This is what I consider "understanding something" ;) Anybody to suggest an application that assist in creating something similar? So far http://biologicalnetworks.net/ looks quite close, but still missing on the ease of use. - Pawel Szczesny
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You could draw a diagram like this in Omnigraffle or Illustrator --I'd probably create layers for each of the different diagrams and export each layer as a different image--and then use Dreamweaver to create the JavaScript (or hand code the JS). Automated drawing of this type of graph is very difficult to achieve. - Hilary
"The world of information may be changing rapidly, but humanists for the most part just don't care. That change may in itself become a major object of humanistic study, and when it does it will be addressed in scholarly monographs and articles. We could only speculate on why change is slow, but I suspect that it's the way they're trained, the long years of discipline they undergo mastering a tradition. It also has to do with the nature of such scholarship. Humanists engage texts and arguments; thus they need texts and arguments to engage. Giving them a nice data set won't please them. Libraries are there to serve scholars, not the other way around." - John Dupuis
Datasets aren't just numbers. A textual corpus is also a dataset. Trust me on this one; I was a lexicographer in a past life... - Dorothea Salo
"Do any of us want to get out of our comfort zones? I work in the humanities. I don't see those science librarians getting out of their comfort zones to understand how the humanities operate, so I don't think it's just we humanities librarians who are special in that regard." - John Dupuis
If somebody walks up to the desk and asks me a humanities question, I'll start, and tell them that they should go to that library if they need more. If an engineer walks up to the humanities desk, the staff run screaming. - DJF
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I do have a bit of a response on the "comfort zone" question. Speaking as a science librarian, I have to say that with the way that the web (and computational methods in general) is transforming both the way science is done and communicated any science librarian that isn't trying to expand their comfort zone at least a little is in danger of becoming irrelevant. Trying new things to reach out to faculty and students who may not see a role for libraries is a must. And whether it's IM reference, blogs... - John Dupuis
...social networks, escience/data sets or, perhaps most importantly, getting a foothold in the classroom with expanded instructional programs, I think most are trying something. - John Dupuis
"I don't see those science libns getting out of their comfort zones to understand how the humanities operate" ... because naturally that's the only possible way a science librarian could stretch him- or herself. John, are you TRYING to set me going? *g* - Dorothea Salo
Srsly, the point is that the OP has his head in the sand. The digital humanities are here, and here to stay. Of course that doesn't mean they're using the same techniques and tools as e-science. It DOES mean that "texts and arguments" are changing, and librarians will have to change with them, in ways that many librarians don't find congenial. (Am amused that OP seems to think I have a science background. Nope. Comp lit, medieval studies, and linguistics.) - Dorothea Salo
Yes, Dorothea, I was trying to set you going *g*. - John Dupuis
While I agree that digital humanities are here to stay, I think the actual number of humanists actually practicing them are v. small at most institutions. And I sympathize with Wayne's point that the library is there to support the faculty research and work habits that they actually practice, not the ones we wish they did. BTW, I'm a humanities librarian that got his start at the Science & Engineering ref desk at UCSD. If your humanities folks scream at science questions, tell 'em I said they are losers. - Steve ✪ Lawson
Well, we also get quite a few humanities questions here at the sci-eng library and we tend not to scream too loudly. The hum-ss library also gets scitech questions and I think they usually manage. There is the occasional puzzled phone call going one way or the other, though. - John Dupuis
With a background in humanities and social sciences, I'm still trying to find my comfort zone with helping students do tax law and accounting research (MPOW has a huge accounting program). - Stephen Francoeur
As always Deepak you're right on point and have great insight on this topic. I think part of the problem could be that scientists aren't willing to scrap their current implementation or workflow for a reported 1-5% performance increase on some dataset that isn't their own. I like the parallel you draw to Google and the search market. In order to beat Google a company can't just be a little better but you have to be MUCH better. The same goes for the researcher who is copying their trusty old charmm.inp around with few modifications from project to project or running/scoring their docking the same way because they know it's worked in the past. The barrier to adopt new methods just seems too high.
