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Victor / Mendeley Team › Comments
Now Cameron is talking about open notebooks
Mike Chelen, mike seyfang and Richard P Grant liked this
the blog as the lab notebook - with links to files, images, comments
- Jean-Claude Bradley
use mobile phone to write to the lab notebook
- Jean-Claude Bradley
he's showing graphs of his lab notebook objects interconnected
- Jean-Claude Bradley
there are no formal semantics in his system but can use tagging very well
- Jean-Claude Bradley
I"m switching to posting comments to my feed - nobody else here :(
- Jean-Claude Bradley
Well I'm here...
- Richard P Grant
true - 4 people :)
- Jean-Claude Bradley
Five!
- Victor / Mendeley Team
six! (JCB - Can you pls link to your 'comments feed'?
- mike seyfang
blogs are great for text, and tagging provides a form of structured metadata. hopefully the next step will be to integrate semantic web technologies
- Mike Chelen
Help! My Mendeley has gone haywire. It seems every time I open it, it thinks I have 20,000 more documents to add? Now it's up to 63,000. I think I only have 1 thousand something actually. This happened after I'd noticed that "folder watching" had somehow stopped working. I reselected the folder, and now this is happening. Any ideas?
Duncan Hull, Nils Reinton, Björn Brembs and Pedro Beltrao liked this
Paulo, any ideas? ;-)
- Neil Saunders
Neil .. lol
- Deepak Singh
More than odd, to say the least! I'll ask support to check... sorry for that!
- Victor / Mendeley Team
Thanks, Victor. Also, FYI I just reopened it, and it only incremented to 62,976, which is good. FYI: I checked my web account, and there are only 98 pages (about 1960 files), which seems correct. If I reinstall Mendeley, will I lose all of the information I've added to fix citations that were generated from PDFs in my library?
- Steve Koch
Steve, you won't lose anything, because you should be able to get the correct info from Mendeley Web. I assume someone from support has gotten in touch with you by now.
- Mr. Gunn
@Mr Gunn, no tech support yet. To clarify: If I reinstall, and then watch those folders again: will Mendely recognize that the PDFs represent the article already in my online database? Or will it essentially double the size of my library with the newly recognized PDFs?
- Steve Koch
Whoops: just noticed a tweet from Mendley support from 11 hours ago. I don't check twitter that often.
- Steve Koch
I would uninstall the-software-that-should-not-be-named and use some actual good service/program, like Citeulike and Zotero.
- Paulo Nuin
I'm neutral on Zotero (tried it too early, probably). Citeulike is very useful and quite different than Mendeley. The folder watching / auotdetect feature of Mendeley is great, especially for extremely lazy people (99% of everyone). I suppose Zotero is similar in that regard. Mendeley looks like they will be the first service to offer simultaneous markup of shared PDFs by multiple...
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- Steve Koch
The only problem with Mendeley is that it sucks. And nothing can change that.
- Paulo Nuin
any suggestions for good screencast software (the sort for making videos of computer actions ...)?
Daniel Mietchen, Mary Canady, Dan Hagon and 3 other people liked this
I like Screenflow for Mac but it costs money. Camtasia for PC similarly is highly recommended. Jing and similar are fine for short videos less than a couple of minutes.
- Cameron Neylon
screenr.com is fabulous, runs in your browser, very quick to use, uploads straight to youtube if you want. Has set window sizes which helps you fit your demonstration window to include all the action you want.
- Jo Badge
Try http://www.screentoaster.com/ - also runs in the browser, and is apparently free (haven't tried it because I bought Camtasia earlier, which is pretty expensive).
- Victor / Mendeley Team
What OS? I like gtk-recordMyDesktop on Ubuntu, others recommend Istanbul.
- Neil Saunders
mac osx ... also open to ubuntu for the more technical stuff. browser-based sounds fab! thanks guys :)
- Anna Croft
Jing is cool if you want quick, easy and short.
- Matt Leifer
I like Jing as well
- François Dongier
I use and like Camtasia but it is not free - although the 30 day trial is fully functional - Camstudio is free and might work for recording but not editing
- Jean-Claude Bradley
Try Screenr.com - excellent.
- AJCann
I recommend ScreenCamera because it makes live real-time screencasts on Skype, UStream, messengers, or wherever you can use a webcam. http://www.pcwinsoft.com/screenc...
- PCWinSoft
ISHOWU is quite amazing ..its only US $10 or so. creates very compact H.264 codec using files
- Hari
@UofILibrary Mendeley syncs with Zotero - anything you add there is automatically added to Mendeley, so you can actually use both!
