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Cameron Neylon
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?
I'm interested in joining the testing. Need to agree on criteria for comparison before starting, though. - Daniel Mietchen
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 - 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: - 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
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 (maths), these would include, for instance, (anthropology), (polar research), or this very life science group at - 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: - 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: - 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: - 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
@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
@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
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 You should be able to login with openids, any problem give me a yell. I would suggest a week by week schedule to dive into and try and use a specific site, give it a good shot and then report as we go. I... more... - Cameron Neylon
Cameron, what do you mean by "stability" - things like a service being bought/shut down vs. server outages? What about one week to agree on parameters and sites to check? I added data portability. - Daniel Mietchen
I was thinking more of medium to long term financial stability - but technical stability is a good criterion in terms of functionality. Data portability is a good point! - Cameron Neylon
Cameron, I spoke with Drew Endy, Bill Flanagan, and a couple other PIs that use OpenWetWare (Maureen, Pam) last week about the future of OWW. There are two major issues (a) funding and (b) overhauling the platform. I think funding will work out, if we can figure out what is the best way to do (b). Bill and Drew have some good ideas at this point, but in my gut I think we're still not... more... - Steve Koch
I guess my easy question for everyone who's familiar with OWW: Do you think with the resources we have (one full-time excellent lead developer) we can transform OWW into a killer openscience resource for many more people going forward? One thought that keeps coming to me is that something could be (needs to be) done to tap into the energy of the user base. I.e., obsessed students who... more... - Steve Koch
Another thing that keeps coming into my head since the conference call last week: FriendFeed is quite possibly very similar to what many people need for OpenScience. As far as science goes, we generate information from all kinds of different sources (Machine-specific data; gel photos; microsoft word; evernote; scratch paper; blogging; etc.). This needs to be aggregated and shared in a... more... - Steve Koch
Oh, and to clarify a bit: I don't want to replace FriendFeed with OWW. I want to use the FriendFeed model as a starting point for the new OWW. As an OpenScienceAggregator / Networking tool. As others have pointed out, much of the value of friendfeed is that it's not limited to scientists generating data. - Steve Koch
Steve, that's a great way of asking the question. I'd go one step further and say how can we make it the framework in which we can integrate all the other things we do on other services. It's never going to be a no-brainer to move from what you use to something else - there is always the simple problem of the activation barrier to change - its a question of the balance. But my guess is... more... - Cameron Neylon
Cameron, I agree with you exactly: I don't want people to switch, and indeed I want to think "one level above." Do you think there's a real possibility for doing that? - Steve Koch
If we could coordinate a series of activities and get proper funding then yes. Quite a lot of interest in the pieces of this (including the grant I'm currently rushing to finish), Chris's ideas further up this thread, OWW obviously, Mendeley/Citeulike/Zotero. But coordination is the hard bit - and getting agreement that its what enough of us want. Do I think we have a clear idea of what... more... - Cameron Neylon
Should we include some discipline-specific ones or are we going for general-purpose only? - Daniel Mietchen
Cameron Neylon
Nice simple starting point. Philosophy here is to make it easy for the user to connect up objects that already exist somewhere on the web when they write up a lab report. - Cameron Neylon
I am particularly interesting in the 'publish-in-database-x' features... someone mumbling ChemPedia? - Egon Willighagen
My thinking at the moment is limited to some sort of centralised data store just so that we can keep things simple in terms of building an exemplar. So objects get pushed via REST to the store and then the store generates RSS feeds. Theory being that in the longer term one can build "plugins" for any service that has a REST deposition system and generates a suitable RSS/Atom feed. - Cameron Neylon
Very interesting. - Jill O'Neill
incidentally the other half of this is something that looks like DropBox on scientific steroids. Files dropped into a directory get posted as blobs to the store with whatever metadata can possibly be captured - as far as possible with no user intervention. - Cameron Neylon
Science Online
Andy Powell
...the semantic web is not about "annotating the web with machine-readable data", it's about annotating the world with machine-readable data
I have a sudden vision of running around town spraying <graffiti> </graffiti> tags - Richard Akerman
Bora Zivkovic
RT @ezraklein Obama also awarded Nobel prize in chemistry. "He's just got great chemistry," says Nobel Committee.