I have hope that community efforts like CAPRI or CASP can make the best methods stand out among the rest and offer that compelling reason to try something new. It's sort of depressing that we even have to talk about stagnation in such promising disciplines. - Adam Kraut
After all, if it's science, shouldn't the drive for innovation be baked-in? - Adam Kraut
That's what I was led to believe growing up. Turns out they lied to me :) - Deepak
... and it pains me a lot. That field is still the one I care about the most and in the end I believe that physical approaches are the ones that will give us the best answers, but we're essentially still stuck in 1983. Explains why I got so excited when MM-PBSA and some of those flexible docking methods came out - Deepak
"Drew Endy, an open source biologist currently working at Stanford, is a good example of why. Along with several researchers at MIT, Endy is working on synthetic biology and the engineering of standardized biological components and devices, known as BioBricks. Endy is also founder of the BioBricks Foundation, a non-profit organization founded by engineers and scientists from MIT, Harvard, and U.C. San Francisco, focused on open source biotechnology. Just as open source software is often shared in online repositories, the BioBricks Foundation has a registry online for open source biological parts." - imabonehead
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not really. I find the deepak/neil tech news aggregator service pretty reliable. The algorithm seems pretty robust to variation in input quality - Cameron Neylon
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not really. I find the deepak/neil tech news aggregator service pretty reliable. The algorithm seems pretty robust to variation in input quality - Cameron Neylon
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not really. I find the deepak/neil tech news aggregator service pretty reliable. The algorithm seems pretty robust to variation in input quality - Cameron Neylon
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That's a generic question. Which ones are you thinking of specifically? - Louis Gray
Cameron, not from the science end. There we're doing quite well, but the tech world just gets to be a bigger echo chamber than ever. No wonder that I spend so much more time on hacker news than on techmeme. - Deepak
Louis, don't want to mention any specifically, but there were a bunch that I read regularly in my feed reader. These days I either find the topics aren't compelling or the writing isn't just as good (too much dilution perhaps). - Deepak
Deepak I think there just hasn't been any good tech news lately. A lot of it has been pretty boring. - Jesse Stay
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Jesse, that's probably true. Explains some of the lack of interesting material. Also feel though that most of the big blogs have added so many writers they're just writing to make up the numbers, so when there is nothing interesting to write about those who are not good writers get shown up - Deepak
Richard, I used that as a template ;) I was looking for a page on open notebook science in particular and didn't find one, so I created one. Everyone feel free to add their contribution, I am not the expert. - Andrew Lang
Be aware that this did exist before and got deleted by the powers that be. I think we've got a much greater case for it now but we need the set of references to the term in the 'real' media to hand when the editors come by... - Cameron Neylon
@Cam: I have been collecting such references here: http://www.simpy.com/user/senn... -- v. small collection so far, perhaps we could use this room to collect more? - Bill Hooker
@Cameron Ah I thought this had existed before, I wasn't sure whether I had imagined that or not. I actually did a few searches to see if I could find a deletion log but nothing showed up. - Richard Akerman
Jean-Claude will know but I think he originally put a page up about 12-18 months ago. Then it go redirected to 'Open Data'. I'm wondering how best to go about writing the article though - as I understand the Wikipedia guidelines both JC and I would be seen non-objective observers - is it better for us not to write any of it? Or restrict ourselves to the discussion page? - Cameron Neylon
@Bill - Jean-Claude also has a google search for 'open notebook science' piped through to an RSS feed I think which should capture a lot of the general media references. - Cameron Neylon
I think if you stick to your guns on the topic, add references, especially anything in mainstream media and/or with a DOI, you have decent start - Deepak
I agree with Deepak that referencing the hell out of a new Wikipedia page is a good way to manage the inevitable assault from the Notability Police. - Richard Akerman
Thanks Andy and everyone with helping out with giving this another try! Cameron is right - I tried a while back and it got redirected to Open Data. As Tony reminded me a few months back this is a good time to do it - Jean-Claude Bradley
Richard/Deepak - yes references are crucial - I added one to an early Precedings document. I think the criticisms portion is very important to give a balanced view - based on the meeting in Southampton maybe Jenny could contribute to that - what do you think Cameron? - Jean-Claude Bradley
@Cam: I think it is appropriate for you and I to add the odd link or make a correction but it would certainly be best if the article were built up by true crowdsourcing. We can certainly try to use the discussion more than just direct edits. - Jean-Claude Bradley
@Jean-Claude I hadn't thought about that - probably helps NPOV and any perceptions of boosterism to include critiques or issues. I'm sure there must be a few writers who think open science is total bollocks... :) - Richard Akerman
