. Bernstein

As far as I know, Ray Ozzie's Groove Networks was close to cracking that nut, but then got swallowed by Microsoft in 2005, never to be heard from again. - Michael R. Bernstein

I see what you're getting at now. A sort of abstraction layer over multiple instances would indeed be cool. The people I've talked to who have expressed interest in this have been thinking much smaller (or more paranoid) than this - just a way to share things with other members of their particular research group. Everyone else seems comfortable with using it as a desktop client... more... - Mr. Gunn

The acid test is this: can I collaborate using this software as easily/effectively as if my collaborator was sitting next to me with a paper and pencil (and maybe laptop). Essentially the answer at the moment is..? I have never used the software you're talking about above. My experience is limited at the moment to blogs and wikis, which are both completely inadequate. Which would you rather use - the wiki method, or the" paper-pencil-coffee" method? - Matthew Todd

It depends on what we're doing. If it's hashing out ideas and prototypes, paper&pencil works great. If it's asynchronous collecting of references or working out a protocol, then a tool that captures this and allows each person to easily see what the other person is doing is probably best. Mendeley http://bit.ly/181tmi does a pretty good job of collecting references and sharing them. The... more... - Mr. Gunn

I'm currently in the process of applying for a grant who will sponsor the development of a collaboration system for scientists: http://docs.google.com/Doc... Leave your input on that document and we might still be able to incorporate it into the grant application. - Björn Brembs

@Björn does not have access to this document? - Abhishek Tiwari

I've requested access, Björn. - Mr. Gunn

Also requested access (no worries if not appropriate). - Neil Saunders

Mat what specifically do you find inadequate about blogs and wikis for open collaboration? - Jean-Claude Bradley

JC - well, data entry is slow (anyone who blogs complains about how long it takes to do one entry), partly because to cross-link data/pages requires very careful curation, which scales monstrously with the volume of data. To collate pages and draw conclusions needs to be quick. Pages from a project need to be linked in a 3D web of relevance, i.e. rather than just links to similar pages,... more... - Matthew Todd

Very interesting random thoughts. We've talked a lot about how you can imagine using a massive touch screen with different elements laid out on it, dragging, dropping, connecting up. Unfortunately Microsoft don't seem to be read to just give us a "Surface" as yet. Can't think why not ;-) - Cameron Neylon

Exactly, a surface or shape where posts/data/elements may be perceived and connected as simply as tracing a line between them. If I want to highlight a key concept on a whiteboard, I circle it several times. If I want to emphasise something to a colleague, I shout/repeat myself. Doing such things using a linear progression of wiki pages at the moment: very difficult to do it effectively in any decent timeframe, or in a way that rapidly engages passing readers. - Matthew Todd

I'm sure Daniel will grant all of you access. - Björn Brembs

Mat - you are right that you can't draw directly on the wiki using your tabletPC and if you are used to that on paper that is probably annoying. Maybe I'm just used to text but I find that I am able to express my points most of the time by leaving a bolded comment in the relevant place on the wiki page that serves as our lab notebook. For the type of work that we do it seems to work quite well. - Jean-Claude Bradley

Access granted for all requests so far. - Daniel Mietchen

Mr. Gunn, I just watched the Groove 2007 demo (somehow I missed that an MS-branded version had eventually been released). Looks reasonably similar to what Groove Networks had, except that certain features seem to have been shorn away as a sort of 'Sharepoint Tax', and of course it is very Office-centric now. - Michael R. Bernstein

As for the need for an 'abstraction layer', that depends on what you mean. Do you consider a syndication feed aggregator (whether server-based like Google Reader, or desktop-based like FeedDemon) an 'abstraction layer' over the blogs you read? For that matter, do you consider FriendFeed itself to be an abstraction layer? - Michael R. Bernstein