Next up -- he'll win a Nobel in Physics for requiring GM's next car to run on HOPE - Benjamin Tseng
Richard Akerman
gandalf_grey: Obama wins peace prize and commits lunar bombing on same day. -
gandalf_grey: Obama wins peace prize and commits lunar bombing on same day. - Richard Akerman
Pierre Lindenbaum
Michael Nielsen
PLoS Biology: Real Lives and White Lies in the Funding of Scientific Research -
"The peculiar demands of our granting system have favoured an upper class of skilled scientists who know how to raise money for a big group... They have mastered a glass bead game that rewards not only quality and honesty, but also salesmanship and networking." I agree with much in this article. Some years back I constructed a list of papers I especially admired, and was surprised to discover that with only a few exceptions they were produced from unfunded research. This was sobering, since it suggest that receiving research grants was (at least according to my judgement of scientific quality) anticorrelated with doing work of the highest quality. Grants seem to be good at sustaining an established area, but not very good at all at producing the conceptual innovations that start new subfields. - Michael Nielsen
Depressing - Rajarshi Guha
@Duncan, oh absolutely. The idea of long contracts (5 - 7 years) makes sense. But these approaches will really require systemic changes - even if I could get by with small amounts of money (say for 1 student), the university won't like the fact that I'm not bringing in gobs of money to pay for electricity - Rajarshi Guha
I agree with Duncan that although the situation is depressing (and quite accurately represented in there), seeing it gain higher profile is refreshing. - Daniel Mietchen
Pushing these issues more and more is vital if we want things to change - even if we don't agree on the solutions, awareness of the problems is a prerequisite for change. - Björn Brembs
To be nitpicky, I'm afraid that the following suggestion is as open to abuse and laziness as the current one: "Everyone should get slotted into a funding category and assessed every five years. If you're productive, you get five more years of resources. If productivity is down, you are moved down a category. If it is high, you can apply to move up. Starting PIs are in a different... more... - Heather
Hmm. can't write English today. The suggested improvement to the system is subject to abuse, as much so as the current system - dead wood will be carried along. No room will be made for younger people moving up the ranks. And I meant "effective". - Heather
Lest we forget: "Trained as a biochemist, Dr. Prasher, 57, was interested in the chemistry of how certain animals are able to glow. In the late 1980s, he applied to the National Institutes of Health for a five-year grant to track down the fluorescent protein gene...'I knew it could serve as a genetic marker and it would be really, really useful, which it has turned out to be.' That application was turned down..." - Richard Klancer
Michael Nielsen wrote above: "Some years back I constructed a list of papers I especially admired, and was surprised to discover that with only a few exceptions they were produced from unfunded research. This was sobering, since it suggest that receiving research grants was (at least according to my judgement of scientific quality) anticorrelated with doing work of the highest quality.... more... - Bora Zivkovic
I don't have a blog post about it. To make the judgement I used a large fraction of what I know as a scientist. I couldn't easily reduce that to a short list of criteria. - Michael Nielsen
Oxford University Press announces take-up rates for their open access option:
Interesting to know what the funder breakdown is. Will try to dig into this later in the week. - Cameron Neylon
Bora Zivkovic
Is there any lit on 'Ethics of information literacy' or 'ethics & access to information'?
What specific sense of "ethics" do you mean here? - Mickey Schafer
For example, from a now apparently non-updated blog: "Information Ethics refers to the responsible creation and use of information in a variety of formats. Information Literacy is concerned with the ability to select and evaluate relevant and credible information resources." ( or "the adoption of appropriate information behaviour to identify,... more... - Mickey Schafer
Another sense would be the more philosophical/societal -- akin to literacy issues in general -- what is the ethical responsibility of a society/culture with regards to the info literacy of its citizens? - Mickey Schafer
How about the "A2k - Access 2 knowledge" movement - - Anders Norgaard
Thank you all...Ethics and information access to scientif. literature, that's the topic - Ana Ivkovic
There's a journal, International Review of Information Ethics. From the home page: [The journal] "envisions an international as well as intercultural discussion focusing on the ethical impacts of information technology on human practices and thinking, social interaction, other areas of science and research and the society itself". Most recent issue: Vol. 10 - February 2009, "Business Intelligence Meets Moral Intelligence", - Jim Till
Victor / Mendeley Team
Yippieh! Mendeley is Nr. 6 in the Guardian's list of Top 100 Tech Media Companies!
