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Arnaldo M Pereira to Arnaldo's feed, Python, Computer programming, TheNextWeb Forum, RWW: The Future of Tech

Socket Benchmark of Asynchronous Servers in Python - http://nichol.as/asynchr...

yesterday from Bookmarklet - Comment - Like - Share

Ho John Lee, Marcos de Carvalho and Scott liked this

"There has already been written a lot on the C10K problem and it is known that the only viable option to handle LOTS of concurrent connections is to handle them asynchronously. This also shows that for massively concurrent problems, such as lots of parallel comet connections, the GIL in Python is a non-issue as we handle the concurrent connections in a single thread. In this post i am going to look at a selection of asynchronous servers implemented in Python." - Arnaldo M Pereira from Bookmarklet

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

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

November 10 - Comment - Like - Share

Sandeep Gautam, rowlikeagirl, Kubke and 19 other people liked this

No mention of friendfeed, so what about writing a correspondence piece on this? It could be based on http://ff4s-paper.wikidot.com/start and perhaps also put the recent NIH grant for a "Facebook for Scientists" ( http://ff.im/beKk7 ) in perspective by providing an overview over existing tools along these lines and why they are not widely used. - Daniel Mietchen

105 more comments

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

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

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

Added some stuff... - Björn Brembs

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

895 words... - Björn Brembs

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

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

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

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

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

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

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

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

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

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

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

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

Otherwise made a few very minor changes - Cameron Neylon

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

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

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

Added mention of polymath project. - Daniel Mietchen

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Apart from inclusion of the RW room, the title has not been decided yet. Two suggestions are in there now (I threw away my older one). - Daniel Mietchen

Also, what about the "like=bookmark" discussion? I would like to see that paragraph go back in. - Daniel Mietchen

I thought that like=bookmark was clear from the context? If not, then it should be easy to add a sentence to make it explicit. - Björn Brembs

Björn - see chat bar - Michael was not comfortable with the notion. Any other opinions? Also turned Shirky quote from title to quote and set the title to "Social filtering of scientific information - a view beyond Twitter". - Daniel Mietchen

Besides, FF search has now been unusably slow for weeks, so I wonder whether we should take this formerly excellent feature off the draft. See also http://ff.im/cO3Jw . - Daniel Mietchen

Two weeks left to submit. I plan to do it on Sat (Dec 19) around noon UTC. Still to address: RW room and perhaps ephemerality of non-Open Source services like FF. I think I saw somewhere that FF have released (part of) their source code, or plan to do so. Anyone know details? - Daniel Mietchen

Added "the permanence of services whose source code is not public" as an unresolved issue. brushing welcome. What about the RW room? - Daniel Mietchen

Also, authors need to identify themselves in the document, or they will be missed. Academic affiliations and FF feeds, please! - Björn Brembs

Like the current version a lot! Also the source code permanence point was important! We should get it ready, clear authorship and author order. My suggestion is Daniel in front, me in the back and whoever feels should have a place in the middle, but I'm flexible (or does author order matter here at all?). From Bill's argument, we should leave the reference to the RW room in, but I'm also flexible there. If there are no storms of protest now, let's keep it the way it is. - Björn Brembs

I did some more brushing - 899 words now without the title (spot landing). As for authoring, I would really like to go for a group pseudonym (as explained above), but the submission process will probably ask for the usual contact information (incl. email) anyway. Order does not matter to me. Will check back in about 36h, with the intention to submit. - Daniel Mietchen

I was only pointing out that if you mention the RW room at all, you might as well name it. The poll stands at 41 votes (~25% representation, but it seems to me that there aren't many more than 41 really active contributors/users). The tally is No - 56%; Yes - 32%; Unsure - 12%. I don't think the piece loses much by deleting the mention of the RW room, and it seems to me that the users prefer to continue to keep quiet for now. - Bill Hooker

I tend to agree with Bill. It seems to me that mentioning (and in doing so effectively naming) the RW room is not what users (that cared to vote) want FULL STOP - Jan Wessnitzer from iPod