Jean-Claude Bradley, Björn Brembs and Richard Akerman liked this
All in good time :-)
- Victor / Mendeley Team
In the meantime, Alexey, you could export RIS. It's not ongoing sync, but it works OK as a one time transfer. I believe you can get RIS for any selected tag or range from connotea, you don't have to get the whole thing.
- Mr. Gunn
From Climax Control Gel to German Shepherd Dogs: The Top 5 Misspellings of Mendeley - http://www.mendeley.com/blog...
My spell-checker suggests Mengele...
- Fergus Gallagher
It must be British spellchecker trained to Mention the War.
- Victor / Mendeley Team
don't mention the war!
- Richard Akerman
Bibliographies here, bibliographies there, bibliographies anywhere! - http://www.mendeley.com/blog...
'Mummi' Thorisson, Steve Koch, Mr. Gunn and AJCann liked this
Showed my 10 undergraduate Junior Lab students Mendeley today. They'll be writing their formal lab reports on OpenWetWare in the next few weeks, and needing some kinds of tools for bibliographies. I hadn't really rehearsed anything, so I just showed them Mendeley desktop and said something like, "There're other things you can use, but this works great, so I'm just going to go ahead and say 'use this'" Then I wowed them with "watched folders" and "copy citation." :)
- Steve Koch
That's awesome, thanks Steve!
- Victor / Mendeley Team
BBC's nature docus never cease to amaze me - stunning! I just wish David Attenborough's narration wasn't so completely devoid of humour.
Careful - you'll be renditioned of you say a word against Saint David. He's up there with the Queen Mother in that respect. Anyway, you're German - what what do you know about humour? :-)
- Fergus Gallagher
In Germany, we take humour very seriously! I am a state-licensed humourist, up to Level 3a (Light Humour with Occasional Yet Recognizable Irony)!
- Victor / Mendeley Team
Do you miss your annual fix of "Dinner for One"?
- Fergus Gallagher
Last weekend, I road-tested Google Folder with three contacts. One response in so far which I've responded to. So having tested this and having previously suggested the likes of Mendeley (which is ace IMO), they asked the following questions. Comments welcome.
Mike Chelen liked this
"Are there any other more low key ways of organising research papers? Something that I can use for my own organising of papers, but can share some papers with other people also. Is there a personal paper organising system that you know of that doesn't need to be signed into, but which through I can share some papers with other people"?
- Graham Steel
Hi Graham - one feature we'll be adding soon is the ability to e-mail papers to others from within Mendeley Desktop, so that the recipient doesn't need to sign up/sign in to Mendeley. In case it helps :-)
- Victor / Mendeley Team
is the goal to avoid your registration for yourself, or for others? zotero website requires signup, but then others can see shared papers through your profile without registering or installing any software, like http://www.zotero.org/mikeche.... there are some sites that can be used entirely without registration, such as http://sharedcopy.com/, it doesn't have understand citation info but can be used for highlighting and commenting on html articles
- Mike Chelen
Hi, I guess you know that if you use citeulike (where I work) your library or a group you set up is public so the others you are sharing with don't need to login (you can't share the actual PDF this way, just the link to the paper on the publisher's website and the metadata). If you want something really low key, where no one needs to login, try Instapaper, but it only allows you to store URL's (no metadata).
- Kevin Emamy
I guess my point here is to build upon this small (but important) project/post on my blog http://mcblawg.blogspot.com/2008... last year. As lay people, we continue to seek methodologies to better allow us to collaborate online in the scientific fields that we have mutual interest in.
- Graham Steel
Hi Chris - the answer is that Mendeley doesn't check the metadata provided in the PDF (because it is usually incomplete and often wrong), but tries to guess the correct metadata from the full-text of the document and checking it against external databases (such as PubMed, CrossRef, arxiv, Google Scholar etc.). However, this is a case where it obviously would make sense to use the PDF's embedded metadata - I just filed an internal ticket for this! Thanks for pointing this out to us.
- Victor / Mendeley Team
merci Mendeley pour la réponse (Cc : @neuromancien @jsicot Bcc: @mendeley_com )
- chris dabin
Just released Mendeley Desktop 0.9.4 -new features include Zotero and LaTeX integration! http://www.mendeley.com/blog/.
Björn Brembs liked this
Is it possible to sync both ways with Zotero? If not, is it planned? Same question applies to citeulike. I would use Mendeley to sync my local and internet(ional) references, which does't really work at the moment. As a consequence, I am not using it at all.
