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Nice interview guys. I’ve been using RB now to tag my “serious” posts on http://www.sciencebase.com/ and http://www.sciencetext.com/ for quite some time now and it certainly makes me feel good to know they’re being taken up by the system.
It’s impossible to analyze referrals because so many people read blog posts and RB via so many different routes now, but I had a couple of hundred new readers via direct referrals from researchblogging.org last year, which is a small number compared with my actual daily visitor rates, but it’s presumably a more targeted audience so definitely a good thing.
As RB itself and awareness of it grows this year, I’d expect those stats to improve and for the scientific threads to pull our community together more effectively as well as to rope in more and more people from outside the various niches too.
Walter introduced me to your blog and I have just now stared to follow you on Twitter (which I have only just started using and boy–is it a good way to keep up on Science 2.0).
Very, very helpful to hear from you, a serious sci/tech blogger, on how you use RB and your thoughts as to its potential.
[...] It is interesting to compare Scientist Solutions with LabRoots. [...]
christina commented on January 28th, 2009:
hmm…i am using researchgate nearly every day, dont have the impression of low activity – but to be honest, i once signed up for labroots and never visited again… hm?
[...] have looked at smaller Science 2.0 sites, such as LabRoots, Scientist Solutions and 2collab, and it is at once clear that NPG is pouring money and talent into [...]
[...] have looked at smaller Science 2.0 sites, such as LabRoots, Scientist Solutions and 2collab, and it is at once clear that NPG is pouring money and talent into Nature Networks. [...]
We’ve “met” briefly in the comments section of Michael Neilson’s blog — my students are the “guinea pigs” whilst I figure out how to introduce science2.0 in a meaningful, useful way to them. I find your evaluation of NPG’s offering very similar to what my student’s found — they liked the variety, but were disappointed by the lack of science rigor. Many of them performed searches similar to yours — fairly specific for things they were interested in — and didn’t turn much up. Most of the blogs they subscribed to feature topics of interest that they don’t quite have time to immerse themselves in. Interestingly, this pretty much covers the blogs I subscribe to — personal interest, professional interest, but not those related to my actual area of expertise (linguistics — it’s funny, ’cause most of what I’ve read related to language makes me want to throw things or sigh “but we’ve done that already”!).
This has left me in something of a jam in terms of explaining why I think this is so interesting — and relevant to them as future MDs. Currently, I’m adding your blog to their reading list since you are taking a sort of pedagogical look at the issue: an “about science 2.0″ perspective, which is incredibly useful. And I’ll have them began their own individual posts in a couple of weeks so they get a feel for the writing side. But that hardly seems to cover it! One of my students recommended an open-source web-building program to use instead of the class blog — I thought that was an interesting option b/c we could use it to talk about how to design personal web spaces that are useful professionally — not just for connecting with colleagues, but for directing patients, too. Science 2.0 is turning out to be a difficult sell because most of them see themselves as practicing MDs rather than as researchers.
Love the phrase “wild web” — very much what it feels like!
Hi, Mickey. Thank you so much for you very interesting note. Now, if this isn’t classic Web 2.0. I learned about Michael Nielsen’s blog from the Science 2.0 room at FriendFeed and visited his blog because of interesting comments he had made about Google’s Knol. I found his blog very interesting reading and your comments there ditto and here you have visited this blog and made some more.
Yes, there just doesn’t seem to be much hardcore scientific rigor at Nature Network. I think that such is to be found in the plethora of specialized blogs on specific topics and in the increasing number of open notebook blogs such as those that Jean-Claude Bradley, Michael Nielsen and Steve Koch either highlight on their blogs or embody at same.
I would recommend that your students visit and contribute to the Science 2.0 room of FriendFeed. I learn a lot there from Jean-Claude’s comments such as, “The term “Open Notebook” refers to a mandatory sharing of all experimental data for a given project. If you didn’t find entries for the past 30 days in a true ON you can infer that no experiments were performed during that time. There is a category in the Wikipedia page on ONS referring to Partial/Pseudo ONS. This would include all attempts at being more open in sharing research without strict adherence to all the implications of ONS.” And his comment on one site, “…it sounds more like a research blog – commenting on papers he reads…”
And my partner here at Next Generation Science, Walter Jessen, just emailed me, “I’ve always considered NN a forum and not a blogging community (even though you can blog there). You are right – all the prominent scientists blogging have their own blogs.”
I loved your comment, “…but we’ve done that already!” If you have the time, you might stop at such blog entries and say so and cite the earlier study. That would be a public service—but who has the time?
I agree with you that it is hard to sell Science 2.0 to front-line clinicians. But more and more of them are getting involved in research even at the community hospital level and so need to know about the world of clinical trials and how that world is changing radically (e.g., the lithium for amyotrophic lateral sclerosis trial led by the online patient community Patients Like Me) thanks to the Web. There is so much in Science 2.0 for future MDs to know about—patient empowerment and firms such as Private Access https://www.privateaccess.info/
that are developing security suites that will enable frontline medical providers, researchers and patients to communicate productively in secure, confidence-building environments. I learned about Private Access at the Health 2.0 Conference and Science 2.0 is not all that abstruse or disconnected from the daily practice of medicine.
Good for you for working so hard and creatively to instill a research mindset in future clinicians and form future clinician discoverers.
It is, as various commenters seem to agree, early days for Web2. NN (and I blog there, so take what I say with that in mind) is more of a social networking site. The blogs rarely deal with ‘hard’ science, and focus more on the human side of things, which seems to be what people want (slightly self-fulfilling, but as you say they seem to be the clear market leaders).
I would love to see the forums (as distinct from the blogs) being more useful somehow. But as that doesn’t appear to be happening one has to ask if that, again, is market-driven? The tools could be there, but maybe it’s too early for them to be successful. We tried getting the ‘Collaboration’ forum going, to little avail.
There are problems with the platform—as a user and a blogger—although we keep nagging them to fix these, and progress occurs. What I will say though is that I got a new job with the strength of my blogging at NN, so I’m not knocking it
@rpg No worries … I’ve updated the link. Thanks for your input. There’s this stigma attached to blogging that it somehow hinders you from advancing in academia. Congrats on the new job and kudos for getting it with your blogging at NN.
and was impressed by the large number of readers you have. You are a one-man social network in and of yourself.
I was interested by your comment, “I would love to see the forums (as distinct from the blogs) being more useful somehow. But as that doesn’t appear to be happening one has to ask if that, again, is market-driven? The tools could be there, but maybe it’s too early for them to be successful. We tried getting the ‘Collaboration’ forum going, to little avail.” I wondered what you meant by “too early.” Too early in what respect? Too early in the evolution and visibility of social networks in the sciences in general or too early in the evolution of that particular forum on Nature Networks?
Given Mickey’s comments here and on FriendFeed that he has difficulty persuading his medical student pupils of the professional value of blogging and of Science 2.0 in general (“This has left me in something of a jam in terms of explaining why I think this is so interesting — and relevant to them as future MDs…”), your comment here is especially valuable and a teachable moment, “What I will say though is that I got a new job with the strength of my blogging at NN, so I’m not knocking it?” Think about that all of you early career scientists and health science students out there.
I found that also quite interesting given that there don’t seem to be prominent examples of scholars who have won plum positions on the basis of self-archiving at institutional repositories and I would be interested to learn if you have done much of that. Librarians often have a hard time convincing scholars that there are career advantages to depositing their papers in institutional repositories that can be then rendered searchable via such search tools/databases as the E-print Network http://www.osti.gov/eprints/ .
Hope, thanks so much for the remarks, and I happily have a bit of success to report. A very short history: last week I was out of the office for 3 days b/c my daughter had pneumonia (thank goodness for wireless routers!). The result was my thesis students (the neuroscience/premeds I’ve been writing about) took it upon themselves to write individual blog entries on our class blog despite not having discussed the assignment yet. Many of them chose to write about exactly the kind of stuff I read everywhere: funding (lots of that!); the impact of the “scientific method” on progress (student titled the entry “slow science”), the potential ineffectiveness of the peer review process (a student found a major research report featuring an incorrect finding with that finding later popping up in reviews as well; she is despairing somewhat!); the elation and disappointment of research itself. The entries are well-written, creative, interesting, reflective — all the things that make me proud to work with this population of students.
But the biggest excitement is that is works! 3 weeks ago, the students were not excited by this. I don’t know yet that I would say they are converts, but they do see the point — one student even blogged about how important writing/comm skills are to scientist/MDs, particularly if they are to convince an audience that their research deserves funding or their particular take on a therapy is superior. Ye gods, I can barely sit still and type!
Okay, before I get to loopy, I’d say the point of this lesson is something many have blogged about: there is great value to just doing it. Smart people in general have interesting things to say, and since work lives frequently allow expression of just a portion of what goes on in their heads, this medium allows participation in the kinds of conversation they value. Now, I believe I will take up your suggestion of joining the FriendFeed science2.0 community b/c I think they’re ready to see the value of it. I can’t say that they will join in as participants, but are perhaps ready to take the next step. Especially given Richard/your comment ““What I will say though is that I got a new job with the strength of my blogging at NN, so I’m not knocking it?” Think about that all of you early career scientists and health science students out there.”
Hi, Mickey–that is all very sweet and immensely touching. I’m just heading out to my day job the library right now so will read all of your comments more thoroughly tonight. In the meantime, would you please tell your students that as someone who knows and loves a kind and gentle person with amyotrophic lateral sclerosis, I can’t think of anything more important than what they’re doing with their lives: studying neuroscience. Theirs is a noble calling and they are lucky to have such an engaged and engaging, enthusiastic, creative, resourceful, dedicated teacher like you.
Hi, Mickey. Thank you so much for the report from the frontlines. It is delightful to hear that your pupils are starting to see the value in blogging and other Science 2.0 types of communication and research.
Yes, funding is perennial problem. I am very interested in amyotrophic lateral sclerosis, so I try hard to list any grants on neurodegenerative diseases in particular and on neuroscience in general on ScanGrants. Good for your students for improving their writing skills—they are going to have to write grant applications at some point in their careers and if they can so quickly and well, the less they will have to farm out at great expense to professional grant writers.
I loved “Slow Science”—cute.
Good for the student who spotted the error and subsequent uses of the flawed data. For the rest of her career she will be on the alert for such things. I did a quick PubMed search and came up with these articles. She might be interested in them:
1: Scientific deception: retraction of a fraudulent paper.
Coats A, Williamson EM.
Int J Cardiol. 2009 Jan 24;131(3):297. Epub 2008 Dec 3. No abstract available.
PMID: 19056136 [PubMed - in process]
2: Falsified papers in high-impact journals were slow to retract and indistinguishable from nonfraudulent papers.
Trikalinos NA, Evangelou E, Ioannidis JP.
J Clin Epidemiol. 2008 May;61(5):464-70.
PMID: 18394539 [PubMed - indexed for MEDLINE]
3: Retraction rates are on the rise.
Cokol M, Ozbay F, Rodriguez-Esteban R.
EMBO Rep. 2008 Jan;9(1):2. No abstract available.
PMID: 18174889 [PubMed - indexed for MEDLINE]
4: Retractions in the research literature: misconduct or mistakes?
Nath SB, Marcus SC, Druss BG.
Med J Aust. 2006 Aug 7;185(3):152-4.
PMID: 16893357 [PubMed - indexed for MEDLINE]
5: Research misconduct, retraction, and cleansing the medical literature: lessons from the Poehlman case.
Sox HC, Rennie D.
Ann Intern Med. 2006 Apr 18;144(8):609-13. Epub 2006 Mar 6.
PMID: 16522625 [PubMed - indexed for MEDLINE]
6: Scientific misconduct. Even retracted papers endure.
Unger K, Couzin J.
Science. 2006 Apr 7;312(5770):40-1. No abstract available.
PMID: 16601165 [PubMed - indexed for MEDLINE]
As to the elation and disappointments of research, I heard a very good talk a few months on ALS by Joseph S. Beckman, Ph.D. Principal Investigator and Ava Helen Pauling Chair, Linus Pauling Institute here in my hometown of Corvallis, Oregon at Oregon State University. It was clear what a talented teacher and dedicated researcher he is. I wish your students the same kind of joy in their research as Dr. Beckman discoursed upon so memorably and know they will share his determination to help those with devastating diseases. I can see why you are proud of your students. Dr. Beckman’s talk was moving and exciting. Writing skills clearly are part of the skill set of any successful scientist.
I definitely recommend that your students follow the Science 2.0 room at FriendFeed. For instance, apropos of the student interested in the peer review process, I came across this item via FriendFeed just now:
gpeerreview
A tool that enables peers to review and sign each others’ works
Very interesting post. Not totally unlike academia, sometimes, though I am fortunate that the particular academic unit I am involved with only “stifles” innovation b/c of budget. Basically, if any of us can demonstrate via simple argument that something will work and we can afford it, then we can do it. I sent this post to my brother who is an aerospace engineer (designs guidance systems) and also a project manager. I’m curious to see what he might say in response.
Another perspective on this issue has to do with management and how people are or are not prepared for the change in responsibilities…I have discovered that even in my fairly low-profile position as coordinator of a couple of projects that there are issues at the administrative level that are not well-understood until you get there. Or perhaps it would be better to say that these issues are not often made clear until one gets to a position of responsibility (ex: inter-departmental relationships with political bite that don’t have to be negotiated when simply a faculty member). I wonder if greater transparency of these relationships would lead to smarter suggestions by all members or if this knowledge would be discouraging. I’m of the personality type that makes suggestions without regard to operational constraints, then winnows ideas according to what is possible (both a strength and weakness!). This is not the case for everyone. What is the best way to educate members of the group so that innovation better matched actual constraints? And even at Google, there must be a vetting process at some level — not to mention that overall, the public is less concerned with what Google fails at (if the public learns much about it at all) whereas NASA is a more visible entity.
I’ve found the same thing in biomedical research: if you can justify an experiment or project (barring fiscal constraints), you can do it. Needless to say, there’s quite a difference between a research experiment and spacecraft design, but the willingness to listen to and think through new ideas should be a shared trait by managers in either environment.
What struck me about this was the lack of technical discussion between administrators and the engineer. The disconnect between the process and the details is surprising given the nature of the job. Perhaps it exemplifies your comment, “there are issues at the administrative level that are not well-understood until you get there.” I wonder what those issues are at NASA?
As I said I might, I sent my brother this entry since he is a project manager at a huge aerospace firm, and has won awards from NASA for his launch successes. I don’t believe he’d want me to post his whole reply…suffice to say that he had a strong, eloquent reaction based largely on the apples to oranges comparison between a private company like Google and a more public company like NASA. While the amount of money flowing through each might be similar, the public and other consequences of failure are not at all the same. He did make a point, though, that is closer to yours above in terms of a “technical discussion” — there is a point for innovation, but it isn’t mid-project. Perhaps there needs to be more discussion up front or a separate line of $$ for mid-project insights that need exploration (an untested piece of Google code may cause embarrassment, but it won’t result in death). Even in academia, a project cannot usually be stopped cold to be re-worked from the beginning; instead, new lines of inquiry are planned.
[...] never will understand why tech firms don’t feature screencasts. LabRoots has one. It is such a no-brainer. Basic, basic, basic. Never make potential customers have to email you for [...]
Thanks for the backlink to my scientists on twitter link, we passed the 200 last week, currently 204 members. All science types with a twitter ID are welcome. Just tweet me, comment on the post, or retweet the link http://bit.ly/scientwists and I’ll add you. (Please make sure you have a non-generic photo, a bio and a website link)
Nicely done interview, Hope! Definitely helps next gen sci live up to goal of providing a forum for those of us still new to web2.0. I am particularly interested in the idea of the “semantic web” — ThinkMap’s (http://www.thinkmap.com/) Visual Thesaurus (though not semantic in the sense I think code creators use the term) is still an interesting model of what happens when technology is modeled after more human forms of cognition and is made to appeal visually. Mozilla project’s ubiquity (http://labs.mozilla.com/2009/02/ubiquity-016-and-release-scheduling/) is also an attempt at the semantic web which is fairly intuitive insofar as we humans are used to thinking of things as verbs and nouns. I think it would be easier for people to pick up a controlled set of verbs for web navigation, especially if an equally obvious set of metatags (I think that’s the term) were commonly used (or, in addition, developed discipline-specifically).
Hi, Mickey. Thank you for your nice note and kind words about Next Generation Science. Walter is doing most of the work right now. I keep wandering away to read the absorbing writings of Jean-Claude Bradley and those of his colleagues that he provides links to in the various Science 2.0-related rooms FriendFeed. There is so much to read about on this topic that I haven’t been writing much about it—except to write comment after comment in FriendFeed urging all those brilliant science bloggers to make sure to place Twitter buttons their homepages so that you and I can tweet particularly useful posts and thereby alert others of blogs they might not have heard of. Twitter really is a powerful tool in the Science 2.0 and Open Science movements.
In my library school courses, they certainly do stress the coming importance of the Semantic Web. Have you been following Tim Berners-Lee’s work in that area? Seems rather heavy on bureaucratic power grabs and obsessive concern with larding with metadata what should be a vibrant, growing organism. I would be very interested to see what people like Jean-Claude think of Berners-Lee’s strategy for standardizing it all.
Apropos of your comments about ThinkMap, here is a superb slideshow put out by the makers of the equally interesting product, Tableau:
Thanks for the heads-up on Ubiquity, which I had not even heard of! Duh, Hope!
Could you provide an example of how this would work in practice, “I think it would be easier for people to pick up a controlled set of verbs for web navigation, especially if an equally obvious set of metatags (I think that’s the term) were commonly used (or, in addition, developed discipline-specifically)?”