(1) The point of the letter is to attract scientists who are not using social media for their work to FF. As far as I can tell, the one single thing that everybody can profit from that doesn't already exist in mailinglists etc. is the sharing of papers. Moreover, this is also the one single aspect that touches every single reader, as nobody has access to all the literature. So while it... more... - Björn Brembs

(2) This has been mentioned before, but I see no reason why one would have any interest other than supporting closed access, in keeping quiet. The purpose of the room clearly is to 'document', so nobody in his/her right mind would think that their actions remain anonymous. This means that everybody participating must have been well aware that one day this documentation will be... more... - Björn Brembs

(3) I have now voted often enough to skew the results to more than 50% 'yes'. Who can verify that this has not occurred before, on the 'no' side? - Björn Brembs

Bjoern, I do agree with your arguments. W.r.t. (3), I was merely trying to argue that the vote should be respected (if it were representative). Allowing multiple votes clearly screwed that up beyond repair! ;) - Jan Wessnitzer

BTW, I voted 'yes' and maybe the only way to do this now is to vote openly here in the Forum! - Jan Wessnitzer

@Bjoern: "I see no reason why one would have any interest other than supporting closed access, in keeping quiet" -- are you going to pay my legal bills for me, if I get sued? That's a completely serious question. I'm one of the heaviest suppliers of papers in the room -- if anyone is targeted, I certainly will be. I have said many times that I don't think I am doing anything wrong OR... more... - Bill Hooker

@Bjoern, cont'd: I see no reason to think that (before you fucked it up :-) ) the vote was not representative, which means that most of the RW room users were less willing than you to take up arms against their closed-access oppressors. Judge that as you will, my friend, but some of us have limited resources. If even one publisher sends even one cease-and-desist letter to FriendFeed we... more... - Bill Hooker

@Bjoern, cont'd: I fucking HATE that I have to make this calculation. I would rather publish and be damned -- if the publishers do send lawyers, mount an international campaign in defense of the room and its users and bring their shitty empire crashing down around their beancounting ears. But I have my newly acquired all-American cowardice to consider: I have no health insurance and my... more... - Bill Hooker

P.S. I do not really think I can be accused of "supporting closed access"... merely of refusing to fight it to -- not my, but my family's -- last drop of cash... - Bill Hooker

Bjoern, I will add that any librarians in this room (and I am not the only one) may have a professional interest in keeping mum. We are pathologically helpful folk, so it's hard to resist sending papers -- but we also belong to a profession that looks incredibly askance at even a HINT of copyright-related impropriety. Are you willing to lose me my job over this? Like Bill's, completely serious question. Remember also that my job is intimately OA-related. - D0r0th34

I cannot sit here and say nothing in light of recent input. I'll be brief simply by saying, 'as Bill and D0r0th34 say(s)'. I too am not willing to put my livelyhood on the line over this (single) issue. All my (OA) eggs in one basket re. this one? I think not. - Graham Steel

Just a couple of points. (1) I'd assumed that most or all contributors voted in good faith, i.e. once, on this issue. (2) Having read through the draft at etherpad, I think it reads as a good summary of the utility of FF, with or without the mention of RW room (which is only one small paragraph). Is this one aspect really so important, really such a major component of the FF science experience? I think our interactions and discussions are much more important and interesting. - Neil Saunders

IMHO, the 'no' voters here are blowing the matter way out of proportion. I'll try and put it back into proportion, which may or may not work :-) - Björn Brembs

@Neil: Good point. I think it may not be all that much of FF for us, but for people not using social media for their work, it may well be *the only* useful thing they can see in this article. That's one of the reasons I'm fighting for it to remain in the letter. I agree, for anybody who is already using this technology, the RW room may only be a minor benefit, compared to the rest of the features. - Björn Brembs

To all those who "are not willing to put their livelihoods on the line": what part of "document" did you not understand when you signed up? Bill used the right description for this kind of behavior: cowardice. But if you really think our little room of 40 scientists with inadequate access to scientific literature will wake a sleeping giant, I have several additional accurate descriptions. - Björn Brembs