- Oliver Schuster
Hi Oliver, two-way sync with CiteULike is in the works. We've also reached out to Zotero about how to achieve a two-way sync, because we can't get it to work by ourselves.
- Victor / Mendeley Team
Good to hear, Victor! Once you got either of them working, you can sign me up as ambassador for Mendeley.
- Oliver Schuster
What are the current feelings on ResearchGate starting it's own preprint (self archive) service? http://blog.researchgate.net/index... Had a talk with my boss about preprint servers on our way home from a meeting. He thought it was dumb, "They'll all end up in PMC eventually."
Daniel Mietchen, François Dongier, Graham Steel and 9 other people liked this
Speaking as an IR manager, yes, a repository perceived as redundant is a tough sell. If I were you I'd turn the question around. "What could a self-archiving service capture that won't ever end up in PMC? Is it worth the work?"
- D0r0th34
Great point.
- Brian Krueger - LabSpaces
I live the idea of decentralized repositories, but only if there's a widely-used standard way of attaching data to the papers (via rel attributes or whatever) so that they can be searched for. I'm waiting to see what they do here.
- Mr. Gunn
I too wonder of the value of this. However, if they provide programmatic access to get the data out, then I dont care where it was origionally "depsosited"
- Frank
Mr. Gunn: check out OAI-ORE.
- D0r0th34
That's exactly what I'm talking about.
- Mr. Gunn
@Frank, I'd be surprised if they did. Most of their "tools" require a registration and login to use them. It seems redundant to me. Why choose researchgate when submission to PMC is automatic, or you could use a much better established service like arXiv
- Brian Krueger - LabSpaces
I thought a preprint server was for material that may or may not be published, but a self-archive was specifically for versions of a published article. Am I wrong about this?
- Ian Mulvany
Nope, your definition is right. Researchgate's plan is to get one or the other. If the publisher doesn't allow self-archiving, then they want the pre-print. I'm not sure how legal self archiving on another company's site and in their database is though. Seems to go against the spirit of the idea of self archiving
- Brian Krueger - LabSpaces
arXiv is a different animal than PMC, so yes, Ian, you're right. Technically, Brian, they're saying they are just acting as the blog host in this case, which I'll buy. I don't own the server my blog is hosted on.
- Mr. Gunn
@MrGunn, I guess, but that's running in the gray area. I'm sure publishers will see it more black and white than that.
- Brian Krueger - LabSpaces
ResearchGATE currently has a non-trivial number of members (140,000), according to an email message that arrived in my inbox today. A copy of the message is at: http://tillje.wordpress.com/2009...
- Jim Till
yeah, Jim, seems like everyone got that email. They also say they're the first to make an directory of self-archived manuscripts and so on. Some think the numbers to not be what they say: http://www.nextgenerationscience.com/science...
- Mr. Gunn
Personally, Brian, I care about how the publishers want to see it about as much as BoraZ cares what their business model is going to be (http://scienceblogs.com/clock...). I care much more about my rights as an author.
- Mr. Gunn
@Mr. Gunn, my own limited experience with the social networking aspects of ResearchGATE is that the groups I've joined (Science & Publication 2.0, Science Communication, Research in Canada, Feedback) don't compare very favorably with Twitter plus FriendFeed. For a more positive review, see: http://openparachute.wordpress.com/2009...
- Jim Till
@MrGunn, I know ;) Just sayin... @Jill, stating the 140k number is very disingenuous. You can have 3 million members, but if they do nothing, then the community isn't very useful. Researchgate's most active area is the methods forum and there's maybe 5 posts a week in there. What are the other 139,995 people doing there??
- Brian Krueger - LabSpaces
"I care much more about my rights as an author" - keep going, @MrGunn, I like the idea of strengthening publishing cultures where authors keep their copyright in the first place. Generally speaking, as long as an open repository (OR) is fully oai-compliant and everyone can see which of the files claim to have passed peer review, all's fine with me (who has lately started to run an OR...
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- Claudia Koltzenburg
Yes, Claudia, that's my take as well. Providing a repository is great, let's have more of that, but make sure it's open and can be part of a web of other open repositories.
- Mr. Gunn
It'll be interesting to see how access to the DB will be handled. Currently you have to be registered to do anything there. The hardest part of getting something like this to work will be compliance. It'd be great if people uploaded and provided their own metadata to a repository like this. But I can see populating this DB with metadata being tedious.
- Brian Krueger - LabSpaces
does e.g. Mendeley provide an oai-compliant OR yet?