Incidentally, the small/paranoid approach is *totally* valid, the only question is how well these solutions support nested, intersecting, and disjoint groups. IOW, how does one use it when one is a member of more than one research group (perhaps with different roles in each)? - Michael R. Bernstein

I started this discussion on April 28 and last looked at it when there were four comments (about five days ago). I checked the thread again this morning to find an active discussion. I guess the secret is to not watch the pot before it boils :-). Collaboration can range from a project beteen two labs "down the hall" from each other to large aboratory, multiorganizational collaborations. The Human Genome Project and SNP Consrtium are examples of the latter. (continued) - Jack H. Pincus

Collaboration between companies or companies and universities is also becoming more prevalent, especially in the biotech and pharma industries. Lilly refers to its new business model as FIPNET (fully integrated pharmaceutical network). It may be possible to do small collaborations with existing tools. But larger collaborations may require a new type of virtual research environment. - Jack H. Pincus

Michael, yes, I would, in the general sense of the word. Just wanted to make sure I understood what you meant when you were talking about federation. - Mr. Gunn

It looks like there's two kinds of collaboration we're talking about here. Small group collaboration where all members are only part of that group is where online sharing of references and annotations works well enough. Larger, distributed collaboration requires the open, federated approach. - Mr. Gunn

Yes, smaller collaborations may be in one location. Document management may also be important for small collaborations. - Jack H. Pincus

I have requested access, too and thank you, Jack, for asking the question that generated this very edifying discussion. - Hope Leman

Mr. Gunn, distributed collaboration requires an open federated approach even when it is *small*, otherwise the overhead of setting up a collaboration space of some sort overwhelms the benefit. Note that distributed collaboration in-the-small therefore always ends up happening via email, an existing ubiquitous federated system that does not require that same coordination overhead. - Michael R. Bernstein

There are three dimensions here: Size of the group, distribution of participants among organizations, and - for lack of a better term - spontaneity. The three aren't entirely unrelated, for example the odds that all participants will belong to the same organization goes down as the number of participants increases, but they can be thought of as orthogonal for most purposes. - Michael R. Bernstein

Similarly, spontaneity decreases with the size of the group (at least at the outset, small groups can grow into larger ones organically). It is unlikely that a large working group will spring into being on it's own without some large-scale negotiations and planning behind it, including setting up a collaboration space. - Michael R. Bernstein

And yet, large-scale spontaneous collaboration *does* happen, when the infrastructure exists to support it. Case in point: Some Wikipedia articles which come together eliciting the contributions of thousands of participants in a very short period of time. - Michael R. Bernstein

Michael, good points on spontaneous collaborations. There are also organized collaborations funded collaborations such as the NIH Clincial Translational Sciences program or established multiorganizational research projects, intercorporate collaborations, or collaborations between corporations and universities. Are there different issues/parameters for these? - Jack H. Pincus

Perhaps we should distinguish between spontaneous collaboration (which can happen within an already organized system/organization, as it does within Wikipedia) and spontaneous organization, ie. ad-hoc group forming, for purposes of collaboration. There are slightly different thresholds to cross in either case. Note that the main advantage of a federated approach is *radically* lowering... more... - Michael R. Bernstein

An example of an effective platform was used in this topic: Google Docs. It allows multiple collaborators to edit a document through a graphical user interface. Concepts through text, and support for presentations and spreadsheets is improving. Access can be controlled, or published to allow collaboration, with compatible machine readable file formats to provide federation. - Mike Chelen

SciBarCamp: Aaron Rowe

It looks like we have a critical mass for a discussion about the future of healthcare; with an emphasis on what patients can do to help themselves, better ways for patients to interact with researchers and each other, policy tweaks that could help everyone, and emerging medical technologies. Who would like to attend?

July 1 - Comment - Like - Share

Attila Csordas, Shirley Wu, Jim Hardy and 2 other people liked this

Shirley Wu

An open letter to Oprah - http://shirleywho.wordpress.com/2009...

