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Lars Juhl Jensen

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

47 minutes ago from SlideShare - Comment - Like - Share

arek, Pawel Szczesny and Marcos de Carvalho 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

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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

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...

23 hours ago - 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

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

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

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

Added some stuff... - Björn Brembs

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

895 words... - Björn Brembs

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

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

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

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

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

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

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

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

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

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

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

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

Otherwise made a few very minor changes - Cameron Neylon

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

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

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

Added mention of polymath project. - Daniel Mietchen

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Christopher Harris

having to resist writing a blog post about free will, how ironic

Sunday from Twitter - Comment - Like - Share

Björn Brembs, Eivind, Pawel Szczesny and Nils Reinton liked this

As you said the other day, it's not science. Or do you have a philosophy blog? - Alexander Kruel

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My blog is a little bit of everything but nevermind, the point is that free will IS entering the scientific language. It's not the free will we're used to (it's not necessarily conscious, it's fully brain based etc) but it's certainly getting in: on the brain science podcast just the other day they embraced it, and a paper I read this weekend is full of intentional concepts despite... more... - Christopher Harris

Yeah, it IS entering the scientific language. But wait, it's not what you think it is. It's really banana juice. Sorry people for the deception. Well, I'm not going to read it. Up next: the reintroduction of evil into the legal system. Again, not what you think, it's just free people doing bad things. Phew... - Alexander Kruel

I think I know why you're so adamant about this. I was raised Christian too and the stress of spending many young years realizing how much of what I'd been told was false and irrational still to this day predisposes me to attack anything that smells like scientifically naive, wishful thinking. Free will used to be a prime target of this anger and frustration as late as a few years ago.... more... - Christopher Harris

Seriously, scientists are also just humans. I've been amazed lately of how dumb educated people can be. Ever heard of Nassim Taleb? What a crank. Anyway, it's really sad to hear this. Free will is the creationism of neuroscience. And if it's true what you're saying, then woo is winning in that field. It's also not ignorance not to read some mathematical musings you may provide underpinning your notion of free will. I don't do it for the same reasons that I don't read papers by Jehovah's Witnesses. - Alexander Kruel

It's not just religious opposition. I'm saying the same when it comes to all the bullshit about consciousness. Or take Roger Penrose, I'd tell him he's making up bs there any time. It's dancing around rainbows end. You don't need expertise for this stuff. It's just flawed reasoning. An oxymoron. Of course, that there is something rather than nothing is a problem that also conflicts with... more... - Alexander Kruel

Well, sometimes there ARE reasons to assume things. For instance we don't know that other people are conscious but the way they talk and act make us assume they are. With recent advances in brain imaging we're starting to be able to distinguish conscious from unconscious brain states which gives us more reason to assume other people are conscious, even though the evidence is not... more... - Christopher Harris

What I meant about bs regarding consciousness is the opinion of some that we cannot tackle this concept with science. The sacrosanct of subjectivity and the first-person perspective. I've written something on topic here: http://friendfeed.com/minds... - Alexander Kruel

"If I cut my throat I may disover that I was dreaming or that I have been playing some advanced virtual reality game all along. Everything is possible. But right now there are safer and more promising options of gaining knowledge. How can I be sure? I can't, but there is evidence which proved to be reliable so far. I have to suspect that it will continue to be reliable based on... more... - Alexander Kruel

Assume free will? No reason. It's a concept that should at best be examined by psychology or the social sciences. It's a cultural idea. - Alexander Kruel

Hey don't despair about free will being studied by scientists, consider this: Even if science truly incorporates free will, such that there are centers for The Neuroscientific Study of Free Will popping up everywhere the way they do around consciousness studies at the moment, then we may still get to a point were we understand the operation of free will in human brains so thoroughly as to be able to predict free decisions. At that point science will truly have killed any traditional notions of free will. - Christopher Harris

