Pierre Lindenbaum - Likes

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

3 hours ago from Science in the open - Comment - Like - Share

Mary Canady, Christina Pikas, Michael R. Bernstein and 13 other people liked this

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

2 more comments

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

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

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

Eric Neumann

Folks in communities like BioPERL, BioPython, and BioRuby would love RDF and existing resources...if they would take the time to try it!

Saturday from Twitter - Comment - Like - Share

Mike Chelen, Ruchira S. Datta, Ted Slater and 7 other people liked this

show us the data! - Jason Stajich

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Agreed with Jason. I like RDF and have played with it out of interest, but not run into lots of available data in my day to day work. - Brad Chapman

Fair enough-- I've been sitting on gigabytes of RDF for awhile, and using it in my commercial business (just because it's the early days); I'd be happy to post a few (possibly) interesting bits to you guys to try out. My only request is that we openly work together on it to do some demos possibly. Cheer! - Eric Neumann

To Eric and everyone who has "liked" this, please explain what this means. I understand the concept of RDF. I do not understand what you want Bio* projects to do with it. - Chris Lasher

Chris. If the public dara were formatted/normalized using RDF, most parsers, SQL queries used to cross the data between two or more datavases would be useless. bio2rdf is a good example: http://bio2rdf.org - Pierre Lindenbaum

Pierre, I interpret your comment as meaning "using RDF, there would be no need to develop nor maintain data and query parsers", which I pretty much agree with. I would hope that would free most informaticists to spend more time writing analytics and views, and less on bit swapping- IMHO... - Eric Neumann

@Eric , yes that's what I tried to say with my poor English skills ;-) - Pierre Lindenbaum

I "like" most mentions of RDF + bioinformatics, it tends to get lively :-) I interpret the post to mean "there is more out there than we realise". If so, as the first 2 comments said, let's see it! I hear a lot of talk, I don't see much in the way of usable data or tools. - Neil Saunders

++ to jason, brad and neil's comments. bio2rdf is a good start, but why do we even need RDF? BioMart is another warehouse that seems to work nicely on good old SQL. I think when people see a tool of comparable utility that depends on RDF they will take notice. - Chris Mungall

Chris- I actually wasn't referring to bio2rdf- as you said it's a nice start, but not key for most imformaticists; alternatively, I have converted GEO, mutdb, and pathway data into rdf. Was hoping you guys would find this useful to try some investigate? - Eric Neumann from iPhone

Attila Csordas

got the advice from my wife that before sleep I should relax w/ other types of literature than programming/biology & w/o backlighted screens

yesterday from Twitter - Comment - Like - Share

Khader Shameer, Piaw Na, Pierre Lindenbaum and 4 other people liked this

Reading anything right before going to bed is bad. Give yourself at least 30 minutes to unwind: lie on the sofa, watch mindless TV - anything that requires no brain! - Neil Saunders

9 more comments

I read Newspaper before sleeping and sometimes those editorials are good for sleep. :) - ashish

sudoku... - Andrew Su

thx guys, were staying up late in the last couple of days due to thinking on coding problems hard instead of sleeping and realized that the iPhones next to my bed are not helping me, probably will move them to another room. - Attila Csordas

Watching TV is a bad way to go to sleep. Reading books is great. - Piaw Na

My 'going to sleep' material is usually science fiction or fantasy. - Michael R. Bernstein

For unwinding I find that if you include a glass or two of red wine, - all of the above works :-) - Nils Reinton

s/red wine/vodka - Bill Hooker

Reading books: history of Science, SF, art, comics - Pierre Lindenbaum

Psychology books or... FriendFeed ;) - Pawel Szczesny

a good novel is my favorite way to relax before sleep - Mike Chelen

Mark H to Mark's feed, ART ROOMََََ

12 Misunderstood Monsters - Travis Louie - My Modern Metropolis - http://www.mymodernmet.com/profile...

2 hours ago from Bookmarklet - Comment - Like - Share

Pierre Lindenbaum, Admiral Anika and atalmatal liked this

"Set in Victorian and Edwardian times, Travis Louie's paintings are hauntingly beautiful. This imaginary world is filled with strange humans, mythical beings and misunderstood monsters." - Mark H from Bookmarklet

The Life Scientists: Benjamin Tseng

Hungry Amoebas Spawn Biggest Viruses Ever - http://www.wired.com/wiredsc... (via http://friendfeed.com/benjami...)