(1) Delusion. If you really think someone like Elsevier is risking their 800 millions annual profit in tax payer money by going after people who can barely support themselves, you must be deluded. The music industry doesn't have any profits left to lose, but publishers do. They wouldn't be making record profits during the worst financial crisis in 80 years if they really were so stupid to go after us. - Björn Brembs

(2) Stockholm syndrome. How many salaries and healthcare plans could you pay from 800 million each year from Elsevier alone? Basically, these guys take your salary and your healthcare and then hold you ransom to shut up and keep your head down - and in response you have nothing better to do than to defend that behavior and cozy up with your captors? You must be the only ones who can see any shred of sanity in such behavior. - Björn Brembs

(3) Hypocrisy. Isn't it hypocritical to oppose a regime on the surface but then support it when real action needs to be taken? Isn't it ironic that a German is arguing for and volunteering to putting your actions where your mouth is and Americans are arguing in favor of personal safety long before any hint of a serious threat is even perceivable? - Björn Brembs

(4) Paranoia. There is no precedence of any publisher going after individuals. Publishers have much more to lose than we. Thus, the only potential threat is purely in your minds. There isn't even the slightest hint of any hazard for any one of us on the horizon, yet you defend yourselves against imaginary future actions of your oppressors. More than any of the above, this paranoia... more... - Björn Brembs

(5) Documentation. This thread, more than any number of exchanged papers documents how bad corporate publishers are for the scientific community. Their stranglehold on the community stifles freedom and liberty, intimidates all community members to the point that they delude themselves, develop paranoia and act hypocritically. I think this thread documents more than anything else in this... more... - Björn Brembs

(6) Anticipatory obedience. It is a well-known consequence of dictatorships around the world that individuals in these dictatorships support the dictator even if there is no explicit force, merely because they imagine some bad consequence for themselves or their family if they wouldn't support the dictator. In Germany, every child is raised with what the term 'anticipatory obedience' means. We are being taught how it works to stop all potential threats to democracy at the roots. - Björn Brembs

1) Elsevier has lawyers on retainer, sending a take down letter costs them very little and makes a point - compare to RIAA - how many college students did they take to court? they are actually legally in their right so you would lose without even a trial 4) it's not paranoia if they really are after you. There is a precedence - in the OSTP letters someone complained about ACM going after a Taiwanese grad student - Christina Pikas

Björn, don't take this for more than the friendly advice that it is: I don't think it will win over many people in a debate (or win you many friends) to accuse those who are not willing to publicly encourage illegal activities of suffering from delusions, Stockholm syndrome, hypocrisy, and paranoia. - Lars Juhl Jensen

Bjorn, you have lost my respect. I am blocking you and leaving this room. My email is findable if you care to apologize. - D0r0th34

Re-reading my posts from this morning, it seems indeed I may have over-exaggerated my points a bit too far. It was and still is my purpose to rouse people and ruffle some feathers on a topic which to me is the worst side of my job. In my frustration that even people who I thought were on my side don't dare to leave their comfort zone for something I find so important, I may have gone a... more... - Björn Brembs

Hadn't voted earlier, but vote now for the references to RW to be included in the article. (nice commentary/response BTW) . RW room is one great thing that you guys are doing and should be proud of. People like me who have no access to any scientific literature (that OA or PNAS or some other because of my country of origination (india) ) are able to do science because of that support;... more... - Sandeep Gautam

I am basically offline now and thus postpone submission until Dec 22. Hope to be able to comment in more detail tomorrow night. - Daniel Mietchen

@Bjoern: I do understand your position, and I cannot disagree with a lot of what you say. But this is my point of view when I step back a little. 1) the number of subscribers to the room cannot claim to represent the sceintific community (they may or may not be representative, but the claim cannot be made based on the numbers). Nor do I think it can claim to represent the scientific... more... - Kubke