The process of putting nouns and verbs together is pretty basic stuff — this distinction exists in virtually all languages (I would say “all” but one should be careful of claiming absolutes:-)) — in Ubiquity, the program pulls up a transparent black box where a set of commands that are pretty familiar to web users can be entered and which can then perform operations with info on one’s hard-drive (the creators are careful to point out this is fairly dangerous, too, and are looking to establish a “trust network” of ubiquity sourcerers (okay, really bad pun there!), umm, code writers (ubiquity is open source) that would provide community-based rankings for a page’s security). I really don’t understand code, but the idea of using this basic distinction b/w noun and verb to navigate seems intuitively appealing. This is at best a hazy idea on my part, and spoken from a position of ignorance in terms of creating code/understanding how code gets created. Rather, it is the opinion of a user dreaming of utopia where the interaction b/w human and machine makes the best use of both capabilities — people are particularly good at creative connection; computers are particularly good at data manipulation. The semantic web idea seems to want to capitalize on these differences.
Sorry, Hope, in reviewing my reply I may have unintentionally come off a bit rude — in that first sentence, I should have said something closer to “Nouns and verbs seem to be a basic distinction common to language…” or something like that. That’s what I meant by “basic stuff” — basic to the human animal. There’s interesting infant studies to show that we respond very early on to differing types of motion. In any case, when I read my answer it didn’t seem quite right. Any chance you could add a preview button? Helps me think my way through before hitting post!
Hi, Mickey. Sorry to be slow getting back to you. Thank you so much for both of your notes and for your very interesting points about how lovely it would be if machines could understand what we are driving it in terms of nouns and verbs. I had that very problem this morning. I was trying to comment on the value of blog carnivals vis-à-vis increasing the visibility of blog posts (say, this one). I typed phrases into the Google search box such as, “to dramatically increase in value” and “to render more valuable.” I then thought that perhaps there was a verb form of “exponentially” but “exponentiate” doesn’t seem to fit that meaning. Maybe it does—you as a linguist would know that better than I. So nice to know linguists.
Your note was not at all rude and I agree with you about the need for a preview feature. One does like to make sure that one’s boo boos are not preserved forever on the Web. We will see what technomeister Walter Jessen can do about that.
I loved “sourcerers” and think it should be adopted forthwith!! I am not sure where we are in terms of the Semantic Web differentiating between nouns and verbs.
Okay, Walter, you’ve almost got me to the point of adding twitter. Almost. I’ll have to employ the “high value” metric you suggest more conscientiously to my current 2.0 activities — it seems that while I’ve done that for the blogs I follow, I still don’t have a way of keeping track of these activities in a way that fits my workflow…maybe I don’t have enough of a workflow!
Nash does make some interesting points in his post, some of which are cultural in nature — just this morning, a pair of local DJs were hashing out whether Facebook’s new look was better — one of them made the observation that in a year, it won’t matter: it will just be the look of Facebook. I’d reply similarly to Nash: for some tools, it’s just a matter of time. They’ll be used because they are used, and if the lab-bound researcher intends to keep up with grads (let alone undergrads, an increasingly large population of researchers b/c NSF provides funding provisions for their inclusion), then real-time text-based comm tools will be a reality.
I do agree the name “twitter” is off-putting — and I’m not convinced that the instant messaging utility of twitter makes it necessary for science groups. Any IM system would work for that. Rather, Twitter offers some kind of “ambient” experience (see Lisa Reichelt’s slideshow and Herot’s thoughts) which is beyond (or at least different from) transmitting messages or consuming information. I think Twitter — and these sorts of 2.0 tools in general — encourage a kind of ambient literacy in which the user builds a dynamic, meta-net understanding that tracks/keeps aware of memic types of happenings — a sort of meta-awareness similar to what we say about the “feel” of a place — only the “place” here is mostly ideas, information. I don’t think selling twitter to scientists as a way of keeping tabs or managing labs (one of Nash’s examples) is how people use twitter or why it is experienced as valuable. I would like to know what about the ambient experience scientists and their kin find valuable.
It would also be interesting to begin some kind of web-based, longitudinal, community wide survey that asked some simple questions about 2.0 use — I think it was Bora who commented after a post (pretty sure it was on NN, but I’d have to look) about the value of science blogging that at the earlier stages of his career, he had a very different relationship with the web — and that as his career progressed (I’m assuming steadied out after the frenzied initial years of achievement), there was (in part) simply more time to find out what other people were doing. But I’m betting we’d find trends in peaks of use and non-use that were career related.
PS — is there anyway I can persuade nextgensci to add a preview button to make sure that links and such worked?:)
Bob commented on March 24th, 2009:
I think there is a general misunderstanding of what Jumper is. Most assume it is typical social networking software – and it is not. It is not a blog. It is not a wiki. And it is not a facebook type application. It enables transparent access to any data stored in a wide variety of different storage devices. This access is provided in a single representation that uses Web 2.0 type of software on the front end that allows end users to directly create representations of data, other users can add knowledge about this data, they can link it to other data, and they can rate it based on its value. It sits in front of your Oracle, DB2, MSSQL databases as well as fileservers and NAS devices to unify search with brokers on the back end for access.
It seems like Connotea has fallen further and further behind in the priorities of its parent company, Nature Publishing Group. Citeulike has upgraded its hardware and Zotero occasionally gets an update, but Connotea hasn’t had a major redesign in years. The interface is dated and more and more painfully slow as time goes by.
If you haven’t given Mendeley a try, I would encourage you to give it a whirl. The thing I like best about it is that it has both a desktop and a web component, so you aren’t forced to choose between simple bookmarklet-based article saving and MS Word integration.
I’m now serving in the role of Community Liaison for Mendeley, so if you’ve got anything you’d like to know, just get in touch!
Excellent discussion from you both. Thanks so much for the outstanding overview of Connotea, Helen. I have Connotea buttons on ScanGrants, but really had not understood it before.
I have just tweeted Mr. Gunn’s blog posting, “I’ve joined Mendeley as Community Liaison.” It should be read by library science students and anyone trying to grasp the matters you both discuss above. I am surprised that more people don’t discuss the usefulness of Twitter as a bookmarking tool. I find that aspect of it very useful indeed. Makes saving stuff (albeit in a stripped-down fashion) a dream. How come you don’t have a Twitter button on your blog, Mr. Gunn?
Very interesting stuff, and I am looking forward to running NetBase through some searches to see what happens. Maybe b/c I’m so used to using key terms and sifting info myself, I’ve found some of the “additional” info provided by some search engines (Iseek, for instance) a bit constraining to get around.
The one difficulty that no search engine can address, though, is access. In healthcare, many practitioners have reading rights only to the publications provided as part of their professional affiliations. Some will also buy into MDConsult, since it is “relatively” inexpensive. How will NetBase address accessibility? Or is it planning to work with publishers, such as the case with Elsevier, to integrate the search platform with existing content? Or have a separate limiter for OA only?
Oh, I see — should’ve looked before I commented! This is a product/service to be integrated into an existing “database” (is that the correct idea?) not a stand-alone search engine like novoseek. I wish I didn’t have to register to try it out!
That is correct. Our current business model is to use our Content Intelligence platform to power other companies search applications like publishers, portals and media companies. We plan to have a free health search demo application up in a few weeks that will include PubMed and other healthcare related data sources.
Thank you, Jens! I’m curious if the Content Intelligence approach incorporates semantic content at the paragraph level, too? While semantic relationships in sentences are important, they are only one part of discourse, and across a paragraph, the import of any particular relationship may be less (or more) weighty than what happens in a single sentence. For example, pronouns (and other shorter lexical forms) usually refer to well-known entities in a paragraph and indicate what is “understood” to be the central topic of the paragraph. Does your system incorporate a formula/algorithm for these kinds of relationships? They are quantitative in nature, so seem like viable candidates, though I am not a code developer (but I had one sit on my doctoral committee and he asked me to model stuff for him — some were easy; for some, I just told him “no”!).
That is a great question Mickey. Today, Content Intelligence does not, in the strictest sense, do what’s called anaphora resolution (e.g. figuring out what “it” refers to in a sentence). We use other tricks to capture context from prior sentences as a back-off. Strict anaphora resolution on massive internet-scale has as far as we know not been done. This is something we are working on and hope to support as a robust commercial feature (anything is possible in the lab) soon.
Awesome read, and am looking forward to your review of DeepDyve as well — but given that it is Friday afternoon on my coast and my eyes are literally spasmodic from so many hours spent reading this week, I will content myself with a comment tingling at the back of my fatigued brain.
Not-so-metaphorically speaking, one thing I’ve noticed about many of the search engines is that the search direction is usually down and/or inward. So, the searcher starts with an query and gets a result screen that will take them deeper into the subject, though the depth may be had by getting more specific or by moving laterally to related concepts (“children” versus “sisters”). For experts, this can be a discovery process. For those new to their field (like undergrad science researchers), these kinds of results may feel a bit overwhelming. A possible consequence is a narrowing of vision to just the literature that very specifically answers a novice’s question, resulting in a lack of discovery. I realize this doesn’t have anything to do with the value of the search engine itself — and I’m also very excited (as both you and Walter are) about the possibilities of the semantic web. But some portion of my teacher-brain wonders about the intersection of inexperience with this sort of information structure. One of the values of a simple, boring meta-data mediated search is the accidental discovery of related material — this happens all the time in classes where students are learning to search the primary literature for the first time. In browsing all those seemingly useless titles, they discern patterns that help them understand new connections and often help them revise research questions to more closely reflect their real interests.
Again, this doesn’t de-value “content intelligent” search engines, but I think it does point at developmental differences in usefulness. We may find a decade from now that semantic-rich searches yield different sorts of discovery patterns than our current “keyword” searching yields, and that some use for each will be valued.
I just ran a search on gopubmed and deep dyve for a current obsession, the relationship/s between prosody and autism. Have to say that I was rather disappointed by deepdyve where even filtering out everything but 2 databases still produced unrelated entries. Could be that their search engine isn’t intuitively obvious to me.
My experience with Gopubmed was quite different — this “metric- insertion-of-dirty-f-word-indicating-extreme-enthusiasm” rocked! Not only did the Find It button bring up 23 beautifully tailored hits, 21 of them were so immediately interesting that it was difficult to remember it was a pedagogical exercise. There is a bit to figure out if one were a true novice to searching, so I created a screen shot to the page with bubbles explaining stuff (I know the search engine itself provides this info, but it does so with tender unobtrusive care, so that I was concerned students might not immediately understand what the buttons could do). I am now going to send out the link with said screen shot (word doc so not sure how to embed the pic or send it along — I can send it via gmail if you’d like) to all my students and colleagues teaching this semester.
Also, you mentioned in DeepDyves that it’s okay to be pretty…woo hoo! That is one of the things I like best about GoPubMed. It’s pretty; easy on the eye, with color intensity cleverly used to help the user navigate. Thanks soooo much for the review!
Hi, Mickey. Thank you so much for your very interesting comments. You are a far better analyst of the complexities of search technologies than I.
I would be most interested in your reaction to the much hyped new search engine, Wolfram|Alpha. I just tired it and was not impressed. I tried my favorite search term, amyotrophic lateral sclerosis and got the response, “Wolfram|Alpha isn’t sure what to do with your input.” Then I tried, ALS and got the result, “Als Island (island).” Then I tried Lou Gehrig’s Disease” and got the same sort of unhelpful answer. Ditto with “motor neuron disease.” I am currently trying, “dog” and am waiting and waiting and waiting…Ah, now I get the message that Wolfram|Alpha is temporarily unavailable (probably because half the world is trying it out today– the servers may have collapsed under the weight of interest.)
I was interested in your reaction to DeepDyve. I like it a lot and not just because it is pretty. Ha.
Good for you for alerting your students and colleagues to GoPubMed. I liked your wording, “beautifully tailored.” I would be very interested to hear back if your students try sample searches in GoPubMed, DeepDyve, Mednar and Wolfram|Alpha.
Your students are lucky to have a teacher who thinks so deeply about how they think and reason.
@Mickey: It’s great to hear that you’re sharing with students and colleagues your experience with GoPubMed. It’s these types of interactions – blog reviews, email discussions (with attached tutorials!) – that foster widespread use of new technologies.
@Hope: Wolfram|Alpha is a computational knowledge engine, not a search engine. Since your queries aren’t being made in the form of a question, the application doesn’t know what to do.
Hi, Eric. James Paul Gee is a sociolinguist and education theorist with a whole series of excellent publications on the value of video games for learning — the most easily accessible (meaning found online for free) are Good video games and good learning (http://tinyurl.com/dgne5f) and Learning by Design: good video games as learning machines (http://tinyurl.com/q5zepw). You’ve probably heard of him, but I find these articles particularly easy to follow.
Hope, I agree that war-based games are not appealing to young girls, but not that it’s video games themselves — at least while they are young. My daughter loves her Leapster L-Max as much as my son, though their preferences for games are somewhat different. It would be great to see more complex games tailored to girls — I wonder if this is likely given the perception that they are an insignificant part of the market? (In fact, girls interest will wane as they perceive that video games are a particular interest of boys, mostly in the effort to disassociate themselves during the pre-teen years). More complex games for girls would have them building and navigating complex tasks but on things more appealing — I know this will sound stereotypical, but girls often respond to nature strongly (how many of us went through the “marine biologist” phase?:-)) — a game which had them build eco-systems with the addition of managing highly social animal groups (lions, wolves, dolphins, monkeys, meerkats, etc!) over time I think would have strong appeal. The same could be said for fantasy environments that are somewhat less dark — let’s say fairies, elves, and gnomes as opposed to warlocks? And while this is particularly stereotyped, building a mall, tying in economics and sociology, would also appeal to a lot of girls. So, I think the possibility exists for video games for girls, but they are clearly not a targeted market overall.
Oops — forgot one last thing, Eric. If you’re interested in these sorts of things, you might find the FriendFeed room “future of education” a fun place to hang out. It doesn’t pick up the traffic that the “science 2.0″ room does, but what get’s posted is mostly pretty good, and it would be great to have more people hanging out there!
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I have two opposing opinions about this. On the one hand, I completely agree that making a digital recording of something against the wishes of the presenter is lame and in many cases egregious behavior.
However, I think you are wrong in the statement “Cameras are great for recording events in life that you want to remember. However, they have no place at scientific conferences or poster sessions where unpublished data is being presented.” I think this can be determined by the meeting and/or the presented. At many conferences I have been at recently, the talks are presented live on the web and also recorded and available for later viewing and downloading. And I personally am trying to post my slides on places like slideshare or the web somewhere and include plenty of unpublished material there. I think that sharing work before publishing is critical to the scientific enterprise and there are many journals that do not exclude the possibility of publishing in that journal even if work is presented previously “published” on the web or in a meeting.
In the end, how one should handle the distribution of posters, talks, etc (and for that matter, papers) varies enormously depending on the situation. I agree that violation of the copyright and intent of the presenter is wrong, but there are many people who are comfortable with broad CC license type distribution of ALL their presentations/publications and I for one enjoy going to these types of meetings enormously.
Oops, I guess I’m doing it wrong. At conferences I print copies of my posters for people to take home with them, and I make my posters and talks available on my website as PDFs. I always thought the purpose of a conference was to expose your ideas to a lot of people, get feedback from them, or initiate a collaboration, not to steal ideas (or data??) for the next grant proposal. I’m sure it happens but if they’re bent on doing it, it won’t matter whether they have an exact replica or not. Most people probably take photos because they appreciate the work and want to take more time to think about it later. Or maybe they just like the color scheme and want to replicate it for their next talk.
This is a really fascinating discussion. The issue of cell phone camera use comes up in the patient care environment, too. Sometimes family members of patients are camera-crazy.
@Jonathan The more I use the Internet for scientific communication, the more I would like to share unpublished data on the web. However, I’ve done research in some pretty competitive areas and worked with people who had unpublished data they presented taken and published before they were able to publish it. Indeed, most of my training has been in labs where the position has been one of guarding unpublished data, not sharing it. I think this is the pervading attitude in science, not the exception. If we’re ever going to have greater communication between researchers and increased sharing of unpublished data, this issue needs to be discussed.
Although you make a good point that the distribution of posters, talks, etc varies on the situation, I think that people shouldn’t assume that unpublished data can be freely recorded. I’d also like to point out that just because talks are presented live on the web and recorded doesn’t mean the presenter is showing you all the unpublished data they would have shown you had they been presenting it in a more private venue where their data wasn’t being digitized and distributed.
The other thing I’d like to point out is that the attitude on this likely differs between disciplines. For example, I’ve noticed that many scientists blogging and using social media tools today tend to be dry-bench scientists than wet-bench researchers. My impression is that sharing unpublished data is much more acceptable to computational scientists than it is to wet-bench researchers.
@Eric I don’t think you’re doing it wrong at all. I don’t have any issue with someone distributing unpublished data. As I said above, the problem is that people to whom you’re presenting shouldn’t assume that your data can be freely recorded without your permission. If you’re handing out copies of your poster, you’re clearly granting permission.
Thanks so much for the streamosphere link — just spent a great 20 minutes doing some broader-based browsing than I get through FF — much more like going to the stacks, so to speak, a topic that came up recently in a discussion regarding the value of hard copy versus digital. So glad I get the RSS from NextGenSci!
[...] Research Blogging is a community-run non-profit organization. The organization was created by bloggers for bloggers, with the input of bloggers and blog readers who like to read about new developments in science and other fields. If you’re a blogger who writes about serious research, Research Blogging offers you a way to distinguish your serious posts from anything else, by directing your regular readers — and new readers — to the posts linking to published articles. You can read more on the idea behind researchblogging.org in this post on nextgenerationscience.com. [...]