Hungry Amoebas Spawn Biggest Viruses Ever - http://www.wired.com/wiredscience/2009/12/giant-viruses/?utm_source=feedburner&utm_medium=feed&utm_campaign=Feed%3A+wiredscience+%28Blog+-+Wired+Science%29 (via http://ff.im/cD0cq)

yesterday - Comment - Like - Share

Deepak Singh, Ami Iida, Steven Perez and 5 other people liked this

Uhh ? Help, I cannot find their citation "Giant Marseillevirus highlights the role of amoebae as a melting pot in emergence of chimeric microorganisms.” By Mickael Boyer & al. PNAS, Vol. 106 No. 48, December 7, 2009" in http://www.pnas.org/content... .... - Pierre Lindenbaum

3 more comments

Curious, I can't find it either -- anyone? - Benjamin Tseng

No sign of it in current issue (which is 106(49) Dec 8, not 106(48) Dec 7) or early edition. Wouldn't be the first time that Wired screwed up a reference. - Neil Saunders

http://www.pnas.org/content... - Thomas Lemberger

Ah, thanks Thomas - Pierre Lindenbaum

Egon Willighagen

I wish the English language had more interesting characters. - http://xn--m-4fanol5b8b4f5bcu8...

12 hours ago from delicious - Comment - Like - Share

Duncan Hull, Carmine Gnolo and Pierre Lindenbaum liked this

Don't the heavy metal umlauts count? - Noel O'Boyle

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there is the occasional é , ö and æ in English. oh and the è used to show up in poetry. - Richard Akerman

@Richard Really? @Noel Two words: Spın̈al Tap. - Chris Lasher

résumé. noösphere. encyclopædia. - Richard Akerman

Did you all note the URL? It does not nicely show up on FriendFeed though.... - Egon Willighagen

References Wanted: Graham Steel

POLL. As a direct result of this FF thread http://friendfeed.com/science... I've created a one question poll. The question is "Is it appropriate to raise the visibility of the References Wanted room outwith FriendFeed?". The possible answers are "yes", "no", or "unsure". I would be really grateful if subscribers to this room would participate.

yesterday - Comment - Like - Share

Piotr Byzia, Pierre Lindenbaum, Egon Willighagen and 3 other people liked this

Poll is here:- http://www.micropoll.com/akira... Thank you in advance. - Graham Steel

10 more comments

Just to expand briefly on Graham's intro: I think the RW room is covered by Fair Use (nota bene, ianal). Nonetheless, the likely result of any legal challenge by publishers would be that FF would shut the room down as a precaution, and we'd have to fight to re-open it. I doubt we have the resources for that fight, so as a matter of realpolitik I'm voting to continue to fly under the... more... - Bill Hooker

^^What Bill said. Yes, the world absolutely needs access to the scientific literature, but we need to work to reform the publishing process and the laws. All things considered, this is a very small room, which is why it hasn't attracted the ire of the publishers. If we advertise and it gets large, the industry will start playing the same whack-a-mole lawsuit game that they do with music or movie sites. - Chris Miller

I voted "No" - Pierre Lindenbaum

Please keep voting folks. A dozen in so far, thanks. - Graham Steel

The referenced thread is about a letter to the journal Cell in which we promote FriendFeed. The RW room will be the single most attractive feature for people who have never used social media. I also think it helps to show a large readership what kinds of hoops we will jump through to get access - and the RW has a great record of people not having access. So in the end, all publicity... more... - Björn Brembs

I'd love to read that Cell paper if possible! http://is.gd/5fQ0D I voted 'unsure' on the poll, perhaps not very helpful, but I thought that my 'yes' might not be as strong as the poll's yes might be demanding. I would like more people to be aware of this helpful service, but to hear of it as word of mouth rather than a 'one to many' broadcast in a journal article. I suppose I'm voting for the status quo (of this room), but with gradual increases in numbers. #fencesitting ;) - Jo Brodie

I would be more concerned about publishers cutting off access to individuals known to be supplying papers in the room for breech of TOS. It has happened to one of our researchers but for other reasons. - suelibrarian from iPhone

Here is the draft of the letter: http://etherpad.com/Microbl... Note that we do not need to spell out the name of the room in the letter, as we do now, just the functionality. I can only re-word my argument from above: cowering before the possible reprisals of 'big publishers' is definitely not the best way to change the current publishing model. In fact, anybody who... more... - Björn Brembs