I don't despair. I'm just worried about the underlying reasons people have to introduce it in the first place. Suspicious. And it may slow down discovery. It highlights a fundamental error in reasoning in that field. That is bad. At the very least, it will always act as a semantic obfuscation for calling randomness, unpredictability and spontaneous behaviour 'free will' when there obviously exist other, more descriptive terms. - Alexander Kruel

blah..."for calling" not not ;-) - Alexander Kruel

We can't know whether there "obviously exist other, more descriptive terms" until we know more about the phenomenon we're naming. 'Random' doesn't cut it, that was the point of Brembs' 2008 paper. 'Spontaneous' doesn't cut it because behaviour is spontaneous even in disease states where autonomous agency is impaired. This is why I want to write a blog post, to list the similarities and... more... - Christopher Harris

Well, nobody can stake a claim to natural language. If you actually want to create your own definition of 'free will', I'll refer to "'free will' as defined by Harris" (or "Free Harris") thenceforward. But what do you say isn't 'cutting it'? What phenomenon? I know that randomness is poriferous. Spontaneous is fatuitous. I commited the mistake to name those terms for the ease of not... more... - Alexander Kruel

Oh no no, I've gone along with trying to articulate and defend the new free will here but I haven't yet decided what I really think about it and it's certainly not my idea. - Christopher Harris

The phenomenon is the generation of will and behaviour by nervous systems - Christopher Harris

I think you're confusing a naive mind over matter attitude with a dynamical systems attitude where emergent properties are important - Christopher Harris

Just forget what I said. Was maybe all bs. A blog post on emergent properties would be cool. Sorry. Thanks. - Alexander Kruel

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

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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

Pierre Lindenbaum

writing a presentation about my genome browser: many slides are a component of my blog. #myblogismynotebook

yesterday from Twitter - Comment - Like - Share

Pawel Szczesny, Neil Saunders and Chris Lasher liked this

Deepak Singh

Questions and information streams - http://mndoci.com/2009...

Monday from business|bytes|genes|molecules - Comment - Like - Share

Pawel Szczesny and Neil Saunders liked this

Steve Koch to Steve's feed, Science 2.0, The Life Scientists, Kochlab

Submitted CAREER proposal & posted to Scribd: http://www.scribd.com/doc... Open proposal for an open science project!

July 21 - Comment - Like - Share

mkz, Michael R. Bernstein, Graham Steel and 20 other people liked this

Thank you to everyone who helped and encouraged on this and offered future support! Among many things, one thing I'm a bit embarrassed about is the lack of details in the "broader impacts" and open science parts of the proposal. Definitely it needs more planning and better writing, and the panelists are going to point that out. Hopefully you all understand that it's a product of spending all my time trying to make the research parts as good as I could. - Steve Koch

12 more comments

good luck Steve! - Jean-Claude Bradley

A small step for a team, but a giant leap for #science . - Daniel Mietchen

Good luck! - Brian Krueger - LabSpaces

Thanks everyone! I sort of dropped off the map after submitting the proposal. One of my most successful attempts at actually vacating during a vacation. - Steve Koch

Bummer! Just found out tonight that the proposal was not funded. I have done one read-through of the reviews. First of all, I am once again amazed at the time and effort the reviewers put into reviewing my proposal. There were 6 reviewers in total and they all had a page or more of feedback. And they all pretty much agreed on the main points: (a) interesting proposal that is worth... more... - Steve Koch

Thank you Jean-Claude, Andy, Cameron, and Drew for the Open Science support letters! I am sure that was key to the very positive reviews for Open Science. Thank you to everyone else on friendfeeed who supports me and our other lab members. We now have 7 months to obtain the preliminary data and get a couple publications, and indeed we are now poised to do so. I am confident the lab members can do this, and by eliminating (b) and (c) above, all signs point towards this being a very strong proposal next time. - Steve Koch

well done all 'round! next time you'll knock 'em dead. - D0r0th34

for the CAREER third time is often the charm - good luck for next round - Jean-Claude Bradley

Thanks, Jean-Claude and Dorothea. The CAREER "3rd time's a charm" effect is part of the reason I submitted without strong preliminary data. (But I also thought we'd be able to generate the data in time for the 2nd submission. Now, though, I'm SURE we can before July :) ) - Steve Koch

After thinking about it for a couple days now, I am still very happy that they viewed the open science so positively. I think that's a big deal. - Steve Koch

absolutely Steve - very good feedback about OS being a positive to the funders - Jean-Claude Bradley

Steve, this looks really really promising. If you can come up with interesting data for the next resubmit, I think you have a great chance to get funded. Congratulations! - Bill Hooker

Thanks, Bill! - Steve Koch

Cameron Neylon

It wasn’t supposed to be this way… - http://blog.openwetware.org/science...