- Claudia Koltzenburg
@Brian. To address the 'tedious-ness' issue: could not metadata for individual (or sets of) papers be harvested from CrossRef on the fly? They offer an OAI-PMH service: http://www.crossref.org/help... (note: I've only recently started looking at OAI, so dunno if this is a silly proposition).
- 'Mummi' Thorisson
@Brian, so far, I've uploaded the full text (PDF) of only one publication into the ResearchGATE repository. There was no requirement to provide metadata. See: https://www.researchgate.net/publica...
- Jim Till
Just added a 2nd full text (another PDF). I've also added a couple of comments about this publication. Haven't tested whether or not the comments can include html tags (can't preview or edit comments): https://www.researchgate.net/publica...
- Jim Till
That's pretty nice. It automatically found the metadata for the article? Or did you have to plug in the title somewhere when you uploaded?
- Brian Krueger - LabSpaces
@Brian, the title of the 2nd publication was obtained (by ResearchGATE) from arXiv. However, the arXiv version of the full text is in html, so I uploaded the PDF (the version in Learned Publishing). BTW, I've just tried adding links to a Comment in ResearchGATE, and they work (with no added html tags required). See: https://www.researchgate.net/publica...
- Jim Till
Claudia, I know Mendeley is currently looking into OAI compliance and it would probably be easy to implement. In fact, they're at the point where they want more input from librarians about this sort of thing, so now would be an ideal time to bring this up. I'll see if I can get a more substantial answer for you.
- Mr. Gunn
Claudia: To answer your question, we're not OAI-compliant yet, but we're looking into releasing APIs to our database soon. Also, as I mentioned during a conversation with Peter Suber back in March (http://www.earlham.edu/~peters...), we've been encouraging our users to self-archive on their Mendeley profiles as well. So if ResearchGate is "the first...
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- Victor / Mendeley Team
@Victor, when they launched they were also the first social network for the sciences (ignoring the fact that Nature Network had been up for a year already).
- Brian Krueger - LabSpaces
Surely the difference with ResearchGate is that they automatically check with RomeoSherpa so that you know whether the publisher of a given paper allows self archiving. Mendeley, SSRN, RePEc etc don't do this
- LibRat
Sounds great! Doing as good and thorough a job as PMC would be a challenge, but it's worth trying and the more decent options researchers have the better.
- Mike Chelen
@LibRat - good point, thx
- Claudia Koltzenburg
@Victor / Mendeley Team, thank for sticking your head out here, in my view of the matter, an automatic check with RomeoSherpa would certainly be a must for any oai open repository (OR) projects for Mendeley, too :-)
- Claudia Koltzenburg
"140,000 members" - but how many signed up, looked around and never went back? And can you delete a ResearchGate account? There are sites (yes, you SciLink) which don't provide a delete link and ignore repeated pleas for deletion. One way to keep the numbers up.
- Neil Saunders
Any concerns about archiving a thread like this one via WebCite and then linking to it in a blog post?
- Jim Till
Neil: I agree, total registered users isn't the best metric - would be more helpful to measure active users, or average time spent on the site.
- Mike Chelen
Jim, you may have already done this, but this item does have a permalink: http://friendfeed.com/the-lif.... Surely it's better to link directly to the item than via a secondary site (also a problem with shortened URLs)?
- Mr. Gunn
@mike, they'd never ever do that. There's a reason they throw around that bloated number.
- Brian Krueger - LabSpaces
@Mr. Gunn, how permanent is the FF permalink URL? I`ve been assuming that both the long URL (http://friendfeed.com/the-lif...) and the short one (http://ff.im/89VkB) will rot. Hope that I'm wrong.
- Jim Till
Jim: as far as web pages go, these are pretty reliable. the URL would stop working if the group name were changed, in which case the ff.im link would still work, unless the topic were deleted. it's also good practice to save a mirror with a bookmarking site such as http://diigo.com or http://sharecopy.com
- Mike Chelen
I've linked to this thread in a comment on my blog: http://tillje.wordpress.com/2009...
- Jim Till
This thread has also been bookmarked on Connotea: http://www.connotea.org/article...
- Jim Till
Getting back to the start of this discussion, why should I be interested in archiving in a repository if there is PubMedCentral? Shouldn't I rather be interested to get more stuff into PubMedCentral, e.g. by starting PubMedCentral UK (already in the works) or PubMedCentral Germany? Both Archiving and searching in a central database is much easier.