I voted no. As I see it, the role of RW is to provide a service, not to instigate a revolution or provide a soapbox for change in the publishing industry. I don't think it's fair to create the potential for unpleasant repercussions through wider publicity for a "cause", certainly not without the full knowledge and agreement of everyone who has ever used the room. - Neil Saunders

@Bjoern, it's not "no big deal" to open another room -- that simply won't work, corporate copyright lawyers are quite good at whack-a-mole and we cannot expect FriendFeed to fight our Death To Toll Access battle with us. As I said above, the fight you are spoiling for is worth having, but I don't want to pick it and then get my ass kicked. If you really want people to fight, you'll need... more... - Bill Hooker

The purpose of the room is explicitly "to document the harm caused by closed/toll-access publication". What's the purpose of collecting this data if we're not going to publish it? Voted yes, apparently against the consensus, whose arguments I'm sympathetic to, but it seems to me like even if we did mention the RW room in a letter it would still only have visibility to a quite small audience. Perhaps the poll choices should have been "yes, publish the RW room/No, don't publish yet"? - Mr. Gunn

Ian Mulvany

#ahm09 interesting, scientists are afraid to share data because others might mis-interpret the data, though this hardly ever happens.

11 hours ago from Twitter - Comment - Like - Share

suelibrarian, Mike Chelen, Richard Akerman and 6 other people liked this

Has there been much research into this (i.e. quantified "hardly ever")? - Sarah Kendrew

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I think a bigger reason is they don't want people seeing errors - every experiment has some kind of "error" - especially an unmeasured quantity that turns out to be important in the end - Jean-Claude Bradley

As I said on twitter, really think this is just an instance of the control imperative. Scientists are for the most part very uncomfortable with relinquishing direct control over anything that affects them - they want to make every decision as far as possible and the idea that for a framework to scale you have to give up control over thing seems very alien. But I too would like to see some data and analysis on the issue - a fair bit of high profile data misinterpretation going on at the moment. - Cameron Neylon

scientists concerns can help be addressed by advancing methods and best practices, and by describing case studies to provide confidence. accuracy is an inherent purpose of knowledge sharing, it is a testament to the high level of skill that it is usually accomplished - Mike Chelen

Well, the imperative to 'show your work' can make people very uncomfortable. I see this all the time in the Open Source world, where developers sit on their code polishing it instead of releasing. - Michael R. Bernstein

Karen James

I wish there was a universal format for submitting peer-reviewed papers; authors could post papers (once!) & then the journals bid on them.

July 30 from Twitter - Comment - Like - Share

Mickey Schafer, Cesar Sanchez, Nir London and 32 other people liked this

Oh, now that's an interesting idea, Karen. - Graham Steel

25 more comments

Cyndy Parr tweets ( http://twitter.com/cydparr... ) "This is kind of what PLOS One envisions -- it goes up there, and then it could get chosen to be part of a hub". Iz true? - Karen James

Thanks, Graham. Having just had a paper rejected by two journals in a row, I'm fed up to here *points to own eyebrows* with spending hours if not days re-formatting to meet the ridiculously precise but in no way substantive guidelines of different journals. It's not even rewriting, it's just pointless fiddling and a silly waste of time. If the taxpayers only knew... - Karen James

There are two issues at hand here. One, a universal format for submission, Two, a bidding process on papers. The Neuroscience Peer Review Consortium points to how the second part of this kind of deal is working right now in some disciplines (http://nprc.incf.org/), the really really sad part about the first issue here is that the big publishers don't care what format you submit in (let... more... - Ian Mulvany

+1 for more standards for paper submissions, starting with reference styles. And for allowing submissions in the NLM DTD format. - Martin Fenner

Ian, you may say they don't care, but when one is submitting a manuscript, one is trying to do everything one can not to give the publisher any possible little excuse to reject your paper without review. - Karen James

Second time in a week that someone stated "publishers don't care about format of submissions". Again I ask: if that's the case, why do all journals make a huge deal about it in their instructions to authors? - Neil Saunders

As for universal format: easily solved by writing our papers on the web. Imagine a simple forms-based interface with fields for title, authors, abstract, introduction... Imagine a button in Google Docs that says "submit this document to <insert journal here>" !! But currently, we all like to use our own word-processing software on our own machines, then upload a document in a multitude of formats. It's going to take a big shift in thinking and work practices. - Neil Saunders