@Kubke: Indeed, very measured words. Last night I've also come to the conclusion that apparently, the situation is not bad enough, yet, for people to seriously push for change. It first has to become a lot worse, before it will get better, I totally agree. - Björn Brembs

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

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

Sorry, won't make it today. Next online time scheduled for 27, just in time. - Daniel Mietchen

GrrlScientist

This Is For All My German Friends: Speak Better English - http://scienceblogs.com/grrlsci...

yesterday from Living the Scientific Life... - Comment - Like - Share

Thomas Brox Røst, Jo Young, Marcos de Carvalho and Björn Brembs liked this

Sein English ist doch besser als mein Deutsch! - Bill Hooker

Duncan Hull

MapReduce: a flexible data processing tool - http://www.citeulike.org/user...

yesterday from CiteULike: dullhunk's library - Comment - Like - Share

Marcos de Carvalho and Pierre Lindenbaum liked this

Steve Koch to Steve's feed, Telomere Biology

Telomere Biology: Web Focus: Nature http://www.nature.com/nature...

Sunday - Comment - Like - Share

Marcos de Carvalho liked this

Björn Brembs

Rammstein: Liebe ist für alle da. - http://brightkite.com/objects...

December 18 from brightkite.com - Comment - Like - Share

Jan Wessnitzer, Andrew Spong and Marcos de Carvalho liked this

You are at a concert? I am deeply envious. - Bill Hooker

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Yup, best Xmas carols I've ever shouted :-) - Björn Brembs from iPhone

Du Hast! - Marcos de Carvalho

Awesome show, ten thousand people, fantastic performance. These guys are outstanding! If you ever get a chance of seeing them, don't miss it. - Björn Brembs

Saw them in '96 and one of the most memorable shows I have seen! - Jan Wessnitzer from iPod

Chris Patil

WTF? anoTHER blog? - http://www.ncbirofl.com/2009...

December 18 from NCBI ROFL - Comment - Like - Share

Marcos de Carvalho and Shirley Wu liked this

This reminds me of Worst. Result. Ever. (http://worstresultever.blogspot.com), a blog my labmate started but it never got past the first three or so posts. But each of us three who graduated this year turned our worst result ever into memorable t-shirt as parting gifts for our advisor... :) - Shirley Wu

Paulo Nuin

Algorithms for locating extremely conserved elements in multiple sequence alignments - http://www.biomedcentral.com/1471-21...

December 18 from Google Reader - Comment - Like - Share

Marcos de Carvalho and tim liked this

Neil Saunders

Sass - Syntactically Awesome Stylesheets - http://sass-lang.com/

December 18 from delicious - Comment - Like - Share

Marcos de Carvalho, Chris Miller and Deepak Singh liked this

Sass makes CSS fun again. Sass is CSS, plus nested rules, variables, mixins, and more, all in a concise, readable syntax. - Neil Saunders

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One one shoulder, an angel of optimism goes "ooh, neat". On the other shoulder, a little demon of doom says "sure, just what you need, more complexity -- you don't grok CSS as it is." - Bill Hooker

if it abstracted away browser hacks, I'd be for it - D0r0th34

I think it does Dorothea. I've been using it a bit myself. You can import sass modules such as reset or IE which take of importing all the crazy additional CSS. - Michael Barton

Khader Shameer

Globally, unrelated protein sequences appear random - http://www.citeulike.org/user...

December 9 from CiteULike: kshameer's library - Comment - Like - Share

Marcos de Carvalho liked this

Daniel Mietchen

What if it's a big hoax and we create a better world for nothing? - http://tomate.soup.io/post...

December 9 from Bookmarklet - Comment - Like - Share

Egon Willighagen, Neil Saunders, Nils Reinton and 2 other people liked this

Lars Juhl Jensen

Data integration: The STITCH database of protein–small molecule interactions - http://www.slideshare.net/larsjuh...

December 9 from SlideShare - Comment - Like - Share

Peter Miller and Marcos de Carvalho liked this

Lars Juhl Jensen

Protein networks: A basis for large-scale data mining - http://www.slideshare.net/larsjuh...