Saturday from Science in the open - Comment - Like - Share

Bill Anderson, Jan Wessnitzer, Duncan Hull and 12 other people liked this

Ah - found a clearer statement from Met Office on data release: http://www.metoffice.gov.uk/corpora... - Cameron Neylon

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I must admit that until 48 hours ago, I never realized the Met Office data was secret. I'd always assumed it would be in the public domain. Silly me. - AJCann

You basically have to send them an email saying what you want and what you're using it for. If you are an appropriate accedited researcher you can get access to the thing you want, but not distribute it I think. Its a classic demonstration of public domain benefits in some ways. - Cameron Neylon

blimey - I never knew that met office data wasn't public record. Is the idea that Ordinance Survey introduced deliberate small mistakes into their map to protect their copyright? Or is that an urban myth. Depressing is about right. - Jo Badge

Brilliant post Cameron. - Andrew Lang

*applause* - Bill Hooker

I've heard from people who do mapping type stuff that the OS errors are real. Can't say I've ever checked myself though. - Cameron Neylon

in the US NOAA NWS data is open, but there's a cost recovery model for some of the historic data sets. I think the art around these parts is to combine NWS stuff with Navy stuff and stuff from the literature, but that's just my impression. - Christina Pikas

My understanding was that most of it was provided at cost - but a lot is in formats that are not terribly useable or useful so they charge for transfer to media and some reformatting. Bottom line is that most of it is government data and therefore in the public domain by definition. - Cameron Neylon

Some interesting comments on the blog itself - first time I've had that many comments in ages! - Cameron Neylon

Duncan Hull

The Identity Project @theidentity asks What is Identity? @ExploreWellcome http://www.wellcomecollection.org/whats-o... worth a visit (and free too!)

Monday from Twitter - Comment - Like - Share

ivanandersson and Pawel Szczesny liked this

novoseek

[Reading] A review of the main #reference #management #softwares http://blog.novoseek.com/index...

Monday from Twitter - Comment - Like - Share

arek and Pawel Szczesny 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

Elizabeth Brown, Jamie McQuay, John Dupuis and 21 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

Paulo Nuin

Top climate scientists share their outlook - This is such a good report and from the Financial Times. I did not expect such quality - and the insights on some of the key climate people is most interesting. - http://www.reddit.com/r...

Saturday from Reddit - Comment - Like - Share

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Iddo Friedberg to Iddo's feed, The Life Scientists

Videos on sequencing - http://bytesizebio.net/index...

Friday from Bookmarklet - Comment - Like - Share

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Mladen Srdić

This must be the funniest email conversation ever - http://thenextweb.com/shareab...

Saturday from Google Reader - Comment - Like - Share

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Fulaan, inna Hebel to Fulaan,'s feed, Future of Education, Higher Education, Science 2.0

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

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Richard G. Lanzara, Torfinn Nome, Marcos de Carvalho and 10 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." - Fulaan, inna Hebel from Bookmarklet

cool - winckel

François Dongier to François's feed, The Life Scientists

Math and Probability for Life Sciences | UCLA Video Course - http://academicearth.org/courses...

Friday from Bookmarklet - Comment - Like - Share

Mr. Gunn, Paul Bacchus, Attila Csordas and 6 other people liked this

"COURSE DESCRIPTION This is a math course aimed at students with life science majors covering elementary probability, probability distributions, random variables, and limit theorems." - François Dongier

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

Marcos de Carvalho, Kristen Fortney, Pawel Szczesny and 4 other people liked this

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

Deepak Singh

Hadoop World video is out - http://mndoci.com/2009...