What Neil said: if journals don't care, why do they make such a damn song and dance about it? Why not explicitly say you can *submit* in any basic AIMRAD format? Worry about format after acceptance: either the journal can send it to India per Ian above, or if they make the authors do it at least they only have to do it once. My next paper (quit laughing) is going out in basic AIMRAD... more... - Bill Hooker

Note: this is easier for me to do than many, because I've basically given up on an academic career as currently constructed. - Bill Hooker

"it's just pointless fiddling and a silly waste of time. If the taxpayers only knew" I think they should / deserve to know! - Björn Brembs

+1 Neil "why do all journals make a huge deal about it in their instructions to authors?" and +1 Björn "I think [the taxpayers] should / deserve to know!" - Karen James

Neil & Bill: maybe "don't care" is to strong a phrase. A manuscript does need to be structured correctly to fit into the journal's content management system (an application note looks different to a letter looks different to a research paper), have images properly resized and references in the right format so that they can be processed by systems that convert to them links etc. - Euan

Also: what happened to that Wolfram word processor for papers that was supposed to do what Neil mentioned above with Google Docs? - Euan

Ah, http://www.wolfram.com/product... but doesn't look like there's a great deal of support for life sci journals (BMC aside) - Euan

the publishers i know would be delighted to standardise to NLM DTD for submissions -- would save lots of editorial time and production costs -- the publisher i know best sends accepted papers to be manually turned into xml which can then be used for PMC deposition and the semi-automatic generation of the HTML and PDF versions. But things like the Publicon app have taught publishers that implementing the technology to do something doesn't mean that it will happen in significant quantities! :) - Joe Dunckley

I used Publicon when it was released a few years ago. Essentially a dead product now. Lemon8-XML does what Neil describes as "Imagine a simple forms-based interface with fields for title, authors, abstract, introduction... ": http://network.nature.com/people.... - Martin Fenner

These interviews (about eXtyles and Editorial Manager) might be interesting to those that care about submitting papers in the NLM DTD format, as I specifically asked that question: http://network.nature.com/people... and http://network.nature.com/people... - Martin Fenner

There is a nascent version of that working in neuroscience http://nprc.incf.org/. Journals have formed a consortium where if an author submits to one journal and it gets rejected, the author can specify that the reviews follow the paper to another journal so that it doesn't need to be re-reviewed. This was viewed as a way for papers that have nothing wrong with them but which don't fit the scope of the journal can be published more quickly and easily. - Maryann Martone

What about replacing "papers" and "journals" in the subject line with "proposals" and funders? - Daniel Mietchen

What if journals said here's our LaTeX template. Put the right text in the indicated field, lotion in the basket, and anything else won't be accepted. - Mr. Gunn

@Daniel Mietchen: Yes, that too! @Mr. Gunn: What I'm advocating is that there's a single LaTeX (or whatever) template - not that you'd re-paste for each journal. - Karen James

karen, yes. The idea being you give them the text and they do whatever they like with the formatting. - Mr. Gunn

Aside from making life easier for authors, it would allow sane computational use of papers. With PDF, you don't even know which image a figure legend refers to, except by guess work. The difficulty is that the journals don't see it as their problem. The solution is for the authors to make it the journals problem - Phil Lord

I like the idea, Karen. Publishing an exciting paper should not a be a torture (for us!) - Betül

Getting access to research papers is already too expensive. Wouldn't it just be more so if we invited a bidding war on each paper? Write good papers, and submit them to PLoS. - Ted Slater

I'd like something similar for the review process. Instead of having to register for each journal/publisher managing logins and passwords for each, have a clearing house that manages reviewer information that the journals subscribe to. - John Hogenesch

Christopher Harris

so much to read and learn :/

12 hours ago from Twitter - Comment - Like - Share

Pierre Lindenbaum liked this

Paulo Nuin

Archiving next generation sequencing data. - http://www.ncbi.nlm.nih.gov/entrez...

12 hours ago from Google Reader - Comment - Like - Share

Peter Miller, Cameron Neylon, Jan Aerts and Pierre Lindenbaum liked this

I still wonder about all the data we are losing from the raw images due to sub-optimal processing. How much are we getting now 50% of the useable data or has it gone up? - Cameron Neylon

The paper doesn't describe the architecture of the database :-/ - Pierre Lindenbaum

Duncan Hull

Workflow matching using semantic metadata - http://www.citeulike.org/user...