December 9 from SlideShare - Comment - Like - Share

Peter Miller, arek, Pawel Szczesny and Marcos de Carvalho liked this

Neil Saunders

Rumours that first dark matter particle found - http://www.newscientist.com/blogs...

December 8 from Google Reader - Comment - Like - Share

Jean-Claude Bradley, Marcos de Carvalho and Steve Koch liked this

"Update: in an email to the blog Resonaances, Nature's senior physical science editor Leslie Sage has squashed the rumours that a paper is about to appear in the journal " - Björn Brembs

Iddo Friedberg to Iddo's feed, The Life Scientists

The Ultimate Rebuttal Letter - http://bytesizebio.net/index...

December 8 from Bookmarklet - Comment - Like - Share

Marcos de Carvalho, Mr. Gunn, Khader Shameer and Mickey Kosloff liked this

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

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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: 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.

December 5 - Comment - Like - Share

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

Likewise - Deepak Singh

Daniel Mietchen to Daniel's feed, Young scientists

APS Observer - A Letter to Young Scientists - http://www.psychologicalscience.org/observe...

December 4 from Bookmarklet - Comment - Like - Share

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"In this, my final presidential column, I thought I would write about what I wish for the young scientists in whose hands the future of our science rests. For help with this task, I turned to a letter from Ivan Pavlov (1936) to young scientists published in Science three months following his death at the age of 87. The letter is a mere 301 words long but is full of wisdom." - Daniel Mietchen from Bookmarklet

3 more comments

Further quotes (fee free to replace "psychological" with your field): "Contemporary psychological scientists stand on the shoulders of those who went before. From this perch it is now possible to see that the bounded fields of the 20th century are related parts of the same landscape. This is a requisite step for bringing research on pieces of related problems together to address bigger... more... - Daniel Mietchen

"the quality of scientific teams is no longer hostage to the quality of the faculty in a particular department, region, or nation." - Daniel Mietchen

"Always respect the data, but play with ideas [...] And when you have succeeded, do it all over again." - Daniel Mietchen

"Be serious and not at all serious about your science, at the same time, all the time." - reminds me of "Schrödinger´s cat walks into a bar.. and doesn´t." (http://ff.im/c3Dkg) - Daniel Mietchen

Itachi to Itachi's feed, Future of Education, Higher Education, Science 2.0

Eureqa | Cornell Computational Synthesis Laboratory - http://ccsl.mae.cornell.edu/eureqa

December 4 from Bookmarklet - Comment - Like - Share

Peter Miller, Mickey Schafer, Richard G. Lanzara and 12 other people liked this

"Eureqa is a software tool for detecting equations and hidden mathematical relationships in your data. Its primary goal is to identify the simplest mathematical formulas which could describe the underlying mechanisms that produced the data. Eureqa is free to download and use. Below you will find the program download, video tutorial, user forum, and other and reference materials." - Itachi from Bookmarklet

cool - winckel

The Life Scientists: Khader Shameer

I am working on a docking experiment to see interactions between phosphorylated peptide(s) with a receptor. I am looking for a reliable tool (software/ web server) for protein-peptide docking - any suggestions ?

April 27 - Comment - Like - Share

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Don't know that any docking is 'reliable', but google 'modpropep' - Neil Saunders from fftogo

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As far as the docked complexes from the tool provides known interactions (from literature) and minimization values are in good range (-ve), I can consider the docking as reliable. Neil, thanks for the suggestion - but am afraid this server is designed exclusively for Kinases, Class-I, and MHC Class-II - am working on phosphatases. - Khader Shameer

1) Dock (full options, difficult to implement), 2) AutoDock (less options, but faster to implement), 3) HEX (even less options, but perhaps the best tool to start). These are all free. In addition, depending on your institutional subscription there are other (expensive) options. - genereg