Michael Nielsen
The impact factor's Matthew effect: a natural experiment in bibliometrics -
"Using an original method for controlling the intrinsic value of papers--identical duplicate papers published in different journals with different impact factors--this paper shows that the journal in which papers are published have a strong influence on their citation rates, as duplicate papers published in high impact journals obtain, on average, twice as much citations as their identical counterparts published in journals with lower impact factors. The intrinsic value of a paper is thus not the only reason a given paper gets cited or not; there is a specific Matthew effect attached to journals and this gives to paper published there an added value over and above their intrinsic quality. " - Michael Nielsen
should have also figured in the year of appearance. if they appeared (were available to be cited) a year apart, that would make a difference in a field with a high immediacy... otherwise very interesting, though. - Christina Pikas
These are fellow UQAM researchers (my school!). Look up Gingras' work. Lots and lots of papers on similar topics. - Daniel Lemire
"duplicates papers as those that are published in two different journals and have the following metadata in common: 1) the exact same title, 2) the same first author, 3) the same number of cited references. Using this method, we have identified 4,918 pairs of papers." is it just me that finds it odd that there are actually 5000 pairs (!) of duplicated papers, same tittle, same 1st author and same references ? I find that amazing in itself. - Pedro Beltrao
It would look strange in a c.v. to have two journal papers with the same titles. - Daniel Lemire
Pedro: Trust me, it's not just you. - Walt Crawford
See also : here Mark Newman demonstrates the Matthew effect for citations in a very detailed way - Ewout ter Haar
i've seen it. also, you might have the case in which it's a conf paper reprinted in a journal and then a journal article - but that's not great either. i'm sort of surprised about the number of citations -that's something i would expect to change as a consequence of review - Christina Pikas
I do know of Emerald's stunt (publishing the same articles and even whole issues in different journals) and, of course, the Australasian Journal of... stuff--but should any of that be in the source database for this study? - Walt Crawford
maybe we should write them an e-mail? - Christina Pikas
The more I think about it, the more this bothers me. There are so many possible confounding factors that could easily play a causal role here (date of publication, how the authors themselves promote the paper at conferences and to colleagues, and so on). The empirical facts reported are interesting, but I'm not sure it's possible to conclude much. In particular, the inference that it's... more... - Michael Nielsen
Show me the duplicate papers data for social sciences. I want to understand how first -- I have seen perhaps one or two qua-duplicates in many years of reading, never two perfect duplicates, at the exception of reprints (articles becoming book chapters in edited collections, for example -- in which case citing the article is no Matthew effect at all). - Fr.
Branwen Hide
RT @mattlingard RT @JISC: How-to guides on web 2.0 technologies launched by JISC Netskills:
Bora Zivkovic
What is better? Twitter, or Flutter or Woofer ?
What is better? Twitter, or Flutter or Woofer ?
Martin Fenner
@kejames You find 28 blog posts about Science Online London (list will soon be out of date) listed here: #solo09
Jay Rosen
Matt Yglesias agrees with my prediction that the term "blogger" will drift into meaninglessnesss
FYI tried the link from my email and from FF- does not go through this morning. - frankiecarl from email
Hysell Oviedo
Kudos to health writer Tara Parker-Pope of the NYT. She's responding to reader's comments & even including additional info from scientists.
I looked around to see if other NYT writers do this and couldn't find any (although my search was not exhaustive). Does anyone know who else is doing this at the times? - Hysell Oviedo
In my past experiences, I haven't seen that kind of interplay too often with regular contributors. However, Op-Ed and other non-regular authors tend to relish this conversational approach with the public regarding their articles... But the fact that the NYT seems to be encouraging this with the Q&A section is great! - Noah Gray
Jay Rosen
What do you think of ? The Tribune launched it today. Blogging Guidelines, which I influenced
Martin Fenner
CiteULike + BibDesk: Sync your references and live smarter: - Nathalie Cornee