13 hours ago from CiteULike: dullhunk's library - Comment - Like - Share

Pierre Lindenbaum liked this

Enro

Les Ernest de la rue d'Ulm, alias TED à la française http://www.les-ernest.fr/ (via @ritontriton)

13 hours ago from Twitter - Comment - Like - Share

Daniel Mietchen and Pierre Lindenbaum liked this

Benjamin Tseng to Benjamin's feed, The Life Scientists

Amazing gel shows Ubiquitin is transferred one-at-a-time and on a millisecond timescale! - http://www.iayork.com/Mystery...

December 3 from Bookmarklet - Comment - Like - Share

Andrew Perry, arek, Jean-Claude Bradley and 16 other people liked this

That's awesome. - Bill Hooker

2 more comments

Ian York rocks, as do the scientists who did this. - Mr. Gunn

Gels still speak, even without lasers... - Mark A Jensen

My initial reaction was "how can anyone pipette that quickly !" ... but it seems they have some fancy quench-flow equipment to get around that problem. Very cool. - Andrew Perry

Yann Abraham

Science sans conscience - http://vidberg.blog.lemonde.fr/2009...

yesterday from Google Reader - Comment - Like - Share

Pierre Lindenbaum liked this

The Life Scientists: 'Mummi' Thorisson

One giant leap for Taverna: workflow: workflow construction workbench used by NASA's JPL in WS-infrastructure - http://www.omii.ac.uk/wiki...

yesterday - Comment - Like - Share

Steve Koch, Pierre Lindenbaum, Pawel Szczesny and 2 other people liked this

"NASA’s Jet Propulsion Laboratory (JPL) created the first American satellite and are now using Taverna for their Web Services-based infrastructure.[..] One of the challenges faced by the research team is the integration of various models that are used to explore the science behind the JPL’s missions. These models have been developed independently and run on different platforms, so their integration is not straightforward. The JPL’s solution is to wrap each model as a Web Service and drive them with a Web Services-enabled workflow." [From the OMII-UK newsletter: http://www.omii.ac.uk/wiki...] - 'Mummi' Thorisson

?!? - Neil Swainston

Rocket Science? - Duncan Hull

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

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

November 10 - Comment - Like - Share

Graham Steel, Cesar Sanchez, Jamie McQuay and 14 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

61 more comments

http://www.cell.com/authors... / Correspondence: "The Correspondence format provides our readers with the opportunity to respond to an article in Cell—either a research article or Leading Edge article—that has been published within the last 2 months. Correspondence should be no more than 900 words in length with up to five references and should be of interest to the broad... more... - Daniel Mietchen

Now that sounds like a good idea! I'm all for it - especially mention the gazillion "facbook for scientists" already out there. - Björn Brembs

I gave it a start at http://etherpad.com/Microbl... - feel free to join in! - Daniel Mietchen

Added some stuff... - Björn Brembs

333 words so far, and once the generic FF description and some highlights from the spreadsheet are in, we will be near the limit. So probably no time to dwell on fb4sci, though I would still like to mention the NIH grant in the hope that those people will build on the ideas we lay out. - Daniel Mietchen

Maybe steer away from a "but we want to talk about friendfeed" towards more "there is a much richer set of tools out there...and here is a good example..."? Might mean the Fb4Sci stuff can get squeezed in? - Cameron Neylon

I would actually prefer the Fb4Sci stuff in there, and the article would be more balanced if we were to name a few more services that offer microblogging (I listed some in the Organization part of the document). FF can then be described in two sentences as a particularly useful example because it provides hierarchies of threaded conversations in which the most current and the most popular entries compete for the top of attention. - Daniel Mietchen

Correspondence has to be submitted within two months, so we got four weeks to go if we are to submit something on the matter. Perhaps we can indeed expand this into a general overview on the potential of web 2.0 stuff for science. To this end, I just started a vote on the "open science breakthrough of the year" at http://ff.im/cidKG . - Daniel Mietchen

thanks guys - a very interesting read (the paper, these responses, the etherpad document). I've added a couple of possibly-relevant points to the etherpad doc. :) - Allyson Lister

...bumping to remind me to try and do something about this before deadline... - Cameron Neylon

To those coordinating this: let me know if you need any extra help with anything... - Allyson Lister