May 11 from I was lost but now I live here - Comment - Like - Share

Mickey Kosloff, Bora Zivkovic, tim and 30 other people liked this

jumping late on the anti-vaccination backlash bandwagon, but was "inspired" by her speech at Duke on Sunday... - Shirley Wu

24 more comments

If we googlebomb this, perhaps Oprah will see it? If we all blog it, and link it to the phrase "open letter to Oprah" -- or is there a better term/phrase to use, any SEO experts here? -- then perhaps it will get picked up. Also, do any of us have msm contacts? They love controversy, and might reprint Shirley's letter. I'd love to see this get some real traction. I plan to blog it anyway, hoping someone can tell me how to give it maximum google juice. - Bill Hooker

Yikes, what have I gotten myself into? :P Really, I'm just rehashing what many others have already said, e.g.... more... - Shirley Wu

I'm aware of the prior conversations, Shirley, but your letter is rather different in tone and strikes me as something that might get a positive (rather than an angry, defensive) response. - Bill Hooker

Good post, Shirley. Twittered http://twitter.com/MatToddChem - Matthew Todd

Saw this comment on Reddit re: my post - "Obviously this crazy person is unaware of the effects the last time people overreacted to bird flu in this country. Vaccines are potentially deadly. This headline ['Why Oprah should not give talk show to a baby killer ' - guess someone felt mine wasn't sensational enough] is crap." Does anyone know what effects s/he is talking about re: bird... more... - Shirley Wu

It's an interesting story. In 1976 a soldier died at Fort Dix from what was diagnosed as an H1N1 (NOT Bird, that's H5N1) strain similar to the 1918 strain of the Spanish Flu: the one that killed millions post WWI. The CDC and various other advisers urged Pres. Ford to start a mass vaccination campaign. Once the campaign started, a few people reported Gullian-Barre syndrome: a rare and... more... - Iddo Friedberg

Ah, thanks, Iddo. Seems like the anti-vaccination folks are still on shaky footing. It still seems strange because vaccines are proven to work, whereas getting sick from them has NOT been proven, and yet people keep following the anti-vaccine bandwagon - Shirley Wu

I guess this boils down to poor understanding of statistics. You receive a vaccine, something (unrelated) happens to you, you blame the vaccine. No matter that 1000 other people received the vaccine with no effects. You believe that your case is "special" and that you are not "a statistic". Understandable in some ways (we all think we're special), if completely wrong-headed. Question is: how better to educate? - Neil Saunders

That's a great question, Neil, and I'll answer Paulo's call to arms from last week http://blindscientist.genedrift.org/2009... by explaining my understand of how better to reach these people. Dave Munger has written about(people who wrote about) the tendency for people to overestimate near-term risks and underestimate larger, further off risks.... more... - Mr. Gunn

Just saw this. As someone from a third world country, where immunization saves more lives that people in this part of the world could possibly fathom, the anti-vaccination movement drives me nuts, especially since I know some relatively sensible people completely buy into it. Mr. Gunn's point about people listening to the fringe rather than the entire scientific community (in all kinds... more... - Deepak Singh

Jim Hardy said her post briefly made it on the top 10 list at wp.com, but I can't find it there now. - Mr. Gunn

I don't know about making the Top Posts, but the blog itself is currently listed at #7 on "Growing blogs" for May 18, 2009: http://botd.wordpress.com/2009.... (Not there on the overall "Growing Blogs" list, though.) Hard to beat CNN, FAIL blog, lolcats, and celebrity babies! - Shirley Wu

@MrGunn Yes, mis-spoke. Growing Blogs *not* Top Posts. Looks like it's faded away for the time being. Actually, I am impressed that there aren't more comments from dissenters. - Jim Hardy

Just got picked up by Bad Astronomy: http://blogs.discovermagazine.com/badastr... Starting to freak me out... - Shirley Wu