[...] combination. As you may know, the NIH awarded almost $30 billion in grants in 2008, and with the American Recovery & Reinvestment Act of 2009 (ARRA) expected to receive an additional $8.2 bill…, it is more important than ever to unlock that valuable insight into federally funded [...]
regarding your answer to the question “how NovoSeek differs from GoPubMed …”, I must say I’m disappointed. Let me tell why: first, what is described here for your search platform was done 6 years ago when GoPubMed first went online. I don’t see any new features above GoPubMed or others. Secondly, your statement: “… lets users search more accurately, in less time and with less effort than any other search offering in the market today” is unproven and just another marketing statement. For “Heart Diseases” you find 163,595 results. We know that at least 848,633 are semantically relevant. It is hart to believe that Novoseek involves any semantics besides synonyms. Using the query “Vitamin C”, NovoSeek is missing (using MEDLINE source) more than 5,000 papers. Additionally, I’m missing all the following features:
· Statistics about queries, ontology terms, persons (co-author network diagram)
· Top author for your query showing the automatically compiled vita references
· Editable author profiles, contact authors
· Curation tools for scientific crowd computing
· Navigation based on MeSH, Gene Ontology and proteins ontologies
· Auto-completion based on MeSH and the Gene Ontology
· Syntax like Pubmed, related articles extracted from Pubmed
· Wiki links with concepts found in abstracts
· UNIPROT links with proteins/genes found in abstracts
· Using the tree: easy option to include and/or exclude concepts in queries
· Easy navigation to dive into the ontologies and find related terms and functions
· The WWWW (WHAT, WHO, WHERE, WHEN) concept: navigation using combination of queries based on concepts, persons, places of affiliation (countries, cities) and/or places cited in abstracts, journals (reviews only, high impact journals) and date (year, months, days)
We are open for any discussion! But let’s move on to the next semantic stages. There are so many open, scientificly interesting and unsolved issues where all should collaborate: ontology alignment, unlearn “old” facts from the ontology and last but not least ontology generation. Let’s go for it!
I went there immediately—as I always note and immediately check out any info about Science 2.0 in Twitter. I am glad that I did because Anton has a tweet that says, “Do you want to help plan ScienceOnline2010 (in RTP over MLK weekend)? Contact me and we’ll get you involved.” And then I found this in FriendFeed:
and saw this comment by one of my heroes, Jean-Claude Bradley: I’ll be there – always a good time
Sure would be exciting to meet Bora and Jean-Claude. I have tweeted Anton and hope to learn more about the conference and hope to attend.
This discussion is a good example of social networking in science. Bora blogs eruditely and compellingly. He is interviewed on this blog and discusses how blogging can lead to print publication, thereby illustrating that blogging actually helps traditional print remain viable (which should raise the comfort level of librarians and publishers with blogging). He mentions figures of note that the reader of this post can then research via Twitter and FriendFeed and discusses interestingly the review in The New Scientist, which one can see only a snippet of without a full subscription—classic case of the frustration of interested readers encounter with old school publishing methods. And as a result of reading this interview with Bora I have just subscribed to the PLoS ONE room on FriendFeed and to the @PLoS Twitter account, and there found a tweet to linking to Michael Nielsen’s seminal essay (must reading), “Is scientific publishing about to be disrupted?”
The differences between novoseek and goPubMed are clear under my point of view. As you put it in your comment, there is a lot of pending research to do regarding ontologies; therefore and although we take that into account, we don’t rely that much on them for our analysis.
As you know, it is not all about getting results or reordering pubmed results based on any type of ontology. It is more about differentiating those documents with the most relevant meaning from those that are there just to keep the user busy.
Regarding functionality, novoseek’s approach is based on keeping the user’s focus on getting the information and we like to make it simple. When we decide to add extra features, we want to make sure that it is really interesting to the user. If we see that there is functionality that people is not using, we just take it away, because it does not help to the final experience. However, I modestly suggest you take a closer look to novoseek because, if aiming to be fair and not only state goPubMed feature list, some of the functionalities you claim to miss are actually present in the tool.
Transinsight’s GoPubMed.com, the semantic search engine for the life sciences, has been recognized with the 2009 red dot: best of the best award in the category communication design – graphical user interfaces and interactive tool. A total of 6,112 submissions were received from 42 countries. The jury selected 470 entries for the “red dot design award.” A group of only 56 submissions were selected as “the best of the best” and will be participating in the final round for the “grand prix award.” The Transinsight team is proud to receive this prestigious award. For further information http://www.transinsight.com
I’m delighted that sales rose after my review appeared.
My review was not aimed at bloggers at all, it was aimed at readers of New Scientist’s print magazine.
I understand this is an emotive issue for Zickovic, but I suggest he reads my comments on the Neurotopia and Laelaps entries he links to before making further claims that bear no relation to the facts.
Hi, all. I got a chuckle out of Michael’s wry comment, “I’m delighted that sales rose after my review appeared.” Now, if we could only determine if those sales were to readers of his review or to those who follow the blogs that criticized his review—which unlike blog postings, is locked up behind a toll access gate and which thus, perforce, will have a limited influence compared to easily accessible blog postings.
And this comment is interesting, “My review was not aimed at bloggers at all, it was aimed at readers of New Scientist’s print magazine.” Are none of those readers science bloggers? I don’t quite follow his characterization of the readership of The New Scientist. I would think some of those readers would object to his dismissal of the revolution in the dissemination of science news that is science blogging.
In any case, it is nice to see such a civil discussion between articulate people on these matters.
Also, to make it clear, I think science blogging is a great thing and I’m all for it. The point I made in the review is that for every RealClimate there’s a Watt’s Up or three. For every Bad Science, there’s a nutty HIV denialism or vaccines-cause-autism blog.
So my suggestion is, what you look at the big picture, at all blogs not just those you or I would call science blogs, that the overall effect of blogging is negative, that it has helped spread myths and lies. I’m not saying this definitely is the case – how do you measure such things? – and I hope I’m wrong, but I think it’s plausible.
The internet has given the nutters a collective voice, and they’re screaming very loudly.
[...] tried to determine what exactly it is — a social network for scientists along the lines of ResearchGATE and BioCrowd for those in the biomedical sciences and [...]
Nice post, Hope! My impression was more hopeful when I reviewed it after it launched, but sadly it doesn’t seem to have gone anywhere since. The major value of the service is its tie-in with ScienceDirect, and it had the potential to really leverage that, but it just doesn’t look like it has gone beyond being just a me-too social bookmarking product.
In fact, both Connotea and 2collab, have been foundering a bit relative to citeulike. Perhaps it’s not surprising that Citeulike is doing better, though. Would an independent project like citeulike necessarily have more energy and commitment than a side project like Connotea and 2collab? Is it a case of 100% commitment of fewer resources relative to 1% commitment of far greater resources or is it just harder to fight off the “what’s your business model” questions when it’s an internal project of a larger company? Maybe it’s something else entirely.
What follows is pure speculation, but …
I have a theory that independent projects start out with more goodwill than products coming from an established brand. There’s always a question of what will happen to the time you’ve invested in a service and the data you’ve accumulated. I think people trust a smaller outfit more because a smaller outfit is more responsive to and more dependent on its users, so they’re less likely to do something bad, and if they do, the users have the power to punish them more effectively than an established brand, which might just shrug off the complaints and can the project. Microsoft and Sony have been guilty of gross misconduct and disregard of their users and have largely gone unpunished for their behavior, whereas a smaller company wouldn’t have. Even Facebook, which is now a big company, had to cave to its users over the Beacon incident.
Imagine a board meeting where people are talking about what possible opportunities exist in Web 2.0. Part of the pitch for developing a competitive product goes like this: “We’re a well-recognized name and we’ve been around for a long time. Clearly we’ve got a marketing advantage over some fly-by-night independent project.”
Now imagine that someone stands up in the meeting, attended by their boss and people from the marketing department, and says, “Maybe our brand isn’t as well-loved as we think it is. Perhaps if we didn’t strongly brand this, the product would do better?”
I could be totally off the mark with this, and certainly resource allocation is part of the reason 2collab isn’t growing as strongly as it could have, but I also think they didn’t realize how important it was to gain the trust of the early adopters and to put a responsive and accountable public face on the project.
Hi, Bill. Thanks for your note below. Sorry to be slow to be getting round to responding to it. I was in transit to Toronto where I am now am attending Medicine 2.0:
I agree with you about 2collab being just a me-too social bookmarking product. Strange that Elsevier didn’t look at Nature Precedings and not see how pretty useless 2collab is by comparison. And interesting that ResearchGATE
seems to working on a me too of Nature Precedings except that ResearchGATE’s
service (as I understand it) is for published articles and not pre-prints
ResearchGATE has a rather vainglorious view of itself vis-à-vis inflated claims of firsts. It says, “We have now launched our Self-Archiving Repository! This project makes full-text articles available to the public, for free – the first application of its kind worldwide.
Currently, there is no way for researchers to access millions of publications in their full version online. We are now changing this by enabling users to upload their published research directly to their profile pages (a system called the “green route” to Open Access).”
That is all balderdash and bogus beyond belief. There are probably dozens of institutional repositories throughout the world at universities and other academic and research institutions. Some scholars have their own personal sites and there is the little matter of PubMed Central. ResearchGATE seems to have a genius for ignoring the efforts of academic librarians and the entire National Library of Medicine. Not the way to win friends in the information science and medical library worlds.
Thanks so much for the disquisition on Connotea, “…foundering a bit relative to CiteULike.” I had not heard that.
Apropos of your comments, “Microsoft and Sony have been guilty of gross misconduct and disregard of their users and have largely gone unpunished for their behavior, whereas a smaller company wouldn’t have,” here is a somewhat comparable instance of bullyboy tactics, this time by Google:
Creepy that Google tried to get a tiny outfit’s grants pulled.
I actually would probably go with a well known name when it came to archiving given that it would be a huge headache if a company went under—which, for instance, the well funded Nature Publishing Group of Nature Precedings is far less likely to do than is the fall smaller ResearchGATE. I would probably go with the revenue-rich Elsevier, but there is nothing much to upload to in 2collab. And then, of course, big names can go under overnight as we saw last year in the world of finance. Scary times in so many respects, huh?
widespread distribution may indeed be a goal, for example to increase interest in an upcoming publication. if the intentions of a presentation are made clear to an audience, unexpected results are less likely.
I guess Nature Network would be the other major initiative. Also nature.com blogs, Nature Videos, Connotea, Scintilla and Streamosphere. There may be others I missed. I see them all as NPG’s experiments in the Web2.0 space.
Thanks guys–I had not heard of Streamosphere–cool! But is is yet another thing to be depressed not to be able to keep up on! So many brilliant people writing so many fascinating things. So what would you consider useful, Neil?
[...] might SciVal Funding fit in with Elsevier’s foray into social networking the sciences, i.e. 2collab? Will there be a way, for instance, for users to determine where potential collaborators might be [...]
[...] I have looked at smaller Science 2.0 sites, such as LabRoots, Scientist Solutions and 2collab, and it is at once clear that NPG is pouring money and talent into Nature Networks. Elsevier may be [...]
Michael Habib commented on September 28th, 2009:
Hi Hope,
First off, thanks for taking the time to write such a detailed review. Sorry to be a little late in my reply, but I was on holiday when this article was published. I would like to take a minute to respond to some of your points.
* 2collab is a social reference management and bookmarking tool. As such, it is roughly in the same space as Connotea and CiteULike. Some of the unique features we have tried to include are:
* More robust group functionalities. As you noted there are a number of public groups that are spam. However, we have seen that there is very limited interest in public groups. The vast majority of interest is in private groups. Researchers are wary to share their current work for fear their competitors will steal their ideas. Our private groups are where more of the interesting collaborations are happening.
* As you mentioned, one of our main advantages comes from integration with other Elsevier products, such as Scopus and ScienceDirect. We had integrated 2collab into ScienceDirect. Any ScienceDirect item bookmarked in 2collab would show up in a box in the sidebar of the article page in ScienceDirect. This box showed number of times bookmarked, comment count, and rating. Unfortunately, we have had to temporarily turn this box off, while we work to improve the performance of 2collab. Worth noting is that this is the first step in determining how best to integrate with related tools such as Mendeley or CiteULike.
* Scopus is integrated in a number of ways. If an article is bookmarked that has a DOI, Scopus is checked and used to pre-populate and clean the reference information. Additionally, bookmarks with a DOI display their citation count from Scopus.
* Scopus Author Profiles are integrated into 2collab user profiles. A user can enter their Scopus Author Profile ID and import their publication list to 2collab. These articles will display as part of one’s profile on 2collab. Additionally, any bookmark can be marked as Authored by the user and will be added to their profile.
* As I mentioned above, a lot of the value of 2collab comes from it being used as a place to experiment with features that could later be added to other Elsevier products. It is our hope to take the best from 2collab, refine, and reuse.
* On a side note, I would like to mention the Spam problems 2collab has been experiencing. It is a major problem that has also caused severe performance issues. Consequently, all our resources are currently devoted to performance improvements and spam prevention.
* This has prevented us from adding some key features that are still needed. One key feature at the top of our list is proper Search. The current search is querying the database rather than a Search index. Once performance and spam are in check this is a top priority.
Since Elsevier began developing 2collab, a lot has changed in the social media realm. We are working to revamp our strategy accordingly.
Just noticed the comment is still awaiting moderation… Copying below, but the format is lost: "Hi Hope, First off, thanks for taking the time to write such a detailed review. Sorry to be a little late in my reply, but I was on holiday when this article was published. I would like to take a minute to respond to some of your points. * 2collab is a social reference management and bookmarking tool. As such, it is roughly in the same space as Connotea and CiteULike. Some of the unique features we have tried to include are: * More robust group functionalities. As you noted there are a number of public groups that are spam. However, we have seen that there is very limited interest in public groups. The vast majority of interest is in private groups. Researchers are wary to share their current work for fear their competitors will steal their ideas. Our private groups are where more of the interesting collaborations are happening. * As you mentioned, one of our main advantages comes from integration with other Elsevier products,…
Just noticed the comment is still awaiting moderation… Copying here: Hi Hope, First off, thanks for taking the time to write such a detailed review. Sorry to be a little late in my reply, but I was on holiday when this article was published. I would like to take a minute to respond to some of your points. * 2collab is a social reference management and bookmarking tool. As such, it is roughly in the same space as Connotea and CiteULike. Some of the unique features we have tried to include are: * More robust group functionalities. As you noted there are a number of public groups that are spam. However, we have seen that there is very limited interest in public groups. The vast majority of interest is in private groups. Researchers are wary to share their current work for fear their competitors will steal their ideas. Our private groups are where more of the interesting collaborations are happening. * As you mentioned, one of our main advantages comes from integration with other Elsevier products, such as Scopus and…
Hi, Michael. Thank you for your courteous and detailed response to my post on Next Generation Science about 2Collab. What you write is all very edifying. Good for you for being so responsive to comments about it and for being candid about various problems. Glad to hear that site search is a top priority. Hang in there—good for Elsevier for trying new things. Hope Leman
Hi, Michael. Thank you so much for your courteous, edifying note. Thank you for making clear exactly what 2Collab is. I appreciate your candor about the spam problems.
Apropos of your comment, “However, we have seen that there is very limited interest in public groups. The vast majority of interest is in private groups. Researchers are wary to share their current work for fear their competitors will steal their ideas. Our private groups are where more of the interesting collaborations are happening” there was an recent, interesting example of FriendFeed of a successful, open collaboration in that environment. See here:
I guess we will just have to revisit the private group/public group matter two or three years down the road to see which model wins out.
Good for you for being open to integrating 2Collab with non-Elsevier tools. Such openness will benefit Elsevier in the long run given that the more integration there is across the Web there is, the better.
Good for you for working on the search matter. I am glad to see that Elsevier is working with NextBio in such areas, at least with ScienceDirect:
Hang in there! Elsevier is a content supremo and we support your efforts to render it discoverable.
Daniel Calto commented on September 28th, 2009:
Dear Hope: Many thanks for your generous and thorough review of the new Elsevier product SciVal Funding. We at Elsevier are excited to launch the product today, especially as we feel it can be a great resource for junior investigators, who face the difficult challenge of transitioning from post-docs to independently funded research scientists.
One of the keys to the product’s success will be to continue to refine and enhance its capabilities over time, and we’re committed to doing so. We look forward to getting crucial feedback from the research community about the product and ways to continue to improve it.
All best wishes,
Daniel Calto
Director of Product Management
Academic and Government Products
Elsevier Inc.
As it happens, I recently attended the Medicine 2.0 conference and at the end of my talk there on ScanGrants, I was asked several questions about the lack of tools for grant seekers in general and junior scientists in particular. I said, “Well, has Elsevier got something in the works for them!”
Good for you for leading the way in innovative thinking when it comes to leveraging the power of Library 2.0, Web 2.0, Science 2.0 and Research 2.0 and linking the worlds of academic and medical libraries and offices of research administration. You are tying those formerly rather distinct realms together much to the benefit of science and scientists and thereby, ultimately, to those of us who will need medical care at some point. Keep up the good work!
I am the always last to know these things, “I’m hoping to moderate two sessions: one on the use of Web 2.0 in health and medicine, and one on Medical Journalism.” Oh? Great!
I wonder how long it´ll be until the first attempts to game the system? (Then again, people already try to ¨game the system¨ with peer-reviewed publications)
Many of my students report that their PIs tell them to consider journal mission first, IF a close second, everything else a distant third. In fact, this is how I learned what IF was a few years back — a student asked me b/c he didn’t know what his PI was talking about (and didn’t want the PI to know that he didn’t know!). I didn’t either. A few clicks and wikipedia reads later, we all knew.