Allyson, help with shortening the FF part and with adding in something on the non-FF alternatives would certainly do something good to push things forward at this stage. Thanks! - Daniel Mietchen

Edited a bit and tried to merge the new contributions into the draft. The word count for the FF part now stands at ~570 excluding FF real science examples. I still don't see how we can give an overview of more than one of these services and accomplish anything better than a boring enumeration without spirit. On the contrary, people will just get the impression that scientists can't make... more... - Björn Brembs

Correction: 660 words... :-) - Björn Brembs

See also Jean-Claude's stylesheet about FriendFeed + Science ? FFscience: https://spreadsheets.google.com/ccc... - Pierre Lindenbaum

Thanks, Pierre, was already mentioned. Just added some examples from this spreadsheet. Word count is now at 760. Tasks remaining (if you agree on the general structure): polishing and final, concluding paragraph. Tasks remaining if you don't agree: re-write :-) - Björn Brembs

have removed a few words, tightened things up. will do more as time permits - Allyson Lister

Getting there ... >800 words. - Björn Brembs

953, so some trimming needed. Mentioned the NIH grant in the roundup section. Which references to take? - Daniel Mietchen

Good job, Daniel! I think the references are fairly clear, most of them are in the text already (i.e., papers from FF). We have until December 30 to get it all finalized, so we have some time, but I'd rather get it there sooner than later. I think a few more runs of polishing and honing and we should get the final author list together and submit. I suggest everybody who wants to be an author leave the URL to their FFfeed at the end, that way readers get an idea of what FF looks like. - Björn Brembs

What about signing with a group pseudonym (something like D H J Polymath; http://arxiv.org/find... ) and a link to this thread or the etherpad? - Daniel Mietchen

I have inquired with them whether links count as references. - Daniel Mietchen

@Daniel as a pseudonym, I suggest to use what Deepak calls the "BioGang" http://openwetware.org/wiki... http://www.linkedin.com/groups... - Pierre Lindenbaum

What about the title? "Should you be sharing science online?" would be my favourite but it is not reflective of the current emphasis. Any suggestions? - Daniel Mietchen

Pierre - good one. Perhaps add FF as initials? - Daniel Mietchen

BTW, the doi does not resolve - anybody has the correct one? - Björn Brembs

895 words... - Björn Brembs

I like Clay's idea for a title: "It's not information overflow, it's filter failure " :) - Allyson Lister

884 words, and a few more slight tweaks. This means we could probably fit an entire sentence about other approaches' existence, if we wanted :) - Allyson Lister

Björn - http://dx.doi.org/10... . - Daniel Mietchen

@Allyson: awesome! @daniel, sorry, meant this one: http://dx.doi.org/10...) - Björn Brembs

Added ref 4: the NAR paper ( http://tinyurl.com/mr5kvm ) - Pierre Lindenbaum

Right now this sentence is a mixture of DOIs & links: which to use? : "Such conference coverage has even received direct (e.g. ISMB09 http://www.iscb.org/ismbecc..., BioSysBio09 http://dx.doi.org/10...) or indirect (e.g. ISMB08) support from the conference organizers, see e.g. http://friendfeed.com/ismbecc... ." We can convert them all to links, & save some of the 5 publications, but all three examples here have papers associated with them (well, ISMB09 paper is accepted) - Allyson Lister

Ah - actually it looks like the ref we would use for ISMB08 is actually ref 1 - am I correct? There isn't much detail in ref 1 yet. That could solve part of the problem - Allyson Lister

I'd also like to find that out, but the DOI does not resolve (for me?). Haven't looked at ref1 yet, to determine if it's redundant. - Björn Brembs

The DOI, if intact, should point to http://genomebiology.com/2009... , which is behind the paywall for me but perhaps Allyson can give us a hint ;-) - Daniel Mietchen

Sorry - yes, @Daniel, the DOI seems broken, but the genomebiology link is the correct one. If we're limited for references, we could just link to the FF room, which is http://friendfeed.com/biosysb... - Allyson Lister

We have 5 references and thus I added Allyson's to make it 5 :-) - Björn Brembs

Question as to whether its advisable to include reference to the RW room. I think someone raised this somewhere but I can't see the discussion now. - Cameron Neylon

Otherwise made a few very minor changes - Cameron Neylon

I'm about adding a ref to O'Reilly/"Beautiful Data". The collaboration for this book started here: http://friendfeed.com/fgibson... - Pierre Lindenbaum