Thanks. I already tried AutoDock with different parameters, but doesn't seems to be a good choice for protein-peptide docking. GRAMM-X is not able to recognize the phosphorylated residues in my peptide. I will try DOCK and HEX. - Khader Shameer

According to this link [ http://tinyurl.com/cp5t9b ] DOCK is not recommended for Protein-Peptide docking. Now am going to try different programs ranked well in CAPRI. - Khader Shameer

if it is not for protein-peptide docking, what it it for :) BTW you do not need the whole protein, you just need to consider its reactive center and the peptide. Also you may wish to try Molegro. It is not free, but you can get a free copy for a 1-month evaluation. The problem is that all commercial programs use their unique output formats not compatible with the standard PDB format and not easy to transform to view and analyze in the external software. - genereg

Ah right, the forgotten phosphatases :) I'd start with a review article; someone must have benchmarked the most-used packages. I've played with zdock, hex and autodock over the years, all with their pros and cons: zdock - 'quick and dirty', hex - easy to use GUI, autodock - the most comprehensive but last time I checked, under very active development and hence poorly documented. - Neil Saunders

Thanks Neil. zdock is always my best friend. but I spend a lot of time with AutoDock as it was ranked as one of the best docking tool in different benchmark reviews. I was hoping that my AutoDock clusters will show nice -ve values for every other docking I tried - but it never happened. Now I am running ZDOCK and planning to get some energy values using minimization routines of Ghemical. - Khader Shameer

Just to update : Due to some inconsistencies in the energy of complexes generated using ZDOCK, I contacted the authors of the program and got to know that ZDOCK consider the phosphorylated-tyrosine as normal tyrosine during the docking process. Now am working on developing an approach similar to that of MODPROPEP specific to phosphorylated peptide. Will update If I get some promising results. - Khader Shameer

I just found this thread. Khader, is this question still relevant ? we've just finished the development of a high-resolution peptide docking algorithm within the Rosetta package... If it's still relevant I could try and model that peptide for you... - Nir London

Nir : Thanks for your note. I proceeded with the superposition approach, but am not so happy with the results. We are still looking for better options. I will be happy to try it if the program can take up *phosphorylated peptides* and perform protein-peptide docking. - Khader Shameer

It works with *phosphorylated peptides* :) or any other kind of short peptides. The code isn't released yet though, as the paper is still under review, If you send me some background, ref. PDBs etc.. I could easily do the docking for you. - Nir London

Thanks, This is great, Nir. I will send you an email with details. - Khader Shameer

Duncan Hull

JBrowse: a next-generation genome browser. - http://www.citeulike.org/user...

December 3 from CiteULike: dullhunk's library - Comment - Like - Share

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Yann Abraham

Charting time series as calendar heat maps in R - http://blog.revolution-computing.com/2009...

December 3 from Google Reader - Comment - Like - Share

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Neil Saunders

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

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

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

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

42 more comments

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Dorothea, sure, not a problem. - Neil Saunders

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Alejandro Montenegro

An alternative cloning strategy: yeast recombinational cloning - http://amontenegro.blogspot.com/2009...

December 2 from MolBio Research Highlights - Comment - Like - Share

Marcos de Carvalho and Steve Koch liked this

Michael Kuhn to Michael's feed, The Life Scientists

A salvo of Science papers by Bork/Serrano/Gavin et al. on Mycoplasma: http://www.sciencemag.org/cgi... http://www.sciencemag.org/cgi... http://www.sciencemag.org/cgi...

December 1 - Comment - Like - Share

Pawel Szczesny, Yann Abraham, Marcos de Carvalho and 10 other people liked this

If I have my story right I think this came out of a criticism from a review panel that the structures and computational bio department was not collaborating enough. They came up with the mycoplasma collaboration that Luis Serrano in particular was very excited about. 3 science papers is not a bad way to show results :). I still have to read them. - Pedro Beltrao

News and Views at MSB: http://www.nature.com/msb... - Pedro Beltrao

Editor's choice at Science Signalling http://stke.sciencemag.org/cgi... - Pedro Beltrao