Many of my students report that their PIs tell them to consider journal audience first, IF a close second, everything else a distant third. In fact, this is how I learned what IF was a few years back — a student asked me b/c he didn’t know what his PI was talking about (and didn’t want the PI to know that he didn’t know!). I didn’t either. A few clicks and wikipedia reads later, we all knew.
Was at David Pendlebury’s "Discover the Power of Quantitative Analysis – The Art & Science of Identifying Future Nobel Laureates", same message don’t use IF as proxy for article influence. Pretty obvious really, but I suppose IF is okay for evaluating journals?
[...] additional tools such as better navigation (I’m thinking specifically of something like novo|seek or GoPubMed) may increase the value of the [...]
[...] differ from an information extraction system and how does CureHunter differ from the much hyped Wolfram|Alpha, which calls itself a computational knowledge engine? And GoPubMed uses the term, [...]
Dear Judge Schonfeld,
the “laundry list” – as far as I understood you right – is the GeneOntology and MeSH (Medical Subject Headings) two well structured ontologies. This is the background knowledge we use to improve search a) guaranteeing completeness and b) giving the user a tool to drill down fast. For example, a search in PubMed for “Heart Diseases” yields 54,231 results. GoPubMed delivers 856,539 results. Why do we get so many more results? It’s because we include all 544 ontological sub-concepts from MeSH and their synonyms found under the concept “Heart Diseases.” This is the big difference between semantic search and key word search and it guarantees completeness of results – of course only as complete as the background knowledge used is. Regarding the comprehensiveness of the article list we can say that we get results from PubMed.org and sort them according to the ontologies (GO & MeSH). We are not better or worse than PubMed, but search results are classified. One last comment to your question concerning the “discovery capabilities” of GoPubMed. Search for Obesity[mesh] and discover for example all associated Nervous System Diseases at a glance. Listed in a well ordered scientifically correct way. This is just one example what other engines can not deliver!
For obesity CureHunter finds 28,067 articles. As seen from GoPubMed more than 130,000 are relevant only in PubMed for obesity. You are missing more than 100.000. I’d argue that CureHunter is not comprehensive.
Best regards, Liliana
Liliana, I apologize for a poor choice of phrase, “laundry list” in talking about extra categorical functions in GoPubMed. The big problem in AI for the last 50 years has not been failure to be inclusive–but how to autonomously execute intelligent discard. CureHunter discards approximately 80-90% of all possible articles that COULD be included–by general search– because its primary design goal was automatic extraction of specific statements of clinical efficacy containing well defined data points that can be used in two types of calculations: Quantified Clinical Decision Support for the use of a drug (relative drug efficacy) and Predictive Analytics, the computational discovery of new disease target applications for existing meds and new cures themselves–using Network Graph Theory Operations over the machine self-extracted data. These calculation systems are built into the CureHunter product and require the input data to be highly filtered to meet the standards typically we associate with hardware-based scientific instruments: Precision, Accuracy, Margin of Error, False Negative Count, False Positive Count, Replicable Results from comparative reference instruments. Because CureHunter is doing predictive data mining and analysis there are vast volumes of “earth” additional material that it does not return to the user. This is not a failure of comprehensiveness but a data filtration decision because we can only use data in calculations that can be specifically quantified. Many articles will comment on many factors of “obesity” or any other disease without ever mentioning that a particular drug, agent, biomarker or other important molecule affects a specific clinical outcome. Thus researchers, patients, or doctors not looking specifically for quantified curative data, should go to GoPubMed and the other good search tools that capture a broad variety of other key subject matter from the library.
Again, I apologize for my poor choice of words.
First, I’d like to recall you that CureHunter and novo|seek do not solve the same problems. Novoseek is meant to help people look for the biomedical literature they need to read in a simple and easy way. The idea of novoseek is that when you look for “warfarin”, the bar on the left presents the most relevant concepts related to this search. Therefore you see that “atrial fibrilation” is the most relevant disease related to it or that “anticoagulant effect” is the biological function most related. Based on these, a novoseeker can refine his search quickly and find the publications interesting him for his research, work, etc. »
In addition, I would like to specify something regarding the bar graphs as you explained above. The bar graphs actually show the relevance of the concept with respect to the current search. We do not only count the volume of information available (that wouldn’t be intelligent searching) but we analyze the available biomedical literature with our semantics techniques to return the most relevant concepts. I would recommend the reading of the following article to get an idea of how our technology works http://blog.novoseek.com/index.php/user-experience/the-importance-of-context-in-text-disambiguation.html/
[...] DeepDyve is a search engine designed to make scientific, technical and medical research more easily discoverable and accessible. Truly accessible. Next Generation Science [@NextGenScience on Twitter] reports that DeepDyve Offers Scholarly Literature Rental Service. [...]
[...] Technologies are coming with will enable the Web, not just for documents, but also for data. The Shared Names Project is working on a format to assign universal resource identifiers as names for publicly available biomedical information records and establish a community managed shared infrastructure for providing durable access to documentation about those names. John Wilbanks, Executive Director of Science Commons, talked about the project in a talk he gave earlier this month on Open Source Science. [...]
Yay! Thanks for selecting our panel: “Broader Impact Done Right” — Karen James, Kevin Zelnio, Miriam Goldstein, Rick MacPherson, Jeff Ives and Beth Beck.
[...] an introduction to the topic and starting point from which to generate discussion (remember, ScienceOnline2010 sessions are held in unconference format, meaning that each will be highly participatory). Medicine 2.0 and Science 2.0 – where do they [...]
[...] I really enjoyed the unconference format. Several sessions I attended were mostly a presentation and not nearly as engaging. For the Medical [...]
Nice interview guys. I’ve been using RB now to tag my “serious” posts on http://www.sciencebase.com/ and http://www.sciencetext.com/ for quite some time now and it certainly makes me feel good to know they’re being taken up by the system.
It’s impossible to analyze referrals because so many people read blog posts and RB via so many different routes now, but I had a couple of hundred new readers via direct referrals from researchblogging.org last year, which is a small number compared with my actual daily visitor rates, but it’s presumably a more targeted audience so definitely a good thing.
As RB itself and awareness of it grows this year, I’d expect those stats to improve and for the scientific threads to pull our community together more effectively as well as to rope in more and more people from outside the various niches too.
keep up the good work.
Walter introduced me to your blog and I have just now stared to follow you on Twitter (which I have only just started using and boy–is it a good way to keep up on Science 2.0).
Very, very helpful to hear from you, a serious sci/tech blogger, on how you use RB and your thoughts as to its potential.
Thanks so much for popping in.
Walter did that interview and very well, too!
[...] It is interesting to compare Scientist Solutions with LabRoots. [...]
hmm…i am using researchgate nearly every day, dont have the impression of low activity – but to be honest, i once signed up for labroots and never visited again… hm?
Hi, Christina. Thank you so much for the feedback and input. Maybe I have sold ResearchGate short.
[...] ResearchBlogging.org: Interview with Dave Munger (Next Generation Science) [...]
[...] have looked at smaller Science 2.0 sites, such as LabRoots, Scientist Solutions and 2collab, and it is at once clear that NPG is pouring money and talent into [...]
[...] have looked at smaller Science 2.0 sites, such as LabRoots, Scientist Solutions and 2collab, and it is at once clear that NPG is pouring money and talent into Nature Networks. [...]
Hi, Hope!
We’ve “met” briefly in the comments section of Michael Neilson’s blog — my students are the “guinea pigs” whilst I figure out how to introduce science2.0 in a meaningful, useful way to them. I find your evaluation of NPG’s offering very similar to what my student’s found — they liked the variety, but were disappointed by the lack of science rigor. Many of them performed searches similar to yours — fairly specific for things they were interested in — and didn’t turn much up. Most of the blogs they subscribed to feature topics of interest that they don’t quite have time to immerse themselves in. Interestingly, this pretty much covers the blogs I subscribe to — personal interest, professional interest, but not those related to my actual area of expertise (linguistics — it’s funny, ’cause most of what I’ve read related to language makes me want to throw things or sigh “but we’ve done that already”!).
This has left me in something of a jam in terms of explaining why I think this is so interesting — and relevant to them as future MDs. Currently, I’m adding your blog to their reading list since you are taking a sort of pedagogical look at the issue: an “about science 2.0″ perspective, which is incredibly useful. And I’ll have them began their own individual posts in a couple of weeks so they get a feel for the writing side. But that hardly seems to cover it! One of my students recommended an open-source web-building program to use instead of the class blog — I thought that was an interesting option b/c we could use it to talk about how to design personal web spaces that are useful professionally — not just for connecting with colleagues, but for directing patients, too. Science 2.0 is turning out to be a difficult sell because most of them see themselves as practicing MDs rather than as researchers.
Love the phrase “wild web” — very much what it feels like!
Hi, Mickey. Thank you so much for you very interesting note. Now, if this isn’t classic Web 2.0. I learned about Michael Nielsen’s blog from the Science 2.0 room at FriendFeed and visited his blog because of interesting comments he had made about Google’s Knol. I found his blog very interesting reading and your comments there ditto and here you have visited this blog and made some more.
Yes, there just doesn’t seem to be much hardcore scientific rigor at Nature Network. I think that such is to be found in the plethora of specialized blogs on specific topics and in the increasing number of open notebook blogs such as those that Jean-Claude Bradley, Michael Nielsen and Steve Koch either highlight on their blogs or embody at same.
I would recommend that your students visit and contribute to the Science 2.0 room of FriendFeed. I learn a lot there from Jean-Claude’s comments such as, “The term “Open Notebook” refers to a mandatory sharing of all experimental data for a given project. If you didn’t find entries for the past 30 days in a true ON you can infer that no experiments were performed during that time. There is a category in the Wikipedia page on ONS referring to Partial/Pseudo ONS. This would include all attempts at being more open in sharing research without strict adherence to all the implications of ONS.” And his comment on one site, “…it sounds more like a research blog – commenting on papers he reads…”
And my partner here at Next Generation Science, Walter Jessen, just emailed me, “I’ve always considered NN a forum and not a blogging community (even though you can blog there). You are right – all the prominent scientists blogging have their own blogs.”
I loved your comment, “…but we’ve done that already!” If you have the time, you might stop at such blog entries and say so and cite the earlier study. That would be a public service—but who has the time?
I agree with you that it is hard to sell Science 2.0 to front-line clinicians. But more and more of them are getting involved in research even at the community hospital level and so need to know about the world of clinical trials and how that world is changing radically (e.g., the lithium for amyotrophic lateral sclerosis trial led by the online patient community Patients Like Me) thanks to the Web. There is so much in Science 2.0 for future MDs to know about—patient empowerment and firms such as Private Access https://www.privateaccess.info/
that are developing security suites that will enable frontline medical providers, researchers and patients to communicate productively in secure, confidence-building environments. I learned about Private Access at the Health 2.0 Conference and Science 2.0 is not all that abstruse or disconnected from the daily practice of medicine.
Good for you for working so hard and creatively to instill a research mindset in future clinicians and form future clinician discoverers.
It is, as various commenters seem to agree, early days for Web2. NN (and I blog there, so take what I say with that in mind) is more of a social networking site. The blogs rarely deal with ‘hard’ science, and focus more on the human side of things, which seems to be what people want (slightly self-fulfilling, but as you say they seem to be the clear market leaders).
I would love to see the forums (as distinct from the blogs) being more useful somehow. But as that doesn’t appear to be happening one has to ask if that, again, is market-driven? The tools could be there, but maybe it’s too early for them to be successful. We tried getting the ‘Collaboration’ forum going, to little avail.
There are problems with the platform—as a user and a blogger—although we keep nagging them to fix these, and progress occurs. What I will say though is that I got a new job with the strength of my blogging at NN, so I’m not knocking it
Heh. And getting my own website URL wrong is just bloody ironic…
@rpg No worries … I’ve updated the link. Thanks for your input. There’s this stigma attached to blogging that it somehow hinders you from advancing in academia. Congrats on the new job and kudos for getting it with your blogging at NN.
Hi, Richard. Thank you for your interesting comments.
I just read your very edifying post, “On the Nature of Networking: Reprise” http://network.nature.com/people/rpg/blog/2009/01/27/on-the-nature-of-networking-reprise
and was impressed by the large number of readers you have. You are a one-man social network in and of yourself.
I was interested by your comment, “I would love to see the forums (as distinct from the blogs) being more useful somehow. But as that doesn’t appear to be happening one has to ask if that, again, is market-driven? The tools could be there, but maybe it’s too early for them to be successful. We tried getting the ‘Collaboration’ forum going, to little avail.” I wondered what you meant by “too early.” Too early in what respect? Too early in the evolution and visibility of social networks in the sciences in general or too early in the evolution of that particular forum on Nature Networks?
Given Mickey’s comments here and on FriendFeed that he has difficulty persuading his medical student pupils of the professional value of blogging and of Science 2.0 in general (“This has left me in something of a jam in terms of explaining why I think this is so interesting — and relevant to them as future MDs…”), your comment here is especially valuable and a teachable moment, “What I will say though is that I got a new job with the strength of my blogging at NN, so I’m not knocking it?” Think about that all of you early career scientists and health science students out there.
I found that also quite interesting given that there don’t seem to be prominent examples of scholars who have won plum positions on the basis of self-archiving at institutional repositories and I would be interested to learn if you have done much of that. Librarians often have a hard time convincing scholars that there are career advantages to depositing their papers in institutional repositories that can be then rendered searchable via such search tools/databases as the E-print Network http://www.osti.gov/eprints/ .
Hope, thanks so much for the remarks, and I happily have a bit of success to report. A very short history: last week I was out of the office for 3 days b/c my daughter had pneumonia (thank goodness for wireless routers!). The result was my thesis students (the neuroscience/premeds I’ve been writing about) took it upon themselves to write individual blog entries on our class blog despite not having discussed the assignment yet. Many of them chose to write about exactly the kind of stuff I read everywhere: funding (lots of that!); the impact of the “scientific method” on progress (student titled the entry “slow science”), the potential ineffectiveness of the peer review process (a student found a major research report featuring an incorrect finding with that finding later popping up in reviews as well; she is despairing somewhat!); the elation and disappointment of research itself. The entries are well-written, creative, interesting, reflective — all the things that make me proud to work with this population of students.
But the biggest excitement is that is works! 3 weeks ago, the students were not excited by this. I don’t know yet that I would say they are converts, but they do see the point — one student even blogged about how important writing/comm skills are to scientist/MDs, particularly if they are to convince an audience that their research deserves funding or their particular take on a therapy is superior. Ye gods, I can barely sit still and type!
Okay, before I get to loopy, I’d say the point of this lesson is something many have blogged about: there is great value to just doing it. Smart people in general have interesting things to say, and since work lives frequently allow expression of just a portion of what goes on in their heads, this medium allows participation in the kinds of conversation they value. Now, I believe I will take up your suggestion of joining the FriendFeed science2.0 community b/c I think they’re ready to see the value of it. I can’t say that they will join in as participants, but are perhaps ready to take the next step. Especially given Richard/your comment ““What I will say though is that I got a new job with the strength of my blogging at NN, so I’m not knocking it?” Think about that all of you early career scientists and health science students out there.”
Hi, Mickey–that is all very sweet and immensely touching. I’m just heading out to my day job the library right now so will read all of your comments more thoroughly tonight. In the meantime, would you please tell your students that as someone who knows and loves a kind and gentle person with amyotrophic lateral sclerosis, I can’t think of anything more important than what they’re doing with their lives: studying neuroscience. Theirs is a noble calling and they are lucky to have such an engaged and engaging, enthusiastic, creative, resourceful, dedicated teacher like you.
Hi, Mickey. Thank you so much for the report from the frontlines. It is delightful to hear that your pupils are starting to see the value in blogging and other Science 2.0 types of communication and research.
Yes, funding is perennial problem. I am very interested in amyotrophic lateral sclerosis, so I try hard to list any grants on neurodegenerative diseases in particular and on neuroscience in general on ScanGrants. Good for your students for improving their writing skills—they are going to have to write grant applications at some point in their careers and if they can so quickly and well, the less they will have to farm out at great expense to professional grant writers.
I loved “Slow Science”—cute.
Good for the student who spotted the error and subsequent uses of the flawed data. For the rest of her career she will be on the alert for such things. I did a quick PubMed search and came up with these articles. She might be interested in them:
1: Scientific deception: retraction of a fraudulent paper.
Coats A, Williamson EM.
Int J Cardiol. 2009 Jan 24;131(3):297. Epub 2008 Dec 3. No abstract available.
PMID: 19056136 [PubMed - in process]
2: Falsified papers in high-impact journals were slow to retract and indistinguishable from nonfraudulent papers.
Trikalinos NA, Evangelou E, Ioannidis JP.
J Clin Epidemiol. 2008 May;61(5):464-70.
PMID: 18394539 [PubMed - indexed for MEDLINE]
3: Retraction rates are on the rise.
Cokol M, Ozbay F, Rodriguez-Esteban R.
EMBO Rep. 2008 Jan;9(1):2. No abstract available.
PMID: 18174889 [PubMed - indexed for MEDLINE]
4: Retractions in the research literature: misconduct or mistakes?
Nath SB, Marcus SC, Druss BG.
Med J Aust. 2006 Aug 7;185(3):152-4.
PMID: 16893357 [PubMed - indexed for MEDLINE]
5: Research misconduct, retraction, and cleansing the medical literature: lessons from the Poehlman case.
Sox HC, Rennie D.
Ann Intern Med. 2006 Apr 18;144(8):609-13. Epub 2006 Mar 6.
PMID: 16522625 [PubMed - indexed for MEDLINE]
6: Scientific misconduct. Even retracted papers endure.
Unger K, Couzin J.