CiteULike Plugin Developer's Kit - - Nathalie Cornee
CiteULike traffic stats - - Nathalie Cornee
CiteULike: Interview with Kevin Emamy - - Martin Fenner
Kevin Emamy talks about CiteULike - Martin Fenner
CiteULike is totally Web-based. I haven't decided yet whether I prefer the web-only approach (Refworks, CiteULike, Connotea) or the web/desktop combo approach (Endnote, Mendeley, Zotero). - Martin Fenner
CiteULike allows PDF uploads. File can only be downloaded by user and private groups. - Martin Fenner
Importing references into Connotea and CiteULike appears to be easier (and faster) than with Endnoteweb and Refworks. - Martin Fenner
Kevin talks about how CiteUlike helps users discover interesting references that they otherwise wouldn't have found. - Martin Fenner
indeed, it's easy to search keywords in citeulike and retrieve other users who have used these tags previously - Nathalie Cornee
Tags and users allow the discovery of interesting related papers. - Martin Fenner
12 citation styles cover 90% of uses, so CiteUlike focussed on those. - Martin Fenner
You can drag & drop citations (in your preferred style) into your word processor document, or you export references as ris or rtf. - Martin Fenner
Other social features of CiteULike: connections, neighbours, and zeitgeist. Neighbours are users that have similar references in their library. Zeitgeist shows you the most popular references over a period of time (e.g. the last 7 days). - Martin Fenner
Kevin shows how PLoS articles have a link to CiteULike (showing the number of users tagging that article in CiteULike). - Martin Fenner
Kevin talks about the business model for a service such as CiteULike. The revenue from advertising alone would not be sufficient. Sponsorship by Springer is major source of income. - Martin Fenner
Really interesting to see the differences in what features are seen as important between Endnoteweb/Refworks and Connotea/CiteULike. - Martin Fenner
I like the CiteGeist feature, and not just because of the terrible pun! - Frank Norman
Interesting social features too - connections (like friends), messages, neighbours, groups. - Frank Norman
To get the bookmarklet to work for PubMed you need to get article URL in browser address bar, before clicking on the "Post to CiteuLike" button - Patti Biggs
Neither of the social bookmarking tools (CiteuLike or Connotea) allow for formatted text, accented characters etc in article titles, author titles - Patti Biggs
Accented chars? Yes we (citeulike) do that. Formatted text too as long as source and output formats compatible. - Fergus Gallagher
But does it capture greek, italic and superscripts from the source? - Frank Norman
I thought so - examples? - Fergus Gallagher
Ah, just realised that the presentations yesterday were all using Pubmed as their source, so wouldn't have a chance of capturing anything except plain text. I'll check this out later. - Frank Norman
Nathalie Cornee
Elsevier Announces the “Article of the Future” -
Scholarly Kitchen asks: "is it lipstick again?" - Nathalie Cornee
Martin Fenner
SciBar Camp: Keynote by Sean Mooney; Biomedical Research in the Age of Cyberinfrastructure
Keynote at an unconference is difficult, an untalk? Will take about why he thinks scientists don't use the internet. - Martin Fenner
hi martin :) - Pedro Beltrao
Is all the discussion on Twitter? - Martin Fenner
seems to be quite a lot over there at #scbPA but we know where the quality is... - Cameron Neylon
Scientists are certainly all connected: email, manuscripts and news on the internet - Martin Fenner
but integration a problem, dissemination of data is a challenge - Cameron Neylon
Most of the tools that his group builds are web-based - Martin Fenner
For the majority of scientists, there is no interest in using tools like Twitter or Facebook. - Martin Fenner
streaming video at - not from me at the moment - Cameron Neylon
His groups built a biorepository inventory management software, community portal software, bioinformatic analysis tools (often web-based). - Martin Fenner
need to get lots of citations of tools to keep getting funding - Cameron Neylon
Individual tools are not in a vacuum, they should be connected together as cyperinfrastructure. - Martin Fenner
lots of web based tools but individual tools are not in a vacuum. The collection of resources is key and how to combine them together - Cameron Neylon
nasa space programme as an analogy for building an integrated cyberinfrastructure - Cameron Neylon
each part can be tightly specificed for e.g. shuttle but harder to push that kind of integration specification for funded research projects - Cameron Neylon