Richard - hopefully we'll get some rational points made - no surprises there: fear of scooping, IP, limitation of publication in some peer-reviewed journals, etc. - Jean-Claude Bradley
Yep, it has to be a well rounded piece, but perhaps with enough material and a list of events where it has been discussed, it will stay there - Deepak
The deletion warning is up on the talk page... - Richard Akerman
In future, perhaps have a more complete article in draft before going live. It seems they're not keen on preliminary articles which sit there a few days without activity - understandable really. - Neil Saunders
Hi Andrew, wikiversity is perhaps a better place to start such things (no deletomanics there), and a scaffold similar to yours is already available at http://en.wikiversity.org/wiki... . Besides, there is also Citizendium where stubbyness is no problem, since they basically only care for approved articles, quality-wise. - Daniel Mietchen
Wikipedia guidelines are that new articles get 7-10 days to be filled out. This article was created 3 days ago, so the request for deletion is premature. On the other hand, more content and references do need to be added with some haste. - Michael Nielsen
Our deletionist appears not to care what the Wikipedia guidelines say. Charming. - Michael Nielsen
Daniel, great and I just linked it to the Open Notebook Science page. If everyone could take five minutes RIGHT NOW to add a sentence or two to the open notebook science page I think it would stick because they look at how many people edit it and where they edit it from. http://en.wikipedia.org/wiki/O... - Andrew Lang
Just got this from the discussion page, thanks to Michael for spotting that: "We have experts in our group who could write an introduction but we have been worried that that may appear self serving and wanted the article to be created exclusively in a crowd-sorcing type manner. Would you mind if the intro was written by an expert in the field rather than someone who is let's say more objective? Romney (talk • contribs) 17:23, 7 October 2008 (UTC)
I understand what you mean. This isn't the same thing as someone who founded a company or other organization posting information about his own operation. There is no reason why experts can't write an article, and in fact I think that's ideal. There's no policy preventing you from writing what you already know. The important thing is that it all be verifiable from neutral third-party sources. I do understand that it can be tedious to identify arms-length resources to cite for material you're able to write out of your own head. But that's the nature of the beast. Yo - Andrew Lang
"FriendFeed's turning one! A year ago today, Bret, Jim, Paul and Sanjeev put our site and service out there and invited some folks. Soon, more people joined—as users, coworkers and friends. The rest, as they say, is history. Although not particularly ancient history." - Bret Taylor
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It's been a year already? Blimey. Happy Birthday! - Tony Ruscoe
Congrats. Trumpets and blowguns to get the rest of us non-FF slimes. Still have those weapons handy. +1 DeWitt, bring in some gears! Got some nice design in mind. +1 Shivanand and the like, how come it never existed before is beyond my understanding, that's how web services win I suppose. Great foundation to build for the future of 'social media'. - Zu aka ElijahBailey
Happy Birthday, FriendFeed! Looking forward to your next 10 years : ) - Jess Lee
Thank you for building my home on the web... Was waiting for a long time. Worth it :) - Christopher Galtenberg
Congratulations Friendfeed and Happy Birthday to you!!! - AJ Batac ♘
I <3 ff! Thanks so much for providing such a great community of wonderful people and great information. :-) - JMShoes
Happy Happy Birthday Friendfeed, best of luck for the future! - Dobromir Hadzhiev
Happy Birthday to you, Happy Birthday dear FF, Happy Birthday to you...and many more!! - Jeff B
CONGRATULATIONS... It has taken me most of the year to figure out how to use and make the most of friendfeed, and now dont' want to live without it.... - amelia arapoff
Unfortunately all our money only exists in RAM, not on hard storage any more. So when you reboot... - Richard Akerman
I'm sure I've got a spare hard disk somewhere - if you just copy all your money on to that I can look after it for you while you reboot... - Cameron Neylon
Mortgage-backed securities and credit default swaps = vapourware? - Richard Akerman
From Russ Altman "Well, maybe you all know this, but I am having a heck of a time coming up with material that is relevant and (hopefully) interesting for this blog. These difficulties are occurring despite help from my blog angel (she knows who she is) who is constantly feeding me excellent ideas. Why are blogs hard?" - Duncan Hull
Agreed. After 3 years......it gets kind of routine. Yet one more daily task. Applies as much to a personal blog as a work blog. - Maxine
Yup, I'm glad I'm not a journalist who *has* to turn out interesting copy on a regular basis. At least with a blog, you can leave it to fester for a few weeks or months... - Duncan Hull
I think a key is to not think of it as an activity separate from your other activities, but an activity that follows from the things you already do. When before you might have had a stimulating conversation with a group of colleagues, formal or casual, and left it in your head or your personal notes, now just dump and sanitize it into a blog post. So much better than random scraps of paper and napkin scrawls, or whiteboards soon to be erased. - Shirley Wu
Good points from Shirley. Do it because it's useful - to you as well as others - and because you enjoy it. If neither of those apply, don't do it. - Neil Saunders