Science. 2006 Apr 7;312(5770):40-1. No abstract available.
PMID: 16601165 [PubMed - indexed for MEDLINE]
As to the elation and disappointments of research, I heard a very good talk a few months on ALS by Joseph S. Beckman, Ph.D. Principal Investigator and Ava Helen Pauling Chair, Linus Pauling Institute here in my hometown of Corvallis, Oregon at Oregon State University. It was clear what a talented teacher and dedicated researcher he is. I wish your students the same kind of joy in their research as Dr. Beckman discoursed upon so memorably and know they will share his determination to help those with devastating diseases. I can see why you are proud of your students. Dr. Beckman’s talk was moving and exciting. Writing skills clearly are part of the skill set of any successful scientist.
I definitely recommend that your students follow the Science 2.0 room at FriendFeed. For instance, apropos of the student interested in the peer review process, I came across this item via FriendFeed just now:
gpeerreview
A tool that enables peers to review and sign each others’ works
http://code.google.com/p/gpeerreview/
And here is an example of a good blog in the neurosciences:
Neuropathology Blog http://neuropathologyblog.blogspot.com/
Hi, Walter.
Very interesting post. Not totally unlike academia, sometimes, though I am fortunate that the particular academic unit I am involved with only “stifles” innovation b/c of budget. Basically, if any of us can demonstrate via simple argument that something will work and we can afford it, then we can do it. I sent this post to my brother who is an aerospace engineer (designs guidance systems) and also a project manager. I’m curious to see what he might say in response.
Another perspective on this issue has to do with management and how people are or are not prepared for the change in responsibilities…I have discovered that even in my fairly low-profile position as coordinator of a couple of projects that there are issues at the administrative level that are not well-understood until you get there. Or perhaps it would be better to say that these issues are not often made clear until one gets to a position of responsibility (ex: inter-departmental relationships with political bite that don’t have to be negotiated when simply a faculty member). I wonder if greater transparency of these relationships would lead to smarter suggestions by all members or if this knowledge would be discouraging. I’m of the personality type that makes suggestions without regard to operational constraints, then winnows ideas according to what is possible (both a strength and weakness!). This is not the case for everyone. What is the best way to educate members of the group so that innovation better matched actual constraints? And even at Google, there must be a vetting process at some level — not to mention that overall, the public is less concerned with what Google fails at (if the public learns much about it at all) whereas NASA is a more visible entity.
Hi Mickey,
I’ve found the same thing in biomedical research: if you can justify an experiment or project (barring fiscal constraints), you can do it. Needless to say, there’s quite a difference between a research experiment and spacecraft design, but the willingness to listen to and think through new ideas should be a shared trait by managers in either environment.
What struck me about this was the lack of technical discussion between administrators and the engineer. The disconnect between the process and the details is surprising given the nature of the job. Perhaps it exemplifies your comment, “there are issues at the administrative level that are not well-understood until you get there.” I wonder what those issues are at NASA?
As I said I might, I sent my brother this entry since he is a project manager at a huge aerospace firm, and has won awards from NASA for his launch successes. I don’t believe he’d want me to post his whole reply…suffice to say that he had a strong, eloquent reaction based largely on the apples to oranges comparison between a private company like Google and a more public company like NASA. While the amount of money flowing through each might be similar, the public and other consequences of failure are not at all the same. He did make a point, though, that is closer to yours above in terms of a “technical discussion” — there is a point for innovation, but it isn’t mid-project. Perhaps there needs to be more discussion up front or a separate line of $$ for mid-project insights that need exploration (an untested piece of Google code may cause embarrassment, but it won’t result in death). Even in academia, a project cannot usually be stopped cold to be re-worked from the beginning; instead, new lines of inquiry are planned.
[...] never will understand why tech firms don’t feature screencasts. LabRoots has one. It is such a no-brainer. Basic, basic, basic. Never make potential customers have to email you for [...]
Thanks for the backlink to my scientists on twitter link, we passed the 200 last week, currently 204 members. All science types with a twitter ID are welcome. Just tweet me, comment on the post, or retweet the link http://bit.ly/scientwists and I’ll add you. (Please make sure you have a non-generic photo, a bio and a website link)
Nicely done interview, Hope! Definitely helps next gen sci live up to goal of providing a forum for those of us still new to web2.0. I am particularly interested in the idea of the “semantic web” — ThinkMap’s (http://www.thinkmap.com/) Visual Thesaurus (though not semantic in the sense I think code creators use the term) is still an interesting model of what happens when technology is modeled after more human forms of cognition and is made to appeal visually. Mozilla project’s ubiquity (http://labs.mozilla.com/2009/02/ubiquity-016-and-release-scheduling/) is also an attempt at the semantic web which is fairly intuitive insofar as we humans are used to thinking of things as verbs and nouns. I think it would be easier for people to pick up a controlled set of verbs for web navigation, especially if an equally obvious set of metatags (I think that’s the term) were commonly used (or, in addition, developed discipline-specifically).
Hi, Mickey. Thank you for your nice note and kind words about Next Generation Science. Walter is doing most of the work right now. I keep wandering away to read the absorbing writings of Jean-Claude Bradley and those of his colleagues that he provides links to in the various Science 2.0-related rooms FriendFeed. There is so much to read about on this topic that I haven’t been writing much about it—except to write comment after comment in FriendFeed urging all those brilliant science bloggers to make sure to place Twitter buttons their homepages so that you and I can tweet particularly useful posts and thereby alert others of blogs they might not have heard of. Twitter really is a powerful tool in the Science 2.0 and Open Science movements.
In my library school courses, they certainly do stress the coming importance of the Semantic Web. Have you been following Tim Berners-Lee’s work in that area? Seems rather heavy on bureaucratic power grabs and obsessive concern with larding with metadata what should be a vibrant, growing organism. I would be very interested to see what people like Jean-Claude think of Berners-Lee’s strategy for standardizing it all.
Apropos of your comments about ThinkMap, here is a superb slideshow put out by the makers of the equally interesting product, Tableau:
http://www.tableausoftware.com/videos/zen
Thanks for the heads-up on Ubiquity, which I had not even heard of! Duh, Hope!
Could you provide an example of how this would work in practice, “I think it would be easier for people to pick up a controlled set of verbs for web navigation, especially if an equally obvious set of metatags (I think that’s the term) were commonly used (or, in addition, developed discipline-specifically)?”
The process of putting nouns and verbs together is pretty basic stuff — this distinction exists in virtually all languages (I would say “all” but one should be careful of claiming absolutes:-)) — in Ubiquity, the program pulls up a transparent black box where a set of commands that are pretty familiar to web users can be entered and which can then perform operations with info on one’s hard-drive (the creators are careful to point out this is fairly dangerous, too, and are looking to establish a “trust network” of ubiquity sourcerers (okay, really bad pun there!), umm, code writers (ubiquity is open source) that would provide community-based rankings for a page’s security). I really don’t understand code, but the idea of using this basic distinction b/w noun and verb to navigate seems intuitively appealing. This is at best a hazy idea on my part, and spoken from a position of ignorance in terms of creating code/understanding how code gets created. Rather, it is the opinion of a user dreaming of utopia where the interaction b/w human and machine makes the best use of both capabilities — people are particularly good at creative connection; computers are particularly good at data manipulation. The semantic web idea seems to want to capitalize on these differences.
Sorry, Hope, in reviewing my reply I may have unintentionally come off a bit rude — in that first sentence, I should have said something closer to “Nouns and verbs seem to be a basic distinction common to language…” or something like that. That’s what I meant by “basic stuff” — basic to the human animal. There’s interesting infant studies to show that we respond very early on to differing types of motion. In any case, when I read my answer it didn’t seem quite right. Any chance you could add a preview button? Helps me think my way through before hitting post!
Hi, Mickey. Sorry to be slow getting back to you. Thank you so much for both of your notes and for your very interesting points about how lovely it would be if machines could understand what we are driving it in terms of nouns and verbs. I had that very problem this morning. I was trying to comment on the value of blog carnivals vis-à-vis increasing the visibility of blog posts (say, this one). I typed phrases into the Google search box such as, “to dramatically increase in value” and “to render more valuable.” I then thought that perhaps there was a verb form of “exponentially” but “exponentiate” doesn’t seem to fit that meaning. Maybe it does—you as a linguist would know that better than I. So nice to know linguists.
Your note was not at all rude and I agree with you about the need for a preview feature. One does like to make sure that one’s boo boos are not preserved forever on the Web. We will see what technomeister Walter Jessen can do about that.
I loved “sourcerers” and think it should be adopted forthwith!! I am not sure where we are in terms of the Semantic Web differentiating between nouns and verbs.
Okay, Walter, you’ve almost got me to the point of adding twitter. Almost. I’ll have to employ the “high value” metric you suggest more conscientiously to my current 2.0 activities — it seems that while I’ve done that for the blogs I follow, I still don’t have a way of keeping track of these activities in a way that fits my workflow…maybe I don’t have enough of a workflow!
Nash does make some interesting points in his post, some of which are cultural in nature — just this morning, a pair of local DJs were hashing out whether Facebook’s new look was better — one of them made the observation that in a year, it won’t matter: it will just be the look of Facebook. I’d reply similarly to Nash: for some tools, it’s just a matter of time. They’ll be used because they are used, and if the lab-bound researcher intends to keep up with grads (let alone undergrads, an increasingly large population of researchers b/c NSF provides funding provisions for their inclusion), then real-time text-based comm tools will be a reality.
I do agree the name “twitter” is off-putting — and I’m not convinced that the instant messaging utility of twitter makes it necessary for science groups. Any IM system would work for that. Rather, Twitter offers some kind of “ambient” experience (see Lisa Reichelt’s slideshow and Herot’s thoughts) which is beyond (or at least different from) transmitting messages or consuming information. I think Twitter — and these sorts of 2.0 tools in general — encourage a kind of ambient literacy in which the user builds a dynamic, meta-net understanding that tracks/keeps aware of memic types of happenings — a sort of meta-awareness similar to what we say about the “feel” of a place — only the “place” here is mostly ideas, information. I don’t think selling twitter to scientists as a way of keeping tabs or managing labs (one of Nash’s examples) is how people use twitter or why it is experienced as valuable. I would like to know what about the ambient experience scientists and their kin find valuable.
It would also be interesting to begin some kind of web-based, longitudinal, community wide survey that asked some simple questions about 2.0 use — I think it was Bora who commented after a post (pretty sure it was on NN, but I’d have to look) about the value of science blogging that at the earlier stages of his career, he had a very different relationship with the web — and that as his career progressed (I’m assuming steadied out after the frenzied initial years of achievement), there was (in part) simply more time to find out what other people were doing. But I’m betting we’d find trends in peaks of use and non-use that were career related.
PS — is there anyway I can persuade nextgensci to add a preview button to make sure that links and such worked?:)
I think there is a general misunderstanding of what Jumper is. Most assume it is typical social networking software – and it is not. It is not a blog. It is not a wiki. And it is not a facebook type application. It enables transparent access to any data stored in a wide variety of different storage devices. This access is provided in a single representation that uses Web 2.0 type of software on the front end that allows end users to directly create representations of data, other users can add knowledge about this data, they can link it to other data, and they can rate it based on its value. It sits in front of your Oracle, DB2, MSSQL databases as well as fileservers and NAS devices to unify search with brokers on the back end for access.
Better useful code than useless marketing…
check it out for yourself. free download.
http://www.jumpernetworks.com/downloads.html
I’ve used Connotea for many years, and just recently made the switch to Mendeley. You can read about my experiences with reference managers here.
It seems like Connotea has fallen further and further behind in the priorities of its parent company, Nature Publishing Group. Citeulike has upgraded its hardware and Zotero occasionally gets an update, but Connotea hasn’t had a major redesign in years. The interface is dated and more and more painfully slow as time goes by.
If you haven’t given Mendeley a try, I would encourage you to give it a whirl. The thing I like best about it is that it has both a desktop and a web component, so you aren’t forced to choose between simple bookmarklet-based article saving and MS Word integration.
I’m now serving in the role of Community Liaison for Mendeley, so if you’ve got anything you’d like to know, just get in touch!
Hi, all. Thank you for the helpful clarification, Bob. It is very edifying to read of what something is not. Not a wiki. Not a blog, etc.
And thanks for the helpful link, Will.
Excellent discussion from you both. Thanks so much for the outstanding overview of Connotea, Helen. I have Connotea buttons on ScanGrants, but really had not understood it before.
I have just tweeted Mr. Gunn’s blog posting, “I’ve joined Mendeley as Community Liaison.” It should be read by library science students and anyone trying to grasp the matters you both discuss above. I am surprised that more people don’t discuss the usefulness of Twitter as a bookmarking tool. I find that aspect of it very useful indeed. Makes saving stuff (albeit in a stripped-down fashion) a dream. How come you don’t have a Twitter button on your blog, Mr. Gunn?
You are very sweet, Graham. Science was nowhere to be seen there! Bummer!
This comment was originally posted on FriendFeed
Very interesting stuff, and I am looking forward to running NetBase through some searches to see what happens. Maybe b/c I’m so used to using key terms and sifting info myself, I’ve found some of the “additional” info provided by some search engines (Iseek, for instance) a bit constraining to get around.
The one difficulty that no search engine can address, though, is access. In healthcare, many practitioners have reading rights only to the publications provided as part of their professional affiliations. Some will also buy into MDConsult, since it is “relatively” inexpensive. How will NetBase address accessibility? Or is it planning to work with publishers, such as the case with Elsevier, to integrate the search platform with existing content? Or have a separate limiter for OA only?
Oh, I see — should’ve looked before I commented! This is a product/service to be integrated into an existing “database” (is that the correct idea?) not a stand-alone search engine like novoseek. I wish I didn’t have to register to try it out!
That is correct. Our current business model is to use our Content Intelligence platform to power other companies search applications like publishers, portals and media companies. We plan to have a free health search demo application up in a few weeks that will include PubMed and other healthcare related data sources.
Thank you, Jens! I’m curious if the Content Intelligence approach incorporates semantic content at the paragraph level, too? While semantic relationships in sentences are important, they are only one part of discourse, and across a paragraph, the import of any particular relationship may be less (or more) weighty than what happens in a single sentence. For example, pronouns (and other shorter lexical forms) usually refer to well-known entities in a paragraph and indicate what is “understood” to be the central topic of the paragraph. Does your system incorporate a formula/algorithm for these kinds of relationships? They are quantitative in nature, so seem like viable candidates, though I am not a code developer (but I had one sit on my doctoral committee and he asked me to model stuff for him — some were easy; for some, I just told him “no”!).
That is a great question Mickey. Today, Content Intelligence does not, in the strictest sense, do what’s called anaphora resolution (e.g. figuring out what “it” refers to in a sentence). We use other tricks to capture context from prior sentences as a back-off. Strict anaphora resolution on massive internet-scale has as far as we know not been done. This is something we are working on and hope to support as a robust commercial feature (anything is possible in the lab) soon.
I encourage your readers to check out this article by Gerry Campbell, CEO of the Real Time search engine Collecta:
http://www.altsearchengines.com/2009/05/05/is-your-realtime-really-realtime
Hi, Hope.
Awesome read, and am looking forward to your review of DeepDyve as well — but given that it is Friday afternoon on my coast and my eyes are literally spasmodic from so many hours spent reading this week, I will content myself with a comment tingling at the back of my fatigued brain.
Not-so-metaphorically speaking, one thing I’ve noticed about many of the search engines is that the search direction is usually down and/or inward. So, the searcher starts with an query and gets a result screen that will take them deeper into the subject, though the depth may be had by getting more specific or by moving laterally to related concepts (“children” versus “sisters”). For experts, this can be a discovery process. For those new to their field (like undergrad science researchers), these kinds of results may feel a bit overwhelming. A possible consequence is a narrowing of vision to just the literature that very specifically answers a novice’s question, resulting in a lack of discovery. I realize this doesn’t have anything to do with the value of the search engine itself — and I’m also very excited (as both you and Walter are) about the possibilities of the semantic web. But some portion of my teacher-brain wonders about the intersection of inexperience with this sort of information structure. One of the values of a simple, boring meta-data mediated search is the accidental discovery of related material — this happens all the time in classes where students are learning to search the primary literature for the first time. In browsing all those seemingly useless titles, they discern patterns that help them understand new connections and often help them revise research questions to more closely reflect their real interests.
Again, this doesn’t de-value “content intelligent” search engines, but I think it does point at developmental differences in usefulness. We may find a decade from now that semantic-rich searches yield different sorts of discovery patterns than our current “keyword” searching yields, and that some use for each will be valued.
Aah, well, onto Deep Dyves!
Hello again!
I just ran a search on gopubmed and deep dyve for a current obsession, the relationship/s between prosody and autism. Have to say that I was rather disappointed by deepdyve where even filtering out everything but 2 databases still produced unrelated entries. Could be that their search engine isn’t intuitively obvious to me.
My experience with Gopubmed was quite different — this “metric- insertion-of-dirty-f-word-indicating-extreme-enthusiasm” rocked! Not only did the Find It button bring up 23 beautifully tailored hits, 21 of them were so immediately interesting that it was difficult to remember it was a pedagogical exercise. There is a bit to figure out if one were a true novice to searching, so I created a screen shot to the page with bubbles explaining stuff (I know the search engine itself provides this info, but it does so with tender unobtrusive care, so that I was concerned students might not immediately understand what the buttons could do). I am now going to send out the link with said screen shot (word doc so not sure how to embed the pic or send it along — I can send it via gmail if you’d like) to all my students and colleagues teaching this semester.