Difference in space program: NASA clearly says what they want, different in bioinformatic tools. - Martin Fenner
Examples of integration (cyberinfrastructure) tools, CaBIG, NCBI, BIRN, homw-grown... - Martin Fenner
talking about different big programs like and - Pedro Beltrao
Administrattors always want "big picture", e.g. asset management, researchers want data analysis. This leads to two kinds of projects. - Martin Fenner
researchers totally focussed on specific problems. Administrators have other concerns, want "asset management" - Cameron Neylon
administrators often misjudge their needs for scientist's needs. Scientists often mistake today's need for tomorrow's needs - Cameron Neylon
NIH has 27 institutes, they all have their own approach to informatics. - Martin Fenner
Traditional approach: domain specific coordination - Martin Fenner
traditional approach is to build a specific system or portal for a consortium of researchers - Cameron Neylon
Data sharing was key to PGRN's value - but not the last place the data might go - Cameron Neylon
horribly complicated workflow with lots of different research foci - Cameron Neylon
i guess this approach creates isolated domain knowledge that is hard to integrate with other domain specific projects - Pedro Beltrao
Need to collect disparate data to pull everything together and then push on to the mandated site - Cameron Neylon
Management needs: secure platform, database eneabled - Martin Fenner
Question: are researchers actually using the web-based tools to collect data? - Martin Fenner
and every lab is probably doing something different to the workflow they say they are using... - Cameron Neylon
but if you designed better to start with (but need heavy resourcing to do this) then it might be - Cameron Neylon
CaTissue is great tool for tissue sampling, was built from the beginning to work for many different situations. - Martin Fenner
Current challenges: connect to bigger projects, next generatin suequencing, etc. - Martin Fenner
pedro asks a good question - is there any mandate for annotation or tagging? Answer from Sean: No, there is money available to support but no compulsion - Cameron Neylon
Big mover in the next 10 years: funding for translational research centers (CTSA). - Martin Fenner
mandates for CTSAs to work together but no idea how that is going to happen in practice - Cameron Neylon
Ask for a laundry list of informatics functionality. Sean "do you know how much this is going to cost" Admin: "No, how much do you need" Sean: "Well all of the money available..." - Cameron Neylon
ability to embed applications in a virtual machine in the web portal. - Cameron Neylon
hub doesn't directly integrate scientific data or handle group collaboration - Cameron Neylon
personal information actually put into their hub implementation by administrative assistants - Cameron Neylon
integration across CTSA informatics projects is not happening, everyone is trying to do everything themselves - Cameron Neylon
And now, the Web2 bit! - Cameron Neylon
popular with adminstrators and funders I think - possibly developers, less so with scientists... - Cameron Neylon
NIH has started to put more grant money into social networking tools, e.g. with the CTSAs mentioned above. - Martin Fenner
but sharepoint very popular in government - never really understood why I have to admit - Cameron Neylon
Challenges faced in Mooney lab: Creation of collaborative documents: manuscripts, proposals, management of datasets, discussion. - Martin Fenner
Laboratre solves problems in Mooney lab. - Martin Fenner
Applications can be embedded in Laboratree using OpenSocial. - Martin Fenner
Web portals for science suffer from under-use. - Martin Fenner
Successful tools are simple. - Martin Fenner
Start with an existing community. - Martin Fenner
Discussion: Open Science is important, but is a long way to go (publishing as example). - Martin Fenner
Discussion: will HTML be used instead of .pdf or .doc? Is a paradigm shift, particular difficult in clinical medicine. - Martin Fenner
One reason to use OpenSocial for Laboratree is the hope that people would build applications that can easily be reused. - Martin Fenner
Discussion: a lot of our data from a years ago is probably no longer relevant to what we do today. - Martin Fenner
Darn, would have loved to be at this session. Some day I will actually make it to one of these - Deepak Singh
I posted the keynote as a video in three parts on my blog: - Naomi Most
Thanks Martin, Pedro, Cameron, Duncan, and Naomi! With so many notes and videos, it is almost like being there :) - Mike Chelen
Brian Kelly
Trying out Twit2go on Android phone. Seems better than Twidroid.