@Shirley How does it feel to be a "blog angel"? :) - Duncan Hull
Initially I just thought of it as a searchability and transparency exercise - why should information that I am *already gathering* end up in a Word document or an email when I can just make it public? However the wider variety of tools that are available tend to diffuse my blogging energies these days. - Richard Akerman
Are there any "independent" organizations that can support concepts of "Open Science" without being "burdened" by the need to compete and standout for the sake of financial sustainability/continuity? So far, it seems like the journals/publishers dominate "Science 2.0" applications like Nature, BMC, PLoS etc. But they use these concepts to boost their own journals, not necessarily advance "Science 2.0" in general. If we agree that there is room or even a need for specialized apps for scholars, do we not also need a platform specifically for scholars as an end itself and not a means to an end? - Wobbler
Science Commons are big on platform development but essentially have charity funding (more on this coming in a later part). Are we not our own organisation in essence. As Chad Orzel said 'We are science' so can we not be 'Science 2.0' a loose confederation of like minded and connected people - Cameron Neylon
Well, the issue I have is not so much with centralized versus decentralized, as long as we can be/are connected, as you say. But I am not sure about having journals/publishers "enable" the underlying foundation. Since their primary objective is not about promoting "Open Science" but about increasing readership/citations of their journals. - Wobbler
I am all for loose confederation and that's where having services and APIs come in. However, this cannot be done in a vacuum. You need the journals, CrossRef etc to provide APIs etc that we can build on. If they can figure out how to monetize them, then we will be in pretty good shape, IMO - Deepak
It's also nice to have financial means to support individuals or projects supporting open science concepts (and to have workshops and meetings) but this seems difficult to generate without a formal organization in place... - Shirley Wu
Shirley - I agree and we're working on that from a number of angles - Jean-Claude Bradley
Wobbler, I can see what you're getting at. But why worry about why the applications are being built if they work well (and are sufficiently open, natch)? If open science gets done then everybody wins. Does it matter who enables it and why? Next big thing could be from a start-up, a grad student with some free time on her hands, two guys in a garage... that's the great thing about web development. Being in it at least partly for the money isn't a bad thing! - Euan
That is a good point. Maybe I am getting a bit too paranoid. I guess the key is indeed the applications being sufficiently open enough. Still, imagine the scholar working on the next big thing that does not specifically help a specific journal (publisher) get readership but promotes "open science" for everybody from all different research fields. Is there an organization that that person can go to for (financial) support (without "compromising" the "openness" of the concept)? - Wobbler
I also think that while publishers are doing a lot of work in this space (and I think that's a good thing - particularly if they want to survive) that a lot of the interesting things are being done in academic research projects, off the cuff side projects, and those loose confederations. They don't always get the exposure and a lot of it doesn't work out but that's where a lot of the innovation is IMO. - Cameron Neylon
As long as no one works in a vacuum. All of these efforts and fine (and there should be multiple different types), but they also have to talk the same language (http for starters :) ) - Deepak
Well I think talking at all would be a good start - that's what this paper is hopefully about... - Cameron Neylon
I am just wondering if an independent academic organization to support a platform for academics for the sake of improving "science" rather than as a means to an end for journal publishers could encourage more scholars to participate. Example, the PLoS ONE rating model is an interesting initiative, but it is limited to helping PLoS (ONE) improve its feasibility. A better approach would be a system that covers all OA journal publications from all OA journals. That would stimulate OA/Open Science more than... - Wobbler
...just a system that is limited the PLoS ONE environment. On the issue of PLoS ONE's system, Björn Brembs suggests taking it a bit further and use reputation systems. Very potential idea to get things moving, but again, limited if it is only for the PLoS ONE environment/community. I think a global reputation system that is based on all the assessment work of scholars for all OA journals gets far more attention (and likely more support/recognition of those same academic communities). - Wobbler
And that would also stimulate fair "quality" competition between journals, and not have a single journal/publisher hog all the "Science 2.0" scholars because they were the earlier ones to start with the rating/comment thing. And fair quality competition (using volunteers, no less) would give a more accurate view of the distribution of (publication) quality among journals. - Wobbler
Some non-publisher organisations are starting to take an interest and funders in general are looking at providing a range of services. We can obviously set up our own platforms but the funding has to be thought through in the long term. Who is going to pay for e.g. a commenting platform? Or, given that ultimately the funders may for everything where will the cost be charged and how do we make sure it's good value for money? - Cameron Neylon