- Martin Fenner
We shouldn't forget that PMC has a limited remit. If you are outside that remit (e.g. publishing plant work, or any non-biomedical field) then your papers are not welcome in PMC. Perhaps ResearchGate has a role for these fields.
- Frank Norman
@Claudia Re. how long will PMC be around, I think it has a better chance of longevity than the majority of online services. It is part of the Natl Lib Med, which is part of NIH. PMC is also mirrored in UK at the Brit Lib and (soon) will be mirrored elsewhere. It would take a lot for all these to fail.
- Frank Norman
@Frank, yes, well, this was a rather implicit footnote of mine pointing to a prevailing cultural habit that seems to say something like: the biggest must surely be those who last longest... hence deserve most trust by scientists, too. hm... @Martin, any decentrality - centrality debate is of course highly important in Computer Science (and LIS) fields. My take on this is that what seems...
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- Claudia Koltzenburg
The BBC Asks, Does Brain Training Work? - http://psychcentral.com/blog...
Bora Zivkovic and Graham Steel liked this
Live on BBC i-player here (UK peeps only) http://www.bbc.co.uk/iplayer...
- Graham Steel
Quite. And with an 'n' of two, scientifically invalid, as they admitted, and far from convincing. Will a larger 'n' produce a statistically significant result/data? Probably not, nut time will tell.
- Graham Steel
"Will the BBC's mass participation experiment be published in a journal"? Yups, I thought about that too and agree that it's (probably) unlikely.
- Graham Steel
J Med Hypotheses - LOL
- Graham Steel
I do find most of the stuff on Bang Goes The Theory rather disappointing... it's thin and stretched even for Pop Science.
- Victor / Mendeley Team
Watch Mendeley live on the Web! Science Hour with Leo Laporte & Dr. Kiki - http://www.mendeley.com/blog...
Ricardo Vidal, Graham Steel and Peter Binfield liked this
I think that "Where" link should be http://live.twit.tv/
- Fergus Gallagher
Thanks Fergus. Updated it!
- Victor / Mendeley Team
Was too late for me to participate in this last night but have just watched it. Currently uploading the download so I can embed & blog about it. Great input, Jason and Pete !!!
- Graham Steel
Box #2 of PLoS swag winging it's away (shortly) from San Fran to Glasgow.Which is nice... #PLOS
Björn Brembs, Karen James, Jim Hardy and 2 other people liked this
It arrived today. Have a stack of PLoS t-shirts in various sizes/designs. I now need to think of a cool way to give them away to folks that will wear 'em (I already have 4) . Any ideas?
- Graham Steel
prizes ;)
- D0r0th34
Exactly. But what for?
- Graham Steel
send them to people who research blog an article from one of the plos journals? Or just people who ask politely? :D
- Allyson Lister
Nice one, Allyson. Will run this by Dave Munger of researchblogging.org
- Graham Steel
And have now done so.
- Graham Steel
Me! Me! Me! Want! Want! Want! (subtle, huh?) :)
- Ricardo Vidal
@ Ricardo, (you is as subtle as a brick shaped object) what size are you? I'll trade you one for a Mendeley one :)
- Graham Steel
Since I've yet to hear back from Dave M, plan T is now underway. Here are the shirts http://www.flickr.com/photos... Top row middle is now winging it's way off to Dr H Gee of Nature.com http://twitter.com/McDawg... even though, this might be rejected via i-stone !!. Ricardo V (shirt size yet to be disclosed) might have another (he has 12 hours left to comment) , so there are still four avaliable for free from me as matters stand. Code = ask politely/candidly. #PLOS
- Graham Steel
After what I suffered in the link posted above, I think I would be extremely happy to have a new PLoS T. Thanks!
- Paulo Nuin
Paulo, one can still do S, or L or XL. (One XL one went to someone in Cromer). Name your size and it will be shipped. ONLY three left now and you folks must try harder to convince me give this stuff away, err convincingly. (Each pack will contain other PLoS goodies too).
- Graham Steel
I will take the L. Can you send me an email with whatever you need? Maybe it's too far for you to ship :-)
- Paulo Nuin
And the L will be shipped to Paulo later in the month. So what's left? After a re-count, 2 S and 1 XL. Rather than simply giving the last 3 away in the manner thus far, one shall devise a competition and three lucky winners will get the last of the pickings.