Also, you mentioned in DeepDyves that it’s okay to be pretty…woo hoo! That is one of the things I like best about GoPubMed. It’s pretty; easy on the eye, with color intensity cleverly used to help the user navigate. Thanks soooo much for the review!
Hi, Mickey. Thank you so much for your very interesting comments. You are a far better analyst of the complexities of search technologies than I.
I would be most interested in your reaction to the much hyped new search engine, Wolfram|Alpha. I just tired it and was not impressed. I tried my favorite search term, amyotrophic lateral sclerosis and got the response, “Wolfram|Alpha isn’t sure what to do with your input.” Then I tried, ALS and got the result, “Als Island (island).” Then I tried Lou Gehrig’s Disease” and got the same sort of unhelpful answer. Ditto with “motor neuron disease.” I am currently trying, “dog” and am waiting and waiting and waiting…Ah, now I get the message that Wolfram|Alpha is temporarily unavailable (probably because half the world is trying it out today– the servers may have collapsed under the weight of interest.)
I was interested in your reaction to DeepDyve. I like it a lot and not just because it is pretty. Ha.
Good for you for alerting your students and colleagues to GoPubMed. I liked your wording, “beautifully tailored.” I would be very interested to hear back if your students try sample searches in GoPubMed, DeepDyve, Mednar and Wolfram|Alpha.
Your students are lucky to have a teacher who thinks so deeply about how they think and reason.
@Mickey: It’s great to hear that you’re sharing with students and colleagues your experience with GoPubMed. It’s these types of interactions – blog reviews, email discussions (with attached tutorials!) – that foster widespread use of new technologies.
@Hope: Wolfram|Alpha is a computational knowledge engine, not a search engine. Since your queries aren’t being made in the form of a question, the application doesn’t know what to do.
See here: Wolfram|Alpha Goes Live in Real Time
Hi, Walter. Oh? Oh. Duh, Hope! What, then, should I ask it in order to get results on amyotrophic lateral sclerosis?
Do you think it has been overhyped bigtime?
Hi, Walter.
Thought you might enjoy another perspective on Wolfram/Alpha — I’m don’t understand the tech itself, so can’t offer an opinion, but thought you might find it of interest:
http://scienceoftheinvisible.blogspot.com/2009/05/dampsquibalpha.html
The one problem is that young girls are not as into gaming as boys and so don’t build up geek nous.
Hi, Eric. James Paul Gee is a sociolinguist and education theorist with a whole series of excellent publications on the value of video games for learning — the most easily accessible (meaning found online for free) are Good video games and good learning (http://tinyurl.com/dgne5f) and Learning by Design: good video games as learning machines (http://tinyurl.com/q5zepw). You’ve probably heard of him, but I find these articles particularly easy to follow.
Hope, I agree that war-based games are not appealing to young girls, but not that it’s video games themselves — at least while they are young. My daughter loves her Leapster L-Max as much as my son, though their preferences for games are somewhat different. It would be great to see more complex games tailored to girls — I wonder if this is likely given the perception that they are an insignificant part of the market? (In fact, girls interest will wane as they perceive that video games are a particular interest of boys, mostly in the effort to disassociate themselves during the pre-teen years). More complex games for girls would have them building and navigating complex tasks but on things more appealing — I know this will sound stereotypical, but girls often respond to nature strongly (how many of us went through the “marine biologist” phase?:-)) — a game which had them build eco-systems with the addition of managing highly social animal groups (lions, wolves, dolphins, monkeys, meerkats, etc!) over time I think would have strong appeal. The same could be said for fantasy environments that are somewhat less dark — let’s say fairies, elves, and gnomes as opposed to warlocks? And while this is particularly stereotyped, building a mall, tying in economics and sociology, would also appeal to a lot of girls. So, I think the possibility exists for video games for girls, but they are clearly not a targeted market overall.
Oops — forgot one last thing, Eric. If you’re interested in these sorts of things, you might find the FriendFeed room “future of education” a fun place to hang out. It doesn’t pick up the traffic that the “science 2.0″ room does, but what get’s posted is mostly pretty good, and it would be great to have more people hanging out there!
This post has been selected for Scientia Pro Publica. Please advertise the carnival on your blog and we hope to see your posts included in the future. Congratulations!
http://network.nature.com/people/primatediaries/blog/2009/05/18/scientia-pro-publica-4-in-memory-of-stephen-jay-gould
I have two opposing opinions about this. On the one hand, I completely agree that making a digital recording of something against the wishes of the presenter is lame and in many cases egregious behavior.
However, I think you are wrong in the statement “Cameras are great for recording events in life that you want to remember. However, they have no place at scientific conferences or poster sessions where unpublished data is being presented.” I think this can be determined by the meeting and/or the presented. At many conferences I have been at recently, the talks are presented live on the web and also recorded and available for later viewing and downloading. And I personally am trying to post my slides on places like slideshare or the web somewhere and include plenty of unpublished material there. I think that sharing work before publishing is critical to the scientific enterprise and there are many journals that do not exclude the possibility of publishing in that journal even if work is presented previously “published” on the web or in a meeting.
In the end, how one should handle the distribution of posters, talks, etc (and for that matter, papers) varies enormously depending on the situation. I agree that violation of the copyright and intent of the presenter is wrong, but there are many people who are comfortable with broad CC license type distribution of ALL their presentations/publications and I for one enjoy going to these types of meetings enormously.
Oops, I guess I’m doing it wrong. At conferences I print copies of my posters for people to take home with them, and I make my posters and talks available on my website as PDFs. I always thought the purpose of a conference was to expose your ideas to a lot of people, get feedback from them, or initiate a collaboration, not to steal ideas (or data??) for the next grant proposal. I’m sure it happens but if they’re bent on doing it, it won’t matter whether they have an exact replica or not. Most people probably take photos because they appreciate the work and want to take more time to think about it later. Or maybe they just like the color scheme and want to replicate it for their next talk.
This is a really fascinating discussion. The issue of cell phone camera use comes up in the patient care environment, too. Sometimes family members of patients are camera-crazy.
@Jonathan The more I use the Internet for scientific communication, the more I would like to share unpublished data on the web. However, I’ve done research in some pretty competitive areas and worked with people who had unpublished data they presented taken and published before they were able to publish it. Indeed, most of my training has been in labs where the position has been one of guarding unpublished data, not sharing it. I think this is the pervading attitude in science, not the exception. If we’re ever going to have greater communication between researchers and increased sharing of unpublished data, this issue needs to be discussed.
Although you make a good point that the distribution of posters, talks, etc varies on the situation, I think that people shouldn’t assume that unpublished data can be freely recorded. I’d also like to point out that just because talks are presented live on the web and recorded doesn’t mean the presenter is showing you all the unpublished data they would have shown you had they been presenting it in a more private venue where their data wasn’t being digitized and distributed.
The other thing I’d like to point out is that the attitude on this likely differs between disciplines. For example, I’ve noticed that many scientists blogging and using social media tools today tend to be dry-bench scientists than wet-bench researchers. My impression is that sharing unpublished data is much more acceptable to computational scientists than it is to wet-bench researchers.
@Eric I don’t think you’re doing it wrong at all. I don’t have any issue with someone distributing unpublished data. As I said above, the problem is that people to whom you’re presenting shouldn’t assume that your data can be freely recorded without your permission. If you’re handing out copies of your poster, you’re clearly granting permission.
Thanks so much for the streamosphere link — just spent a great 20 minutes doing some broader-based browsing than I get through FF — much more like going to the stacks, so to speak, a topic that came up recently in a discussion regarding the value of hard copy versus digital. So glad I get the RSS from NextGenSci!
[...] Research Blogging is a community-run non-profit organization. The organization was created by bloggers for bloggers, with the input of bloggers and blog readers who like to read about new developments in science and other fields. If you’re a blogger who writes about serious research, Research Blogging offers you a way to distinguish your serious posts from anything else, by directing your regular readers — and new readers — to the posts linking to published articles. You can read more on the idea behind researchblogging.org in this post on nextgenerationscience.com. [...]
[...] combination. As you may know, the NIH awarded almost $30 billion in grants in 2008, and with the American Recovery & Reinvestment Act of 2009 (ARRA) expected to receive an additional $8.2 bill…, it is more important than ever to unlock that valuable insight into federally funded [...]
Dear Ramón Alonso-Allende,
regarding your answer to the question “how NovoSeek differs from GoPubMed …”, I must say I’m disappointed. Let me tell why: first, what is described here for your search platform was done 6 years ago when GoPubMed first went online. I don’t see any new features above GoPubMed or others. Secondly, your statement: “… lets users search more accurately, in less time and with less effort than any other search offering in the market today” is unproven and just another marketing statement. For “Heart Diseases” you find 163,595 results. We know that at least 848,633 are semantically relevant. It is hart to believe that Novoseek involves any semantics besides synonyms. Using the query “Vitamin C”, NovoSeek is missing (using MEDLINE source) more than 5,000 papers. Additionally, I’m missing all the following features:
· Statistics about queries, ontology terms, persons (co-author network diagram)
· Top author for your query showing the automatically compiled vita references
· Editable author profiles, contact authors
· Curation tools for scientific crowd computing
· Navigation based on MeSH, Gene Ontology and proteins ontologies
· Auto-completion based on MeSH and the Gene Ontology
· Syntax like Pubmed, related articles extracted from Pubmed
· Wiki links with concepts found in abstracts
· UNIPROT links with proteins/genes found in abstracts
· Using the tree: easy option to include and/or exclude concepts in queries
· Easy navigation to dive into the ontologies and find related terms and functions
· The WWWW (WHAT, WHO, WHERE, WHEN) concept: navigation using combination of queries based on concepts, persons, places of affiliation (countries, cities) and/or places cited in abstracts, journals (reviews only, high impact journals) and date (year, months, days)
We are open for any discussion! But let’s move on to the next semantic stages. There are so many open, scientificly interesting and unsolved issues where all should collaborate: ontology alignment, unlearn “old” facts from the ontology and last but not least ontology generation. Let’s go for it!
Sincerely yours
Michael
Gentlemen: Thank you both for your fascinating contributions to this discussion of important topics.
Hope
This was really fascinating–thanks for the link to
http://twitter.com/mistersugar/
I went there immediately—as I always note and immediately check out any info about Science 2.0 in Twitter. I am glad that I did because Anton has a tweet that says, “Do you want to help plan ScienceOnline2010 (in RTP over MLK weekend)? Contact me and we’ll get you involved.” And then I found this in FriendFeed:
http://friendfeed.com/coturnix/0dad9914/confirmed-scienceonline-10-will-be-on-15-17th
and saw this comment by one of my heroes, Jean-Claude Bradley: I’ll be there – always a good time
Sure would be exciting to meet Bora and Jean-Claude. I have tweeted Anton and hope to learn more about the conference and hope to attend.
This discussion is a good example of social networking in science. Bora blogs eruditely and compellingly. He is interviewed on this blog and discusses how blogging can lead to print publication, thereby illustrating that blogging actually helps traditional print remain viable (which should raise the comfort level of librarians and publishers with blogging). He mentions figures of note that the reader of this post can then research via Twitter and FriendFeed and discusses interestingly the review in The New Scientist, which one can see only a snippet of without a full subscription—classic case of the frustration of interested readers encounter with old school publishing methods. And as a result of reading this interview with Bora I have just subscribed to the PLoS ONE room on FriendFeed and to the @PLoS Twitter account, and there found a tweet to linking to Michael Nielsen’s seminal essay (must reading), “Is scientific publishing about to be disrupted?”
http://michaelnielsen.org/blog/is-scientific-publishing-about-to-be-disrupted/
Thank you Bora and Walter for such a scintillating colloquy.
Dear Mike,
The differences between novoseek and goPubMed are clear under my point of view. As you put it in your comment, there is a lot of pending research to do regarding ontologies; therefore and although we take that into account, we don’t rely that much on them for our analysis.
As you know, it is not all about getting results or reordering pubmed results based on any type of ontology. It is more about differentiating those documents with the most relevant meaning from those that are there just to keep the user busy.
Regarding functionality, novoseek’s approach is based on keeping the user’s focus on getting the information and we like to make it simple. When we decide to add extra features, we want to make sure that it is really interesting to the user. If we see that there is functionality that people is not using, we just take it away, because it does not help to the final experience. However, I modestly suggest you take a closer look to novoseek because, if aiming to be fair and not only state goPubMed feature list, some of the functionalities you claim to miss are actually present in the tool.
Thank you for your comments.
A very gentlemanly exchange. Thank you both for educating all of us on these matters.
As to the question, “What do you think of Buzz Aldrin’s challenge to America? Should the U.S. go back to the moon?”
No more moon. If that money were put into molecular biology, think of the suffering that could be prevented.
Transinsight’s GoPubMed.com, the semantic search engine for the life sciences, has been recognized with the 2009 red dot: best of the best award in the category communication design – graphical user interfaces and interactive tool. A total of 6,112 submissions were received from 42 countries. The jury selected 470 entries for the “red dot design award.” A group of only 56 submissions were selected as “the best of the best” and will be participating in the final round for the “grand prix award.” The Transinsight team is proud to receive this prestigious award. For further information http://www.transinsight.com
For the record:
I read The Open Laboratory from cover to cover.
I’m delighted that sales rose after my review appeared.
My review was not aimed at bloggers at all, it was aimed at readers of New Scientist’s print magazine.
I understand this is an emotive issue for Zickovic, but I suggest he reads my comments on the Neurotopia and Laelaps entries he links to before making further claims that bear no relation to the facts.
Hi, all. I got a chuckle out of Michael’s wry comment, “I’m delighted that sales rose after my review appeared.” Now, if we could only determine if those sales were to readers of his review or to those who follow the blogs that criticized his review—which unlike blog postings, is locked up behind a toll access gate and which thus, perforce, will have a limited influence compared to easily accessible blog postings.
And this comment is interesting, “My review was not aimed at bloggers at all, it was aimed at readers of New Scientist’s print magazine.” Are none of those readers science bloggers? I don’t quite follow his characterization of the readership of The New Scientist. I would think some of those readers would object to his dismissal of the revolution in the dissemination of science news that is science blogging.
In any case, it is nice to see such a civil discussion between articulate people on these matters.
Hi Hope
I’m sure a few New Scientist readers are bloggers, but certainly only a small minority. See my comment here:
http://scienceblogs.com/neurotopia/2009/04/part_the_4th_in_which_the_new.php
Also, to make it clear, I think science blogging is a great thing and I’m all for it. The point I made in the review is that for every RealClimate there’s a Watt’s Up or three. For every Bad Science, there’s a nutty HIV denialism or vaccines-cause-autism blog.
So my suggestion is, what you look at the big picture, at all blogs not just those you or I would call science blogs, that the overall effect of blogging is negative, that it has helped spread myths and lies. I’m not saying this definitely is the case – how do you measure such things? – and I hope I’m wrong, but I think it’s plausible.
The internet has given the nutters a collective voice, and they’re screaming very loudly.
For every Demon-Haunted World, there are a dozen paperbacks by Sylvia Browne and her fellow charlatans. Is the overall effect of the book negative?
[...] had looked and written about ResearchGATE last week and it is striking how much BioCrowd surpasses it in sleekness of look and the [...]
Lively social networking in the sciences: I like the sound of that!
Hi, Lisa. To find that, you really need to try The Life Scientists of FriendFeed http://friendfeed.com/the-life-scientists
First response – "oh, not another one." But this is a detailed, helpful and quite glowing review, so may be worth a look.
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OK, gave in, signed up. Not bad. One gripe – does not seem to have imported my feeds. Unless this takes some time.
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[...] tried to determine what exactly it is — a social network for scientists along the lines of ResearchGATE and BioCrowd for those in the biomedical sciences and [...]
[...] « Previous article The Potential of BioCrowd Next article [...]
[...] does enable users to email other members, via 2collab’s mediation. But GoPubMed does that and so does [...]
Nice post, Hope! My impression was more hopeful when I reviewed it after it launched, but sadly it doesn’t seem to have gone anywhere since. The major value of the service is its tie-in with ScienceDirect, and it had the potential to really leverage that, but it just doesn’t look like it has gone beyond being just a me-too social bookmarking product.
In fact, both Connotea and 2collab, have been foundering a bit relative to citeulike. Perhaps it’s not surprising that Citeulike is doing better, though. Would an independent project like citeulike necessarily have more energy and commitment than a side project like Connotea and 2collab? Is it a case of 100% commitment of fewer resources relative to 1% commitment of far greater resources or is it just harder to fight off the “what’s your business model” questions when it’s an internal project of a larger company? Maybe it’s something else entirely.
What follows is pure speculation, but …
I have a theory that independent projects start out with more goodwill than products coming from an established brand. There’s always a question of what will happen to the time you’ve invested in a service and the data you’ve accumulated. I think people trust a smaller outfit more because a smaller outfit is more responsive to and more dependent on its users, so they’re less likely to do something bad, and if they do, the users have the power to punish them more effectively than an established brand, which might just shrug off the complaints and can the project. Microsoft and Sony have been guilty of gross misconduct and disregard of their users and have largely gone unpunished for their behavior, whereas a smaller company wouldn’t have. Even Facebook, which is now a big company, had to cave to its users over the Beacon incident.
Imagine a board meeting where people are talking about what possible opportunities exist in Web 2.0. Part of the pitch for developing a competitive product goes like this: “We’re a well-recognized name and we’ve been around for a long time. Clearly we’ve got a marketing advantage over some fly-by-night independent project.”
Now imagine that someone stands up in the meeting, attended by their boss and people from the marketing department, and says, “Maybe our brand isn’t as well-loved as we think it is. Perhaps if we didn’t strongly brand this, the product would do better?”