December 2 from business|bytes|genes|molecules - Comment - Like - Share

Neil Saunders, Jeremy Leipzig, Benjamin Tseng and 3 other people liked this

Only took, what, 2 months to post this... - Shiran Pasternak

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Watching now. BTW, you've convinced me to try "hundreds of slides" approach some day - I wasn't sure it works in more scientific talks. - Pawel Szczesny

Pawel, I wasn't sure either, but I've had a chance to do deeper dives now (at Supercomputing) and it seems to work, especially as I get more comfortable talking science in this format. If I had to choose an alternate one it would be a pure storytelling/figure format, i.e. about some of your core results and work backwards if required. - Deepak Singh

that was a really great talk! - Jeremy Leipzig

Jeremy, thanks - Deepak Singh

Deepak Singh

Sysbionetwork - http://sysbionetwork.org/

December 3 from delicious - Comment - Like - Share

Pawel Szczesny and Mike Chelen liked this

This resource is currently maintained by the Duke Center for Systems Biology which is within the Duke Institute for Genome Sciences & Policy. DCSB is one of nine National Centers for Systems Biology in the United States, supported by the National Institute of General Medical Sciences' Systems Biology Initiative. - Deepak Singh

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

Duncan Hull

Big science, little science - http://www.citeulike.org/user...

December 2 from CiteULike: dullhunk's library - Comment - Like - Share

Pawel Szczesny liked this

The real disease is the creeping hegemony of 'big science' over 'little science' and the issue of who sets priorities in biomedical research.--Gregory Petsko (EMBO Journal) - Duncan Hull

Deepak Singh

RT @peteskomoroch: Nice slide deck from @dataspora "An Interactive Introduction To R" http://www.slideshare.net/dataspo...

December 2 from Twitter - Comment - Like - Share

Pawel Szczesny, Steve Koch, Rajarshi Guha and Neil Saunders liked this

all of their slideshare stuff is worth a look - Neil Saunders

Ian York

HA structure showing mutating amino acids1 Anyone who’s taken a virology class, and many who haven’t, know about “antigenic drift” and “antigenic shift”. These... - http://www.iayork.com/Mystery...

December 2 from Mystery Rays from Outer Space - Comment - Like - Share

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Yann Abraham

Visualization of genomic data with the Hilbert curve - http://www.citeulike.org/user...

December 2 from CiteULike: Yanno's library - Comment - Like - Share

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Bioinformatics, Vol. 25, No. 10. (15 May 2009), pp. 1231-1235. In many genomic studies, one works with genome-position-dependent data, e.g. ChIP-chip or ChIP-Seq scores. Using conventional tools, it can be difficult to get a good feel for the data, especially the distribution of features. This article argues that the so-called Hilbert curve visualization can complement genome browsers and help to get further insights into the structure of one's data. This is demonstrated with examples from different use cases. An open-source application, called HilbertVis, is presented that allows the user to produce and interactively explore such plots. Availability: http://www.ebi.ac.uk/huber-s... Contact: sanders@fs.tum.de Supplementary information: Supplementary Data are available at Bioinformatics online. 10.1093/bioinformatics/btp152 Simon Anders - Yann Abraham

Marcin Wojnarski to Marcin's feed, Data Mining, The Life Scientists

Data mining / bioinformatics challenge: analysis of DNA microarray data - http://tunedit.org/challen... (prizes for best solutions)

December 2 - Comment - Like - Share

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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

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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

Cameron Neylon

Article-Level Metrics and the Evolution of Scientific Impact - http://www.citeulike.org/user...