Showed the open letter post to my mom and she's happy I did. She's now forwarded it to her friends. Let's see if her chain-mail pals can make it into the soccermomsphere. :-) - Ricardo Vidal

@Jim, I'm a bit surprised as well that the comments have been so one-sided so far. Maybe just a matter of time. I won't have made it unless I get a troll or two, right? - Shirley Wu

Now the dissenters are coming out... sit back and grab the popcorn? - Shirley Wu

Jeez, I just checked back for the comment thread! You're braver than me, I can't deal with that level of discussion. Popcorn indeed... - Neil Saunders

To what extent does the passion of the "concernedmama" types come from making the choice to either blame themselves or blame vaccines? Obviously there's no role for blame here, but I can see a worried mother going back over things in her head (was it because I didn't eat right, was it that glass of wine I had, was it chemicals in my food ...) and looking for an answer. From an emotional... more... - Mr. Gunn

Passes the popcorn ... anyone wants butter or salt? - Lars Juhl Jensen

salt and pepper on mine please. And maybe some aspirin... - Shirley Wu

@Shirley. Aspirin's not good for you, it contains acetylcyalic acid. Stick with the salt & butter. - Iddo Friedberg

Hm, now that I think of it, corn is bad (see Michael Pollan), salt is bad (low/no-sodium diets), and butter is dairy (and thus equivalent to cocaine). Just handfuls of pepper for me thanks. - Shirley Wu

Shirley: with fresh corn Pollen would have no criticism based on food processing ;) - Mike Chelen

It always comes full circle to Alice in Wonderland. Pepper, lots of pepper.. - Jim Hardy

Martin Fenner

What is the right reference manager for you? - http://www.slideshare.net/mfenner...

May 17 from SlideShare - Comment - Like - Share

Mike Chelen, Shirley Wu, Berci Mesko, MD and 16 other people liked this

Cool! Can I use that for my student lecture on scientific publishing? - Björn Brembs

9 more comments

Björn, you can of course use the slideshow. And feedback is appreciated. - Martin Fenner

Nice, but I was hoping for a flowchart :) - Chris Miller

Very cool, Martin! A flowchart translated from your comparison chart would be a useful addition. - Mr. Gunn

Nice, Martin. Does anyone know if one of those allows multiple people to annotate the same PDF simultaneously? That is: not having to worry about sync issues from multiple people editing a PDF file. I would really like my group to be able to make notes and highlight on a common PDF, but that's tough to do without some kind of online stored version of the PDF. - Steve Koch

great job Martin! I was enjoying the presentation. Keep going! - Alexey

I don't think any of them let you do annotation simultaneously. I suspect that is a tough problem, dealing with real time editing and rendering while hiding from people the issues of where the file actually is being held. - Cameron Neylon

I know they're working on sharable annotations in the next version of Mendeley, but whether or not that's concurrent, I don't know. I'll ask! - Mr. Gunn

What the Mendeley developers tell me is that annotations are shareable via shared groups, and they're working on annotations saved within the PDF. They're aware of the need for non-overlapping concurrent edits aka "conflict resolution". - Mr. Gunn

Thanks for checking, MG. This worked before, so I'll try it again: "I command them to make it happen" :) - Steve Koch

Well, AFAIK, it's planned for the next release in June. There's some serious technical issues to work, though. - Mr. Gunn

Mary Canady

RT @easternblot: @jamiemcquay RE #sbcPA challenge (invite s'one who hasn't been to a barcamp before) - I did, and she signed up for sbcPA!

May 14 from Twitter - Comment - Like - Share

Jamie McQuay liked this

Jean-Claude Bradley

NASA Open Notebook Science Talk April 09 - http://usefulchem.blogspot.com/2009...

April 16 from Useful Chemistry - Comment - Like - Share

Andrew Lang, Jamie McQuay and John Dupuis liked this

Pawel Szczesny

Interview went fine. I got a position in academia; starting in May.