I could be totally off the mark with this, and certainly resource allocation is part of the reason 2collab isn’t growing as strongly as it could have, but I also think they didn’t realize how important it was to gain the trust of the early adopters and to put a responsive and accountable public face on the project.
Hi, Bill. Thanks for your note below. Sorry to be slow to be getting round to responding to it. I was in transit to Toronto where I am now am attending Medicine 2.0:
http://www.medicine20congress.com/ocs/index.php/med/med2009
I agree with you about 2collab being just a me-too social bookmarking product. Strange that Elsevier didn’t look at Nature Precedings and not see how pretty useless 2collab is by comparison. And interesting that ResearchGATE
seems to working on a me too of Nature Precedings except that ResearchGATE’s
service (as I understand it) is for published articles and not pre-prints
http://blog.researchgate.net/index.php?/archives/98-Self-Archiving-Repository-goes-online.html
ResearchGATE has a rather vainglorious view of itself vis-à-vis inflated claims of firsts. It says, “We have now launched our Self-Archiving Repository! This project makes full-text articles available to the public, for free – the first application of its kind worldwide.
Currently, there is no way for researchers to access millions of publications in their full version online. We are now changing this by enabling users to upload their published research directly to their profile pages (a system called the “green route” to Open Access).”
That is all balderdash and bogus beyond belief. There are probably dozens of institutional repositories throughout the world at universities and other academic and research institutions. Some scholars have their own personal sites and there is the little matter of PubMed Central. ResearchGATE seems to have a genius for ignoring the efforts of academic librarians and the entire National Library of Medicine. Not the way to win friends in the information science and medical library worlds.
Thanks so much for the disquisition on Connotea, “…foundering a bit relative to CiteULike.” I had not heard that.
Apropos of your comments, “Microsoft and Sony have been guilty of gross misconduct and disregard of their users and have largely gone unpunished for their behavior, whereas a smaller company wouldn’t have,” here is a somewhat comparable instance of bullyboy tactics, this time by Google:
http://www.consumerwatchdog.org/corporateering/articles/?storyId=25100
Creepy that Google tried to get a tiny outfit’s grants pulled.
I actually would probably go with a well known name when it came to archiving given that it would be a huge headache if a company went under—which, for instance, the well funded Nature Publishing Group of Nature Precedings is far less likely to do than is the fall smaller ResearchGATE. I would probably go with the revenue-rich Elsevier, but there is nothing much to upload to in 2collab. And then, of course, big names can go under overnight as we saw last year in the world of finance. Scary times in so many respects, huh?
widespread distribution may indeed be a goal, for example to increase interest in an upcoming publication. if the intentions of a presentation are made clear to an audience, unexpected results are less likely.
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[...] « Previous article 2collab: Basic Blah Social Bookmarking Next article [...]
Precedings is by far the best of the NPG experiments, in my opinion.
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Hi, Neil. Would you please list for the edification of us all what all the others are?
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I guess Nature Network would be the other major initiative. Also nature.com blogs, Nature Videos, Connotea, Scintilla and Streamosphere. There may be others I missed. I see them all as NPG’s experiments in the Web2.0 space.
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Hi, Neil. Very helpful–thank you! Any thoughts on ResearchGATE, Biocrowd and 2collab?
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Nature Precedings is the most polished one, although streamosphere is pretty neat
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(1) no, (2) not really, (3) no
I find very few of these things useful, to be honest.
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Thanks guys–I had not heard of Streamosphere–cool! But is is yet another thing to be depressed not to be able to keep up on! So many brilliant people writing so many fascinating things. So what would you consider useful, Neil?
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Hope – FriendFeed
My opinion is that X fails when it becomes "X for scientists".
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Hi, Neil. Good point–I am not a scientist and I get to learn from you in good old FF.
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[...] might SciVal Funding fit in with Elsevier’s foray into social networking the sciences, i.e. 2collab? Will there be a way, for instance, for users to determine where potential collaborators might be [...]
[...] I have looked at smaller Science 2.0 sites, such as LabRoots, Scientist Solutions and 2collab, and it is at once clear that NPG is pouring money and talent into Nature Networks. Elsevier may be [...]
Hi Hope,
First off, thanks for taking the time to write such a detailed review. Sorry to be a little late in my reply, but I was on holiday when this article was published. I would like to take a minute to respond to some of your points.
* 2collab is a social reference management and bookmarking tool. As such, it is roughly in the same space as Connotea and CiteULike. Some of the unique features we have tried to include are:
* More robust group functionalities. As you noted there are a number of public groups that are spam. However, we have seen that there is very limited interest in public groups. The vast majority of interest is in private groups. Researchers are wary to share their current work for fear their competitors will steal their ideas. Our private groups are where more of the interesting collaborations are happening.
* As you mentioned, one of our main advantages comes from integration with other Elsevier products, such as Scopus and ScienceDirect. We had integrated 2collab into ScienceDirect. Any ScienceDirect item bookmarked in 2collab would show up in a box in the sidebar of the article page in ScienceDirect. This box showed number of times bookmarked, comment count, and rating. Unfortunately, we have had to temporarily turn this box off, while we work to improve the performance of 2collab. Worth noting is that this is the first step in determining how best to integrate with related tools such as Mendeley or CiteULike.
* Scopus is integrated in a number of ways. If an article is bookmarked that has a DOI, Scopus is checked and used to pre-populate and clean the reference information. Additionally, bookmarks with a DOI display their citation count from Scopus.
* Scopus Author Profiles are integrated into 2collab user profiles. A user can enter their Scopus Author Profile ID and import their publication list to 2collab. These articles will display as part of one’s profile on 2collab. Additionally, any bookmark can be marked as Authored by the user and will be added to their profile.
* As I mentioned above, a lot of the value of 2collab comes from it being used as a place to experiment with features that could later be added to other Elsevier products. It is our hope to take the best from 2collab, refine, and reuse.
* On a side note, I would like to mention the Spam problems 2collab has been experiencing. It is a major problem that has also caused severe performance issues. Consequently, all our resources are currently devoted to performance improvements and spam prevention.
* This has prevented us from adding some key features that are still needed. One key feature at the top of our list is proper Search. The current search is querying the database rather than a Search index. Once performance and spam are in check this is a top priority.
Since Elsevier began developing 2collab, a lot has changed in the social media realm. We are working to revamp our strategy accordingly.
Best,
Michael
Just noticed the comment is still awaiting moderation… Copying below, but the format is lost: "Hi Hope, First off, thanks for taking the time to write such a detailed review. Sorry to be a little late in my reply, but I was on holiday when this article was published. I would like to take a minute to respond to some of your points. * 2collab is a social reference management and bookmarking tool. As such, it is roughly in the same space as Connotea and CiteULike. Some of the unique features we have tried to include are: * More robust group functionalities. As you noted there are a number of public groups that are spam. However, we have seen that there is very limited interest in public groups. The vast majority of interest is in private groups. Researchers are wary to share their current work for fear their competitors will steal their ideas. Our private groups are where more of the interesting collaborations are happening. * As you mentioned, one of our main advantages comes from integration with other Elsevier products,…
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Just noticed the comment is still awaiting moderation… Copying here: Hi Hope, First off, thanks for taking the time to write such a detailed review. Sorry to be a little late in my reply, but I was on holiday when this article was published. I would like to take a minute to respond to some of your points. * 2collab is a social reference management and bookmarking tool. As such, it is roughly in the same space as Connotea and CiteULike. Some of the unique features we have tried to include are: * More robust group functionalities. As you noted there are a number of public groups that are spam. However, we have seen that there is very limited interest in public groups. The vast majority of interest is in private groups. Researchers are wary to share their current work for fear their competitors will steal their ideas. Our private groups are where more of the interesting collaborations are happening. * As you mentioned, one of our main advantages comes from integration with other Elsevier products, such as Scopus and…
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Hi, Michael. Thank you for your courteous and detailed response to my post on Next Generation Science about 2Collab. What you write is all very edifying. Good for you for being so responsive to comments about it and for being candid about various problems. Glad to hear that site search is a top priority. Hang in there—good for Elsevier for trying new things. Hope Leman
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Hi, Michael. Thank you so much for your courteous, edifying note. Thank you for making clear exactly what 2Collab is. I appreciate your candor about the spam problems.
Apropos of your comment, “However, we have seen that there is very limited interest in public groups. The vast majority of interest is in private groups. Researchers are wary to share their current work for fear their competitors will steal their ideas. Our private groups are where more of the interesting collaborations are happening” there was an recent, interesting example of FriendFeed of a successful, open collaboration in that environment. See here:
http://friendfeed.com/yokofakun/11ee2366/gene-wiki-community-intelligence-applied-to
I guess we will just have to revisit the private group/public group matter two or three years down the road to see which model wins out.
Good for you for being open to integrating 2Collab with non-Elsevier tools. Such openness will benefit Elsevier in the long run given that the more integration there is across the Web there is, the better.
Good for you for working on the search matter. I am glad to see that Elsevier is working with NextBio in such areas, at least with ScienceDirect:
http://trainingdesk.elsevier.com/node/397
Hang in there! Elsevier is a content supremo and we support your efforts to render it discoverable.
Dear Hope: Many thanks for your generous and thorough review of the new Elsevier product SciVal Funding. We at Elsevier are excited to launch the product today, especially as we feel it can be a great resource for junior investigators, who face the difficult challenge of transitioning from post-docs to independently funded research scientists.
One of the keys to the product’s success will be to continue to refine and enhance its capabilities over time, and we’re committed to doing so. We look forward to getting crucial feedback from the research community about the product and ways to continue to improve it.
All best wishes,
Daniel Calto
Director of Product Management
Academic and Government Products
Elsevier Inc.
Hi, Daniel. Thank you for your nice note.
As it happens, I recently attended the Medicine 2.0 conference and at the end of my talk there on ScanGrants, I was asked several questions about the lack of tools for grant seekers in general and junior scientists in particular. I said, “Well, has Elsevier got something in the works for them!”
Good for you for leading the way in innovative thinking when it comes to leveraging the power of Library 2.0, Web 2.0, Science 2.0 and Research 2.0 and linking the worlds of academic and medical libraries and offices of research administration. You are tying those formerly rather distinct realms together much to the benefit of science and scientists and thereby, ultimately, to those of us who will need medical care at some point. Keep up the good work!
I am the always last to know these things, “I’m hoping to moderate two sessions: one on the use of Web 2.0 in health and medicine, and one on Medical Journalism.” Oh? Great!
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Fwd: RT @wjjessen @NextGenScience: ScienceOnline2010 – Conference on Science and the Web [link to post] #scio10 (via http://ff.im/8XiBL ) http://friendfeed.com/e/cf905352-2a79-4f8b-bb95-ab47c6459f31
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ScienceOnline2010 – Conference on Science and the Web [NGS] [link to post] #scio10
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ScienceOnline2010 – Conference on Science and the Web [link to post] #scio10
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RT @wjjessen @NextGenScience: ScienceOnline2010 – Conference on Science and the Web [link to post] #scio10
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RT @BoraZ: RT @wjjessen @NextGenScience: ScienceOnline2010 – Conference on Science and the Web [link to post] #scio10
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The NGS Interviews – An ongoing series of interviews with Science 2.0 leaders & key products [Next Generation Science] [link to post]
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♻ @NextGenScience The NGS Interviews – An ongoing series of interviews with Science 2.0 leaders & key products [link to post]
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RT @NextGenScience: An ongoing series of interviews with Science 2.0 leaders & key products [Next Generation Science] [link to post]
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RT @tigressse: RT @NextGenScience: An ongoing series of interviews with Science 2.0 leaders & key products [link to post]
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RT @NextGenScience: A series of interviews with Science 2.0 leaders & key products [link to post] (via @tigressse)
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RT The NGS Interviews – interviews with Science 2.0 leaders [link to post] (via @NextGenScience)
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RT: @genomepop: Nature Precedings: a Fusion of Science 2.0, Open Science, Research 2.0 and Social Networking: [link to post]
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Nature Precedings: a Fusion of Science 2.0, Open Science, Research 2.0 and Social Networking: [link to post] (@nextgenscience)
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RT @NextGenScience: @ALSUntangled: Interview with Richard Bedlack [NGS] [link to post] #ALS
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ALSUntangled: Interview with Richard Bedlack [NGS] [link to post] #ALS
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RT @NextGenScience Open access week Building communities of learning with free, unrestricted, online access. [link to post] #Oaweek
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Open Access Week Around the Web [NGS] [link to post] #OAweek #oaw09
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RT @NextGenScience Open access week. Building communities of learning with free, unrestricted, online access. [link to post] #Oaweek
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Open Access Week Around the Web: Posted by CharlesWBaileyJr to oa.new on Wed Oct 21 2009 [link to post]
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RT @NextGenScience: Open Access Week Around the Web [NGS] [link to post] #OAweek #oaw09
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The Open Laboratory: Interview with Bora Zivkovic | Next Generation Science [link to post]
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New NGS Writer: Graham Steel [NGS] [link to post]
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Open Source Science Commons [NGS] [link to post] #open #science
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Open Source Science Commons [link to post] #open #science
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Thank you RT @wjjessen: Open Source Science Commons [link to post] #open #science to @boraz
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RT: @NextGenScience Open Source Science Commons [NGS] [link to post] #open #science
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RT @wjjessen: Open Source Science Commons [link to post] #open #science
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RT @VeroniqueR Thank you RT @wjjessen: Open Source Science Commons [link to post] #open #science to @boraz
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Open Source Science Commons – [link to post] http://friendfeed.com/e/3155b8c1-1453-45fe-8ace-226b4f603896
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RT @BoraZ RT @wjjessen: Open Source Science Commons [link to post] #open #science
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RT @BoraZ RT @wjjessen: Open Source Science Commons [link to post] #open #science (via ehealthgr)
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RT @NextGenScience: Open Source Science Commons [NGS] [link to post] #open #science
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This Week is Open Access Week: [link to post] http://friendfeed.com/e/23333bfd-ed93-44fc-8fa4-4f03c27caffc
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Science Spotlight – October 29th, 2009 [NGS] [link to post]
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The End of Impact Factors as a Measure of Research Quality [NGS] [link to post] #article-level #metrics #PLoS
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Dare I believe that "end the impact factor" is gaining momentum? It feels that way sometimes. Or is it just in my own small networks?
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Liked “The End of Impact Factors as a Measure of Research Quality [NGS]” [link to post]
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The End of Impact Factors as a Measure of Research Quality [link to post] #PLoS (via @NextGenScience)
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@Neil: One of the most sought after talks that I give is the one on publishing and the feedback is always in favor of getting rid of IFs.
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The End of Impact Factors as a Measure of Research Quality [NGS] [link to post]
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What will Thompson isi do? RT @wozzza: The End of Impact Factors as a Measure of Research Quality [NGS] [link to post]
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The End of Impact Factors as a Measure of Research Quality [link to post]
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Thumbs Up! ->The End of Impact Factors as a Measure of Research Quality [link to post] #article-level #metrics #PLoS
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Hens Teeth or Flying pigs? The End of Impact Factors as a Measure of Research Quality [link to post] #article-level #metrics #PLoS
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I wonder how long it´ll be until the first attempts to game the system? (Then again, people already try to ¨game the system¨ with peer-reviewed publications)
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Reading “The End of Impact Factors as a Measure of Research Quality” on NGS by @wjessen [link to post]
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RT @Berci: The End of Impact Factors as a Measure of Research Quality [link to post]
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The End of Impact Factors as a Measure of Research Quality [link to post] #article-level #metrics #PLoS
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RT @BoraZ: The End of Impact Factors as a Measure of Research Quality [link to post] Znanstvena srenja: VELJA prisluhniti!!!
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RT @BoraZ: The End of Impact Factors as a Measure of Research Quality [link to post] #article-level #metrics #PLoS
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Liked “The End of Impact Factors as a Measure of Research Quality [link to post] #article-level #metrics #PLoS” http://ff.im/-aV1yx
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Many of my students report that their PIs tell them to consider journal mission first, IF a close second, everything else a distant third. In fact, this is how I learned what IF was a few years back — a student asked me b/c he didn’t know what his PI was talking about (and didn’t want the PI to know that he didn’t know!). I didn’t either. A few clicks and wikipedia reads later, we all knew.
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Many of my students report that their PIs tell them to consider journal audience first, IF a close second, everything else a distant third. In fact, this is how I learned what IF was a few years back — a student asked me b/c he didn’t know what his PI was talking about (and didn’t want the PI to know that he didn’t know!). I didn’t either. A few clicks and wikipedia reads later, we all knew.
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Was at David Pendlebury’s "Discover the Power of Quantitative Analysis – The Art & Science of Identifying Future Nobel Laureates", same message don’t use IF as proxy for article influence. Pretty obvious really, but I suppose IF is okay for evaluating journals?
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[...] additional tools such as better navigation (I’m thinking specifically of something like novo|seek or GoPubMed) may increase the value of the [...]
[...] tools such as better navigation (I’m thinking specifically of something like novo|seek or GoPubMed) may increase the value of the [...]
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Article-level metrics RT @notinmy: “The End of Impact Factors as a Measure of Research Quality”: [link to post]
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DeepDyve Offers Scholarly Literature Rental Service [NGS] [link to post] #DeepDyve #research
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“The End of Impact Factors as a Measure of Research Quality”: [link to post]
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RT @NextGenScience: DeepDyve Offers Scholarly Literature Rental Service [NGS] [link to post] #DeepDyve #research
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[...] « Previous article CureHunter: Interview with Judge Schonfeld, part I Next article [...]
[...] « Previous article DeepDyve Offers Scholarly Literature Rental Service CureHunter: Interview with Judge Schonfeld, part II Next article [...]