@Cameron - yep, a few of us have brought up that point (me and michael and some others I think in the etherpad doc). I'm happy to go with whatever the owners of the room, or the general consensus, wants :) - Allyson Lister

Cameron, do you have a reference for the second grant? I am only aware of http://www.labgrab.com/users... . - Daniel Mietchen

Added mention of polymath project. - Daniel Mietchen

Found reference mentioning both grants: http://www.nih.gov/news... . - Daniel Mietchen

RW room discussion is in the header of the document. IMHO there are several crucial reasons for finally going public: it's a grey area probably still fair use; more subscribers mean more access; readers will see the usefulness of this room, even if they don't get any of the other features; the kinds of hoops we have to jump through to get access need to be made public and the room has a significant record now. - Björn Brembs

I think we need to drop ref 6 since we only have 5 and it's not a journal article, correct? - Björn Brembs

With Etherpad deleting everything by March 31, we should think of ways to archive existing pads - particularly relevant for this one, as it was meant to be citable. As far as I can tell, none of the currently available options preserves the version history, so if we want to have that, we should do a screencast. - Daniel Mietchen

Indeed, we need to think of something! - Björn Brembs

Incidentally, the threat of such services disappearing certainly contributes to the hesitation of people to adopt social networks, and the best ways I see to cope with that problem is to have either open standards on data portability, or - better still - social networks (or at least one of the most suitable ones) that are built entirely open source platforms, with open configuration (and of course data portability too). Any suggestions on whether and how this could fit into the concluding paragraph? - Daniel Mietchen

Isn't it already in there, sort of? Where we write that these tools are in development and NIH funded? - Björn Brembs from iPhone

Haven't seen mention of open source and open standards in the news on these NIH grants, so it may be worth making more clear that this is needed. - Daniel Mietchen

Interesting turn: Etherpad will remain operative until at least when they release their source code. http://etherpad.com/ep... . - Daniel Mietchen

Upon feedback from Graham, I took the RW reference out. Still think some mention of Open Source would be good. http://www.nih.gov/news... does not mention it. 816 words. - Daniel Mietchen

Can we be part of that feedback, please? I find the RW functionality so convincing for non-social web users that I fear the whole article might be wasted, i.e, preaching to the converted, without this component. - Björn Brembs

It was in a DM that I just forwarded to you (dunno whether that works), and I asked him to comment here too. - Daniel Mietchen

Did anyone manage to do a screencast? I could try and do that today if its useful? But maybe better to wait until you feel is finished? - Cameron Neylon

I think we should wait until it's basically submitted. - Björn Brembs

@Daniel: DM was blocked (private). - Björn Brembs

Nothing wrong in testing, otherwise I'd also wait till it's submitted. @Björn - sent you screenshot. - Daniel Mietchen

I'll comment once I get back form work (only have internet access here during lunch hour). - Graham Steel

Right. 1) Having consulted with Bill, we have (the same) mixed views vis a vis raising the visibility of the RW room. 2) We don't feel that we "own" the room though, it belongs to everyone who uses it. 3) We agree that a poll should be set up for subscribers of the RW room to vote on the issue of whether or not they feel it appropriate to raise visilbility of the room outwith FF. 4) The poll is http://www.micropoll.com/akira... and I'll post a link to it in the RW room shortly. - Graham Steel

Dan Brickley

LODE: An ontology for Linking Open Descriptions of Events - http://linkedevents.org/ontolog...

yesterday from delicious - Comment - Like - Share

Nakao M. and Pierre Lindenbaum liked this

Neil Saunders

@mndoci There's an awful lot of data/tools at NCBI, but much of it is buried away behind multiple clicks. They need more AJAX and REST :-)

Monday from Twitter - Comment - Like - Share

Deepak Singh, Khader Shameer, Pierre Lindenbaum and Richard Akerman liked this

Kubke to Kubke's feed, ScienceOnline2010

Anyone interested in exploring cloudworks as an aggregating site for Scionline2010? http://cloudworks.ac.uk/cloudsc...