April 9 from Twitter - Comment - Like - Share

Daniel Swan, J. Abdul-Qahhar, Steve C and 40 other people liked this

Congratulations :) - Ricardo Vidal

34 more comments

Congrats! - Simon Cockell

Thank you :) - Pawel Szczesny

Congrats! - Shirley Wu

Congratulations! - Steve Koch

That's great Pawel, congratulations! - Walter Jessen

Congratulations! - John Dupuis

Congrats! - Meryn Stol

Congratulations!!! Where, when, how, what and why? Give us more info on the place and project, etc. - Bora Zivkovic

Well done on escaping the real world! - Bob O'Hara

nice! - Jean-Claude Bradley

Congrats! +1 Bora: details? - Iddo Friedberg

congratulations, hope you enjoy writing grants and peer-reviewing papers :) - Frank

Congrats! Entering the rat race.... - Jim Hardy

Thank you all. I will hold assistant professor position at Warsaw University. I will do the thing I like the most - building big picture ;) At first it will be molecular basis of some genetic diseases (currently I try to understand spherocytosis), however, since it's a kind of independent position, I'm free to change my mind at any time. - Pawel Szczesny

Frank, I don't like writing grants, so I applied for this position (I don't need three grants to get half of salary anymore :) ). Jim, I don't treat it as a rat race - I'm buying myself couple of calm years I can spend doing something (finally!) significant. - Pawel Szczesny

good job, Pawel. - Attila Csordas

Thanks Attila. - Pawel Szczesny

Congratulations! - Bill Hooker

Thank you Bill. - Pawel Szczesny

Congratulations! - Lars Juhl Jensen

Well done and good luck with it! - Cameron Neylon

congrats! - Björn Brembs

Congratulations! - Chris Lasher

Congrats! =) - FFing Enigma (aka Tina)

Congratulations! - Ruchira S. Datta

Congrats, Pawel! I will follow your path in 5 months. :) - Berci Mesko, MD

Great news Pawel. - Andrew Perry

Thank you all :) I wasn't expecting such overhelming response - I've only found a job ;) - Pawel Szczesny

Congratulations, Pawel! - Michael Nielsen

Dude, there's no "only" about finding a job, especially a faculty slot, in this economic climate. - Bill Hooker

Congratulations! - Yann Abraham

Bill, it looks little different here, especially in academia. We still ride on EU money and competition for academic jobs in not that huge, because almost all young people with recognizable scientific output move west (notable exceptions are people with rich partner) or work in accounting/marketing/transport (truck drivers). - Pawel Szczesny

Still, I'm very happy because of all of responses. Thank you all again :) - Pawel Szczesny

Congratulations :) - Michael Barton

congratulations !!! - Abhishek Tiwari

Jonathan Eisen

The physics of why bicyclists hate stop signs - Hard Drive - http://blog.oregonlive.com/commuti...

April 13 from Bookmarklet - Comment - Like - Share

Roland Krause, Jamie McQuay, Shirley Wu and 4 other people liked this

I will print this and carry it with me as I ride ... - Jonathan Eisen from Bookmarklet

3 more comments

I'm glad someone finally wrote this down. Brilliant. - Thomas Sharpton

I'm ambivalent about this issue. As someone who commutes by bicycle, I understand the frustration of having to stop but I also understand that in a contest between me and a motor vehicle I will almost always lose. By the way, might there be an analogy between this and jaywalking? you could argue that having to go to the crosswalks, while by default safer, is also very inefficient in most cases. - Shirley Wu

Oh, there are other posts about it, see this: http://xark.typepad.com/my_webl... and http://xark.typepad.com/my_webl... - Bora Zivkovic

Speaking as a pedestrian, this Special Pleading would be more impressive if I didn't find that I need to watch out for cyclists more than for cars--because the spandex-clad variety would as soon run me over as grant right of way, and feel Entitled to do anything they damn well please. - Walt Crawford

Jamie McQuay › Likes