[...] differ from an information extraction system and how does CureHunter differ from the much hyped Wolfram|Alpha, which calls itself a computational knowledge engine? And GoPubMed uses the term, [...]
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CureHunter: Interview with Judge Schonfeld, part II [NGS] [link to post]
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@jackbullion the semantic search capabilities of GoPubMed [link to post] http://bit.ly/3ZXLGk
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Dear Judge Schonfeld,
the “laundry list” – as far as I understood you right – is the GeneOntology and MeSH (Medical Subject Headings) two well structured ontologies. This is the background knowledge we use to improve search a) guaranteeing completeness and b) giving the user a tool to drill down fast. For example, a search in PubMed for “Heart Diseases” yields 54,231 results. GoPubMed delivers 856,539 results. Why do we get so many more results? It’s because we include all 544 ontological sub-concepts from MeSH and their synonyms found under the concept “Heart Diseases.” This is the big difference between semantic search and key word search and it guarantees completeness of results – of course only as complete as the background knowledge used is. Regarding the comprehensiveness of the article list we can say that we get results from PubMed.org and sort them according to the ontologies (GO & MeSH). We are not better or worse than PubMed, but search results are classified. One last comment to your question concerning the “discovery capabilities” of GoPubMed. Search for Obesity[mesh] and discover for example all associated Nervous System Diseases at a glance. Listed in a well ordered scientifically correct way. This is just one example what other engines can not deliver!
For obesity CureHunter finds 28,067 articles. As seen from GoPubMed more than 130,000 are relevant only in PubMed for obesity. You are missing more than 100.000. I’d argue that CureHunter is not comprehensive.
Best regards, Liliana
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at NGS, interviews with Curehunter’s founder: [link to post]
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Liliana, I apologize for a poor choice of phrase, “laundry list” in talking about extra categorical functions in GoPubMed. The big problem in AI for the last 50 years has not been failure to be inclusive–but how to autonomously execute intelligent discard. CureHunter discards approximately 80-90% of all possible articles that COULD be included–by general search– because its primary design goal was automatic extraction of specific statements of clinical efficacy containing well defined data points that can be used in two types of calculations: Quantified Clinical Decision Support for the use of a drug (relative drug efficacy) and Predictive Analytics, the computational discovery of new disease target applications for existing meds and new cures themselves–using Network Graph Theory Operations over the machine self-extracted data. These calculation systems are built into the CureHunter product and require the input data to be highly filtered to meet the standards typically we associate with hardware-based scientific instruments: Precision, Accuracy, Margin of Error, False Negative Count, False Positive Count, Replicable Results from comparative reference instruments. Because CureHunter is doing predictive data mining and analysis there are vast volumes of “earth” additional material that it does not return to the user. This is not a failure of comprehensiveness but a data filtration decision because we can only use data in calculations that can be specifically quantified. Many articles will comment on many factors of “obesity” or any other disease without ever mentioning that a particular drug, agent, biomarker or other important molecule affects a specific clinical outcome. Thus researchers, patients, or doctors not looking specifically for quantified curative data, should go to GoPubMed and the other good search tools that capture a broad variety of other key subject matter from the library.
Again, I apologize for my poor choice of words.
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New Endeavours in Science Online [NGS] [link to post]
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Dear Judge & readers,
First, I’d like to recall you that CureHunter and novo|seek do not solve the same problems. Novoseek is meant to help people look for the biomedical literature they need to read in a simple and easy way. The idea of novoseek is that when you look for “warfarin”, the bar on the left presents the most relevant concepts related to this search. Therefore you see that “atrial fibrilation” is the most relevant disease related to it or that “anticoagulant effect” is the biological function most related. Based on these, a novoseeker can refine his search quickly and find the publications interesting him for his research, work, etc. »
In addition, I would like to specify something regarding the bar graphs as you explained above. The bar graphs actually show the relevance of the concept with respect to the current search. We do not only count the volume of information available (that wouldn’t be intelligent searching) but we analyze the available biomedical literature with our semantics techniques to return the most relevant concepts. I would recommend the reading of the following article to get an idea of how our technology works http://blog.novoseek.com/index.php/user-experience/the-importance-of-context-in-text-disambiguation.html/
Regards,
The novoseek team
[...] DeepDyve is a search engine designed to make scientific, technical and medical research more easily discoverable and accessible. Truly accessible. Next Generation Science [@NextGenScience on Twitter] reports that DeepDyve Offers Scholarly Literature Rental Service. [...]
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Microsoft Bing Search Begins Using Wolfram|Alpha API [NGS] [link to post]
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[...] Technologies are coming with will enable the Web, not just for documents, but also for data. The Shared Names Project is working on a format to assign universal resource identifiers as names for publicly available biomedical information records and establish a community managed shared infrastructure for providing durable access to documentation about those names. John Wilbanks, Executive Director of Science Commons, talked about the project in a talk he gave earlier this month on Open Source Science. [...]
BioKM: Cloud-based Research Knowledge Management [NGS] http://bit.ly/64puDl #research #knowledge #management
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They do not have Latin America timezones on the registration form. WTF?
The Latin American timezones are now on the BioKM registration form. Sorry about that bug. Hope you’ll give it another shot Marcos.
I think the aim here is research continuity and maybe the aspiration is the kind of infrastructure that would support linked data of the sort discussed in this recent thread: http://friendfeed.com/neilfws/92700c3a/has-our-quest-for-completeness-made-things-too
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Nextgenerationscience has a review of BioData’s lab management service: http://bit.ly/4N2sv3
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Thank you Alex, I will surely register and recommend BioKM now.
BioKM: Cloud-based Research Knowledge Management http://bit.ly/64puDl
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BioKM: Cloud-based Research Knowledge Management [link to post]
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RT @wjjessen: BioKM: Cloud-based Research Knowledge Management [link to post] …A cool product. Looks great for acad research labs.
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BioKM: Cloud-based Research Knowledge Management [NGS] [link to post] #research #knowledge #management
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RT @NextGenScience: BioKM: Cloud-based Research Knowledge Management [NGS] [link to post] #research #knowledge #management
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2009 Top 10 Innovations in the Life Sciences [NGS] http://bit.ly/6VjIQa
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+1 @NextGenScience thanks a great BioKM™ review (and tips): NGS: Cloud-based Research Management http://bit.ly/56YmmW
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+1 @NextGenScience thanks a great BioKM™ review (and tips): NGS: Cloud-based Research Management [link to post]
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checkout the NGS review on #BioKM
http://bit.ly/5JIJoo , many thanks to @NextGenScience
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Woo Hoo ! we got a review on NGS, and some tips also (working on those) http://bit.ly/5JIJoo . thanks to @NextGenScience
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Woo Hoo ! we got a review on NGS, and some tips also (working on those) [link to post] . thanks to @NextGenScience
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checkout the NGS review on #BioKM
[link to post] , many thanks to @NextGenScience
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Nextgenerationscience’s review of BioKM lab management service, good stuff: http://bit.ly/56YmmW
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BioKM: Cloud-based Research Knowledge Management http://bit.ly/64puDl …A cool product. Looks great for acad research labs.
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BioKM: Cloud-based Research Knowledge Management [link to post] …A cool product. Looks great for acad research labs.
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Cloud-based Research Knowledge Management http://bit.ly/64puDl
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[...] 2009-12-20T09:00:08 Cloud-based Research Knowledge Management [link to post] [...]
Want to know more about @BioKM – read a review by Next Generation Science http://bit.ly/56YmmW (via @BioKM)
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[...] The Open Laboratory: Interview with Bora Zivkovic(article #32; 3,398 page views) [...]
[...] BioKM: Cloud-based Research Knowledge Management(article #58; average: 34 page views/day) [...]
The Best of Next Generation Science 2009 – The Year in Review [NGS] http://bit.ly/5Uktob
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The Best of Next Generation Science 2009 – The Year in Review [NGS] [link to post]
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Just posted The Best of 2009 – The Year in Review for Highlight HEALTH http://bit.ly/8b2ogL and NGS http://bit.ly/5Uktob
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Just posted The Best of 2009 – The Year in Review for Highlight HEALTH http://bit.ly/8b2ogL and NGS [link to post]
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RT @NextGenScience: The Best of Next Generation Science 2009 – The Year in Review [NGS] [link to post]
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[...] Focusing on Science via FriendFeed(article #63; average: 65 page views/day) [...]
[...] Open Source Science Commons(article #49; average: 19 page views/day) [...]
The Best of Next Generation Science 2009 – The Year in Review by Walter Jessen http://bit.ly/7PUtij
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The Best of Next Generation Science 2009 – The Year in Review by Walter Jessen [link to post]
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[...] The End of Impact Factors as a Measure of Research Quality(article #51; average: 26 page views/day) [...]
Excellent review of @BioKM by @NextGenScience http://bit.ly/4F64ql
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Science Spotlight: January 6th, 2010 http://bit.ly/6nsPU8 (via @NextGenScience, @wjjessen)
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Our interview with BenchFly founder Alan Marnett in NGS’ science spotlight, thanks NGS!: http://bit.ly/6nsPU8 (@NextGenScience, @wjjessen)
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ScienceOnline2010: Sessions to Attend [NGS] http://bit.ly/5mHRTC .. includes a program PDF #scio10
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ScienceOnline2010: Sessions to Attend [NGS] [link to post] .. includes a program PDF #scio10
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ScienceOnline2010 program PDF – RT @NextGenScience: ScienceOnline2010: Sessions to Attend [NGS] http://bit.ly/5mHRTC #scio10
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ScienceOnline2010 program PDF – RT @NextGenScience: ScienceOnline2010: Sessions to Attend [NGS] [link to post] #scio10
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Yay! Thanks for selecting our panel: “Broader Impact Done Right” — Karen James, Kevin Zelnio, Miriam Goldstein, Rick MacPherson, Jeff Ives and Beth Beck.
We’ll see you Sunday, January 17 at 9:00 am.
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RT @NextGenScience ScienceOnline2010: Sessions to Attend [NGS] [link to post] .. includes a program PDF #scio10
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Thanks Walt!
I too, have been reading through the wiki site trying to decide on which talks to attend. It makes me wish I could clone myself.
There all sound so interesting and it’s so hard to decide. The pdf will be very helpful.
[...] an introduction to the topic and starting point from which to generate discussion (remember, ScienceOnline2010 sessions are held in unconference format, meaning that each will be highly participatory). Medicine 2.0 and Science 2.0 – where do they [...]
ScienceOnline2010: Sessions to Attend | Next Generation Science http://ff.im/-e6fFx
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FriendFeed Science Focus: Week #02, 2010 [NGS] http://bit.ly/8rA1Xa
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Display the ScienceOnline2010 Twitter Hashtag Feed On Your Blog [NGS] http://bit.ly/8gEqEb #scio10
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Display the ScienceOnline2010 Twitter Hashtag Feed On Your Blog [NGS] http://bit.ly/8gEqEb #scio10 (via @NextGenScience)
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Display the ScienceOnline2010 Twitter Hashtag Feed On Your Blog [NGS] http://bit.ly/8gEqEb #scio10 (via @NextGenScience)
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@davemunger Re: Taking your blog to the next level. Display the #scio10 Twitter Hashtag Feed On Your Blog http://bit.ly/8gEqEb
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Fwd: ScienceOnline2010 program PDF – RT @NextGenScience: ScienceOnline2010: Sessions to Attend [NGS] [link to post] #scio10 (via http://ff.im/e3c5K) http://friendfeed.com/e/b3fd5cff-d2a6-448f-9a48-5f78b15045ce
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ScienceOnline2010: Sessions to Attend | Next Generation Science – I will probably simply roll dice to decide [link to post]
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The Open Laboratory: Interview with Bora Zivkovic | Next Generation Science http://ff.im/-ejAl2
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@wilbanks Disappointed you couldn’t make it to talk about Open Source Science. Link to your Oct talk in Cincy: [link to post] #scio10
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The Ope… [link to post]
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FriendFeed Science Focus: Week #03, 2010 [NGS] http://bit.ly/5JDdQ3
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FriendFeed Science Focus: Week #03, 2010 [NGS] http://bit.ly/5JDdQ3
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FriendFeed Science Focus: Week #03, 2010 [NGS] http://tinyurl.com/yeduyjj
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FriendFeed Science Focus: Week #04, 2010 [NGS] http://bit.ly/8uXbvg
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[...] I really enjoyed the unconference format. Several sessions I attended were mostly a presentation and not nearly as engaging. For the Medical [...]
Discussing ScienceOnline2010: Four Questions [NGS] http://bit.ly/aok9h7 #scio10 #science #communications
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Discussing ScienceOnline2010: Four Questions [NGS] [link to post] #scio10 #science #communications
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Discussing ScienceOnline2010: Four Questions http://bit.ly/aok9h7 #scio10 #science #communications
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Discussing ScienceOnline2010: Four Questions [link to post] #scio10 #science #communications
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The passover version of #scio10 RT @galleyproofs Discussing ScienceOnline2010: Four Questions http://bit.ly/aok9h7 (who’s the wise child?)
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The passover version of #scio10 RT @galleyproofs Discussing ScienceOnline2010: Four Questions [link to post] (who’s the wise child?)
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RT @NextGenScience Discussing ScienceOnline2010: Four Questions [NGS] [link to post] (expand) #scio10 #science #communications
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RT @NextGenScience Discussing ScienceOnline2010: Four Questions [NGS] [link to post] #scio10
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Fwd: Discussing ScienceOnline2010: Four Questions [link to post] #scio10 #science #communications (via http://ff.im/f9DEC) http://friendfeed.com/e/bf7266a8-3783-43ed-9035-8aa318466fd7
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RT @BoraZ: RT @NextGenScience Discussing ScienceOnline2010: Four Questions [NGS] [link to post] #scio10
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RT @BoraZ RT @NextGenScience Discussing ScienceOnline2010: Four Questions [NGS] [link to post] #scio10
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Next year I HAVE to get there. RT @galleyproofs Discussing ScienceOnline2010: Four Questions http://bit.ly/aok9h7 #scio10 #science
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Next year I HAVE to get there. RT @galleyproofs Discussing ScienceOnline2010: Four Questions [link to post] #scio10 #science
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RT @eclecticechoes: Next year I HAVE to get there. RT @galleyproofs Discussing ScienceOnline2010: Four Questions [link to post] #scio
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Discussing ScienceOnline2010: Four Questions | Next Generation Science http://ow.ly/12vDO #sci010 Great collaborative post
I’d
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Discussing ScienceOnline2010: Four Questions | Next Generation Science [link to post] #sci010 Great collaborative post
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RT @f1000 Discussing ScienceOnline2010: Four Questions | Next Generation Science [link to post] #sci010 Great post /via @andrewspong ^SP
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Discussing ScienceOnline2010: Four Questions | Next Generation Science [link to post] #sci010 Great post /via @andrewspong ^SP
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RT @andrewspong: Discussing ScienceOnline2010: Four Questions | Next Generation Science [link to post] #sci010 Great collaborative post
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RT @simon_frantz: RT @andrewspong: Discussing ScienceOnline2010: Four Questions | Next Generation Science [link to post] #sci010 Great c
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FriendFeed Science Focus: Week #05, 2010 | Next Generation Science http://bit.ly/bclUrG
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Free Access to the Cloud: A Step Backwards for Open Science [NGS] http://bit.ly/aiP3aS #cloud #computing #open #science
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Free Access to the Cloud: A Step Backwards for Open Science [NGS] [link to post] #cloud #computing #open #science
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Cloud computing – a step backward for Open Science? http://bit.ly/cU7ihb
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Cloud computing – a step backward for Open Science? [link to post]
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RT @cshperspectives: Cloud computing – a step backward for Open Science? [link to post]
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FriendFeed Science Focus: Week #07, 2010 [NGS] http://bit.ly/dls6VH
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Science Spotlight: February 16th, 2010 [NGS] http://bit.ly/aOEwwb
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The Panton Principles for Open Data in Science [NGS] http://bit.ly/cCG3n2 #opendata
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FriendFeed Science Focus: Week #08, 2010 [NGS] http://bit.ly/a0pTT6
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FriendFeed Science Focus: Week #09, 2010 [NGS] http://bit.ly/92y4Im
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FriendFeed Science Focus: Week #10, 2010 [NGS] http://bit.ly/bfvYfS
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FriendFeed Science Focus: Week #09, 2010 [NGS] http://bit.ly/92y4Im
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FriendFeed Science Focus: Week #11, 2010 [NGS] http://bit.ly/9pqJ98
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FriendFeed Science Focus: Week #11, 2010 [NGS] [link to post]
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RT @NextGenScience: FriendFeed Science Focus: Week #11, 2010 [NGS] [link to post]
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RT @NextGenScience: FriendFeed Science Focus: Week #11, 2010 [NGS] [link to post] http://ff.im/-hDqje
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FriendFeed Science Focus: Week #11, 2010 | Next Generation Science http://bit.ly/aEhpo6
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FriendFeed Science Focus: Week #12, 2010 [NGS] http://bit.ly/bkdN8j
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FriendFeed Science Focus: Week #12, 2010 [NGS] [link to post]
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FriendFeed Science Focus: Week #13, 2010 [NGS] http://bit.ly/a0Ypwp
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Networked Science and StackExchange [Next Generation Science] http://bit.ly/95F52J
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RT @NextGenScience: Networked Science and StackExchange [Next Generation Science] [link to post]
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Networked Science and StackExchange [Next Generation Science] [link to post]
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Networked Science and StackExchange [Next Generation Science] http://bit.ly/95F52J
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ResearchGATE: Gateway to Nowheresville [link to post] #science #social #network
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@a__muse Here’s a blog post about it: [link to post]
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Thanks! RT @mrgunn: @a__muse Here’s a blog post about it: [link to post]
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