Michael Ridley
Murray-Rust "The librarian of the future will not come from the librarian of the present. Librarian of the future will be a revolutionary"
Seb Paquet
Brian Kelly
Twitterers Subvert Dail Mail’s Racist Poll -
Underfunded Scientists Force Lipstick-Covered Rat With Cancer To Run Through Maze -
Underfunded Scientists Force Lipstick-Covered Rat With Cancer To Run Through Maze
I'm sorry....but I can't stop laughing at this poor beast........ - Noah Gray
"... Mendel, a blind 1-year-old albino Norwegian rat with advanced non-Hodgkin's lymphoma, has served as the subject for every experiment the lab has performed." - pn
Stop it, stop it.....can't.....breathe........ - Noah Gray
She has been kept as comfortable as possible, given the nature of animal-based lab research," Cho said. "Not that any living organism pumped full of that much serotonin could possibly be having a bad time. - pn
"The lab's shoestring budget, which forces the scientists to conduct their research in the facility's kitchenette, has reportedly inspired several serendipitous discoveries. Cho said the most notable of these is documented in a study entitled 'The Effects Of Acute Toothpaste-Induced Fluoride Toxicity Coupled With Extreme Steroid Abuse After Hot Coffee Has Been Spilled Into A Surgical Incision Resulting From The Removal Of A Genetically Grown Ear.'" - Noah Gray
Better results than these guys - pn
Geoffrey Bilder
Blog posts, papers, and the brave new digital world: your thoughts are welcome « Sauropod Vertebra Picture of the Week -
Interesting thread on citing blog posts, other non-traditional scholarly communication. - Geoffrey Bilder
The comments capture a good cross-section of different community views which is quite interesting to read - Cameron Neylon
'Mummi' Thorisson
e-Infrastructure / e-Science case study video: research into Trypanosomiasis in cattle using analysis workflows -
e-Infrastructure / e-Science case study video: research into Trypanosomiasis in cattle using analysis workflows -
The e-Infrastructure Use Cases and Service Usage Models (eIUS) Project - - have produced a video about “e-infrastructure case study Bioinformatics”. The video discusses the application of Taverna for Trypanosomiasis research and the sharing of workflows on myExperiment. It includes appearances from Carole Goble, David De Roure, Andrew Brass and Paul Fisher. - 'Mummi' Thorisson
"We would not have been looking more widely simply because we didn't have the tools to look" -- quote pulled from last few seconds of video -- How much better an explanation does one need?? - Mickey Schafer
The similar post on archeology was also terrific -- a different emphasis in this one, somewhat more on the impact of digital tools on data collection in addition to sharing and collaboration -- - Mickey Schafer
I agree with Mickey on the value of these videos as teaching tools. Get the kids interested in science. These are perfect--thanks Mumi. I had never heard of myExperiment before. - Hope Leman
Bill Hooker
Question for the LazyWeb: what's like Library Thing, but doesn't suck fourteen different kinds of ass?
is the upper border for ass 13, then? :) like Library Thing how? Shelfari is a competitor, but I don't remember it being as good. - Christina Pikas
I prefer a maximum of one or two kinds of ass in my web apps. :-) Yeah, I was looking for competitors -- I looked at Shelfari, GoodReads, aNobii and GuruLib. They all suck at least fifteen kinds of ass, making LibraryThing the least sucky of a sucky batch. - Bill Hooker
I did "solve" the worst problem with LT, which is that adding a book takes about a million clicks and requires a search -- yes, search for an author, add a book, repeat the search, add a book, and so on. But you can "batch add" in GoodReads (sort of; it's not good but faster than repeated searches) and LT's import function will slurp up GR's RSS page (not as a feed, just as a static page). You still have several clicks to go after that, too. See what I mean about suck? - Bill Hooker
Am about to try weRead, will report back here if it's any good, otherwise assume continued suckage. - Bill Hooker
Why don't you just use a cuecat? Or are you importing from a list you already have? EDIT: I entered by hand by isbn a few years ago, but if I were doing it now I'd use the bar code reader. - Katy S
Not sure how you're trying to import into LT but I got a couple hundred in at once about 2-3 years ago with a text (delimited somehow) file. - Mar₭ Liŋdŋer
@Katy: I don't have a barcode reader. Not the kind of thing I tend to have lying around, somehow. @Mark: the LT import is slow but it works well enough, so long as there are ISBNs to slurp up. Problem is that rather than just adding the imports to your bookshelf, it then sends you, for each imported book, to a page to choose which edition you want to list (even though you fed it ISBNs!). Gah. - Bill Hooker
Bookshare on Facebook, plainly. ;p - Euan
weRead's interface is OK but its recommendation engine is total crap. I want to keep track of what I've read and get decent recommendations, so I'll probably use LibraryThing because although it's a pain to get your backlog entered, after that it's not bad and their recommendations look good. - Bill Hooker
... though if you're after less suckitude an app that's actually regularly developed by a well funded team of people is probably a better bet. - Euan
I get the impression that Google is headed down this road with some of the new features built on Google Books. For example, you can use a barcode reader to import your books into "My Library": - Hilary
Bill - the barcode readers librarything sells are $15. If I were starting from book #1, I would buy one. As it is, now that my books are entered, it is pretty easy to add books as I acquire them. I use goodreads, too, but I find LibraryThing is better when it comes to adding and using tags. I added and tagged most of my items while watching tv and then while helping out after my mom's hip-replacement surgery, fwiw. - Katy S
Ah yes, Bill. That is suckitude. I don't believe it did that at all when I did it but like I said it was a couple years back. - Mar₭ Liŋdŋer
Brian Kelly
@aarontay I cite Wikipedia in my blog and my talks. Wikipedia often gives a readable summary of topics & a useful starting point.
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