(cont my own rant for a sec). And whether it is "Science 2.0" or full OA that comes first, it is not going to matter: either of them significantly increases the value of digital scholarly communication. And when that time comes nothing screams (financial) continuity harder than having a big community of capable people doing valuable work for you, free of charge. And on that account, Nature is doing a hell of a job building that community. Others, including PLoS, are trying to do the same. - Wobbler
And the rest are in danger of fighting for "scraps" (e.g. for helpful and capable users and papers). I am not sure if that is truly desirable. Although admittedly, Nature's Connotea is a pretty sweet non competitive service (other than for marketing, but that is more me being nitpicky). Cameron: I think those are indeed important questions to ask. - Wobbler
There is a real danger of getting poor tools because of a powerful incumbent or early mover with good PR. I think this is likely to happen with researcher UIDs for instance. Whoever manages to make the first effective move will probably end up in control - whereas what would be best is probably some form of federated open standard with multiple authorities that the user can choose from. - Cameron Neylon
If you mean how many people involved we have currently 2 with 2 more coming on board this week and hoping that more join - with SA donating compounds hopefully that will help - Jean-Claude Bradley
If you mean how many measurements we aim for I think Rajarshi can start working with the modeling after we have over 100 - Jean-Claude Bradley
FriendFeed helped me achieve my first Google PR5 ranking - Glenn Batuyong
YEAH!!! Congratulations FriendFeed!! What an amazing and productive first year...very impressive!! So happy for you guys!! Thank you Robert for reminding us of their birthday and to appreciate their product!! - Susan Beebe
Thank you FriendFeed, Robert Scoble and everyone else that has made FF the useful and entertaining tool that it is! - David Ward
I must thank the Twitter outages for pushing me here. - Eric @ CS Techcast
I look forward to seeing how FF moves forward, very good service, thanks to Paul and the team for their hard work creating a very useful utility. - Jeremy Campbell
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FriendFeed is so useful that I don't even know what I'd do without it. Congrats on completing your 1st year FF!! - J. D. Ebberly
Wow, its hard to believe that FF is already a year old. - Josh Smith
It took you almost a year to get me onto friendfeed? Dude, WTF? - Alex "Maverick" Scoble
I predict that I will be unemployed by this time next year if my first month's activity on FF is any indciation of what the next year will bring. :D I joke. I think. - ♥ pea ♥..!..♥..!..♥
Shannon: that wasn't even the private beta. That was the "are you a sibling of Bret beta," of which you were the only participant :) - Bret Taylor
"We leveraged up and if you have a 20 percent fall in value of a $20 trillion asset, that’s $4 trillion. And when $4 trillion lands — losses land in the wrong part of this economy, it can gum up the whole place.”
People should have known better but in some way’s it’s unavoidable with markets: “People should always know better. … I mean people — people don’t get — they don’t get smarter about things that get as basic as greed and you can’t stand to see your neighbor getting rich. You know you’re smarter than he is, and he’s doing these things, you know, and he’s getting rich, and your spouse is getting unhappy with you because you aren’t doing — pretty soon you start doing it. And so you get what I call the natural progression, the three I’s: the innovators, the imitators, and the idiots. And that’s what happens. Everybody just kind of goes along. And you look kind of silly if you disagree." - Paul Buchheit
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Can someone please engrave this on a plaque somewhere? Maybe we could have it etched into some tablets from the mountaintop and have churches predicated on these words. - Christopher Sacca
Right on! Yep, i am very "silly" ...not a jonesy type anymore.... we gave away much of our "cool stuff" and now have a mimimalist home ...MUCH BETTER and the best part, no stinking debt, except house and 1 car. The bank was all too ready to sock us deep into debt. We decided against that and are very happy with our decision to borrow only half what was offered (more realistic with cushion to $pare) - Susan Beebe
Unsure imitators and idiots don't simply continue on their merry way under bailout. - AJ Kohn
@AJ all the bailout does is buy time. We're merely delaying the inevitable, I think. If the imitators and the idiots keep doing what they're doing, we'll just be right back here again, except probably even worse off. - Victor Ganata
A lot of people have criticized Paulson, here's what Buffett says: "I don’t think you can have a better secretary of the Treasury than Hank Paulson … he knows markets, he knows corporations’ work, he knows money, and he’s got the interests of the country at heart." - Sanjeev Singh
One more nail in the Impact Factor coffin! - Bill Hooker
Absolutely! It just drives me crazy that they do this year after year and that they just can't seem to learn from abject failure. - John Dupuis
Guh. And T&P committees buy this crap. The power of heuristics over common sense, I guess. - Dorothea Salo
Haven't read the article, seen past versions. In physics at least, we all know who will win it the year the LHC succeeds in identifying a Higgs Boson: Higgs. In physics, you win the Noble when there's experimental evidence you were right. And impact factors don't matter. - DJF