Monday - Comment - Like - Share

Konrad Förstner, Pierre Lindenbaum, Pawel Szczesny and 2 other people liked this

I was introduced to it today. It allows interaction/liveblogging/commenting in a way similar to FF, but an advantage I see is that it can also aggregate tweets based on the hashtag, and these can get archived through a function called twapper that gets set up when one sets up the cloudspace. It is not open source at this time, but I am told that will be happening in the near future. I am not sure I can assess its functionality/advantages/disadvantages on my own :). I also don't see in it the ability for it to take in my feeds from other social network sites, but that might result in keeping the space of discussion cleaner. The space is by definition open, there is no option to create closed discussions within the site. My understanding is that it was created originally with funding from the UK goverment as an open collaborative educational tool. Any thoughts? - Kubke

4 more comments

Looks interesting! Need to check it out... - Björn Brembs

You might want to check out the ascilite 2009 (or ascilite09) tags. The meeting is being blogged through there. Might provide a good template of how the dynamic works. - Kubke

Not quite sure what 'cloudstream' and 'cloudscape' entail, but this service really looks very promising. Good stuff! - Björn Brembs

The cloudscape is like a group of clouds (could be like a wave, or like a group, eg, the meeting). The cloudstream is more like an individual thread within that cloudscape (the sessions), but can belong to more than one cloudscape. What I am not sure is how collaboratively each cloudstream can be generated. I like that you can add references, comments, and links in its own space (would... more... - Kubke

I am sorry, my error. The cloud is the individual element (where the session liveblogging would be done). The cloudstream is the stream of clouds (it tells you what is happening within the cloudscapes you are following) - Kubke

Meme-Dini to Meme-Dini's feed, Photo Gallery, Photographing, ART ROOMََََ

Norman Rockwell’s Photo Realism | PDN Photo of the Day - http://www.pdnphotooftheday.com/2009...

Monday from Bookmarklet - Comment - Like - Share

Pierre Lindenbaum, gumbit and Xenophilius liked this

popo-realism - Meme-Dini from Bookmarklet

laura

"I used to think that the brain was the most wonderful organ in my body. Then I realized who was telling me this".-Emo Phillips

Monday from Twitter - Comment - Like - Share

JoeCamel, Björn Brembs, Christopher Granade and 6 other people liked this

Timothée

http://www3.interscience.wiley.com/cookie_...

Monday from Twitter - Comment - Like - Share

Pierre Lindenbaum liked this

Tom Roud

Nouveau billet : comment l'homme va (peut-être) évoluer http://darwin2009.blog.lemonde.fr/2009... (sur le blog darwin2009)

Sunday from Twitter - Comment - Like - Share

Pierre Lindenbaum liked this

Fulaan, inna Hebel to Fulaan,'s feed, The Life Scientists, Science 2.0, Highfalutin

Science: The looming crisis in human genetics | The Economist - http://www.economist.com/display...

Saturday from Bookmarklet - Comment - Like - Share

Thomas Brox Røst, Mary Canady, Kol Tregaskes and 19 other people liked this

"Human geneticists have reached a private crisis of conscience, and it will become public knowledge in 2010. The crisis has depressing health implications and alarming political ones. In a nutshell: the new genetics will reveal much less than hoped about how to cure disease, and much more than feared about human evolution and inequality, including genetic differences between classes, ethnicities and races." - Fulaan, inna Hebel from Bookmarklet

2 more comments

we'll know more than before - surely a good thing....... - winckel

For a different perspective, see the Nature article "Let's celebrate human genetic diversity" http://ff.im/9PbOx - Ruchira S. Datta

Uh-Oh... - Christopher Harley

The Life Scientists: Ami Iida

Gallery: The Year's Most Amazing Scientific Images　　　http://www.popsci.com/node...

Saturday - Comment - Like - Share

Steve Koch, Nakao M., Pierre Lindenbaum and 4 other people liked this

Inner ear hair cells. Colored scanning electron micrograph (SEM) of sensory hair cells from the organ of corti, in the cochlea of the inner ear. These cells are surrounded by a fluid called the endolymph. As sound enters the ear it causes waves to form in the endolymph, which in turn cause these hairs to move. The movement is converted into an electrical signal, which is passed to the brain. The V-shaped arrangement of hairs lies on the top of a single cell. Magnification: x21,000 when printed 10cm wide. - Ami Iida

The Life Scientists: Oliver Hofmann

New portal for cloud computing in bioinformatics, set up by Justin Johnson at JCVI: http://www.cloudbiolinux.com/ Really looking forward to this collaboration.

Saturday - Comment - Like - Share

Paul Bacchus, Marcos de Carvalho, Pierre Lindenbaum and 5 other people liked this

Likewise - Deepak Singh