November 17 from CiteULike: CameronNeylon's... - Comment - Like - Share

Bill Anderson, Bill Hooker, Anders Norgaard and 37 other people liked this

Article on ALMs by myself and Shirley Wu - Cameron Neylon

27 more comments

Terrific. Are we still maintaining that list of "outputs resulting from FriendFeed"? - Neil Saunders

I was planning on doing a demo of annotation at PLoS before the end of the year - perhaps this article would be a good candidate. As always, anyone willing to join is welcome. - Daniel Mietchen

@ Neil: It's at http://spreadsheets.google.com/ccc... , and I have added the article as #25 (details missing). - Daniel Mietchen

i added a note once, but now it won't let me add any other notes :( I don't see a rule about one note per person. I should have held off for a good one. - Christina Pikas

I also just noticed that my "annotation" - provided the link to StackOverflow - shows up in the general discussion, where the title "Link" certainly is not helpful, and there is no way I can edit it. - Daniel Mietchen

maybe something is broken, my note appears in general comments but also in that portion of the text as a comment. maybe that's why I couldn't add other notes? - Christina Pikas

Not sure why you can't add more notes. Certainly been able to in the past. I see both notes where they are supposed to be I think. But they will also appear in the general comments as well I think. - Cameron Neylon

Great article! I really need to add some comments or notes, just to prove the authors' point :-) - Björn Brembs

BTW, when does PLoS finally get karma? I've been asking for proper 'show off' userprofiles for like ever :-) - Björn Brembs

As in PLoS Overflow? - Cameron Neylon

Cameron, et al. - What's the most useful thing I could do to nurture and support this renewed interest in article level metrics? (not from a competing data product point of view, but a let's get some good technologies out there with good visibility) - Mr. Gunn

@Cameron: Exactly! I even think having a profile where you can post a pic and see how many papers and comments were published, papers edited, etc.was the very first thing I asked for when I signed up :-) - Björn Brembs

But it needs to be federated across publishers... :-) - Cameron Neylon

if authors put in their 'customer' weight, this will go faster, so why not go syndicate :-) - Claudia Koltzenburg

I think I'll use this paper in my spring thesis class -- this is the main one where I discuss publishing models -- and maybe I'll demo Diigo with this as a class project next to an article that discusses IF. - Mickey Schafer

While we're on the subject of functionality wish lists, I would also like an embed functionality for PLoS papers. Collecting my publications together but don't want to duplicate copies and reduce googlejuice for the journal - at least not for the OA papers anyway... - Cameron Neylon

Whilst not a darts-player http://www.flickr.com/photos... , I think Cameron has hit the "triple-twenty" there :) - Graham Steel

BTW, why isn't there a way to register this thread with the article? Why are we posting here and not on the article? There's got to be a lesson to be learned from this :-) - Björn Brembs from iPhone

http://bullseyevaluation.com/yahoo_s... - Graham Steel

Done. See comment #4. - Graham Steel

Search results: http://topsy.com/s... from Topsy http://labs.topsy.com/about/ - Jim Till

I've included a link to this thread in a blog post: Article-level metrics getting attention http://ff.im/bGuNY - Jim Till

+1 Bjoern :-) another question along these lines would be: why does Cameron's intial FF message link to CiteULike and not to http://www.plosbiology.org/article..., or plainly doi:10.1371/journal.pbio.1000242 ? - Claudia Koltzenburg

Because that was the way I brought the link in. I think that that pointer is appropriate. It is a pointer to the fact that I bookmarked it. Other people linked to the paper directly. Perhaps the issue is that we accidentally aggregated around the "wrong" item to talk about the paper. I'm not sure this is a problem as long as the referral works - its a UI irritation not a problem with... more... - Cameron Neylon

well, not directly, maybe in this ff-thread we're just providing some material for what you say in your paragraph "Technical Solutions to Social Problems", namely: "approaches that gather information from processes that are already part of the typical research workflow are also much more likely to succeed." - even though ff may not be part of 'the typical research workflow' (yet?) - and... more... - Claudia Koltzenburg

That's true, and certainly conversation sparked by the paper. But how to capture that in a way that is useful further down the line might be tough... - Cameron Neylon

I am still wondering if we would not need at least one metric for each 'scientist type' as described in http://dx.doi.org/10... - joergkurtwegner

joergkurtwegner -I'm interested to see what tenurometer comes up with re: h-index correction factors for disciplines. - Mr. Gunn

Harold Jarche

Success depends on who we work with - http://www.jarche.com/2009...

December 1 from Harold Jarche - Comment - Like - Share

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