- Graham Steel
Hmmm - somehow this comment thread dropped off my first few FF pages... Good luck with the competition, I might be a M but I'm not a S, so I'll pass :)
- Allyson Lister
Competition Idea ! As matters stand, me thinks it's boiling down to some form of pub quiz thang down in the, err pub after Science Online London http://www.scienceonlinelondon.org/blog... It will last for 5 - 10 mins and will be called "Who's Round Is It Anyway" Whilst the rules will be made up as we go along, the Host (not me) will ensure 'fair-play'. Cheating will be allowed within reason. 10 Prizes up for grabs inc. a priceless mystery top prize !! #solo09
- Graham Steel
Above comment updated, nudge.
- Graham Steel
Graham - I'll happily take you up on the trade-for-Mendeley shirt! :-) Yes yes yes!
- Victor / Mendeley Team
Game on. Must dash - I have a train to catch...whooosh
- Graham Steel
I recently posted on researchblogging.org and have published in PLoS ONE. Does that qualify me for one of the red or black ones in size M?
- Karen James
Did I read Mendeley shirt? (am actually wearing one of my PLoS One shirts right now...)
- Björn Brembs
By the time I got round to playing "Who's Round Is It Anyway" most folks had gone, so I adopted a new strategy under the circumstances. In the end, the priceless mystery top prize was won (at random I hasten to add) by Brian Kelly:- http://farm3.static.flickr.com/2664... On Monday, 2 shirts went to Victor and Jan @ Mendeley. Thanks guy's for the Mendeley shirt in return...
- Graham Steel
Plenty of Fringe Frivolous and Science Online London 2009 Pictures! http://www.mendeley.com/blog...
Michael Habib, F1000, Duncan Hull and 2 other people liked this
Great pictures! Please add them to the Flickr group: http://www.flickr.com/groups...
- Martin Fenner
Done :-)
- Victor / Mendeley Team
Far out: Speculations on science communication 50 years from now: John Gilbey
Martin Fenner, Bora Zivkovic and AJCann liked this
John introduces the University of Rural England, a fictional place where students and faculty suffer the same weaknesses.
- Martin Fenner
Dead tree media will become history?
- AJCann
Google wave will be history?
- AJCann
+1 AJCann
- Bob O'Hara
i can tell my future involves a nice cold pint :)
- Ian Mulvany
Forget the monkeys, black swans loom over the horizon.
- AJCann
For many people the present is the future. People born before 1980 still know a world without computers and for us a lot what we use today is futuristic.
- Martin Fenner
Ian, so your clairvoyance only extends about 90 minutes into the future?
- Victor / Mendeley Team
Them, Martin? Are you really that young?
- Bob O'Hara
Climate change and tipping points?
- AJCann
when the lizards rule, experiments on monkeys will be a lot less controversial
- Ian Mulvany
At least Second Life will be history.
- AJCann
Ian, they turned off the air condition so we buy more at the bar downstairs ;).
- Martin Fenner
Bob, I'm younger in my mind. But was born before Woodstock took place.
- Martin Fenner
A backup is not an archive.
- AJCann
We need robust mechanisms to protect knowledge offline.
- AJCann
This is the third time in a few weeks that I heard about the importance of making backups of digital information as a great challenge in the future. Have to think more about this. John was showing an old floppy disk with a PhD thesis on it. My thesis is on a floppy disk written with a word processor/operating system that has been dead for many years.
- Martin Fenner
You don't have paper copies of your thesis Martin? I do of mine.
- AJCann
Of course I have paper copies. This just shows that analog formats might still be the safest format for storing information.
- Martin Fenner
The technology horizon is 5-7 years. Predictions beyond that are speculation.
- AJCann
Question is: Why hasn't the future happened yet? :-)
- AJCann
Sigh. Paper is an inherently unstable medium. We should be publishing on stone (Twitter -> Chipper?)
- AJCann
(This was a great way to finish the presentations at Solo09. Thanks!)
- Allyson Lister
http://twitter.com/stressr... "As a geologist, I find "set in stone" to be a very odd metaphor for permanence."
- Bora Zivkovic
so what exactly happens at the "technology horizon"? just another fancy word for the allmighty singularity?
- laura
Jeremy John of the digital archives project at the British Library can read all these old formats in the digital scriptorum he's built. Impressive. (includes paper tape and punch cards which were not shown in this presentation but which I recall my parents using way back when).
- Maxine
After the conference is before the conference: would really like to see a session on digital archives in a future conference.
- Martin Fenner
a session on digital archives sounds good, Martin. Perhaps librarians and infoscientists can do one in January in NC? Rile them up!
- Bora Zivkovic
Jeremy John would be my recommendation. Was an evolutionary biologist before heading up the BL digital lives project.
- Maxine
Thanks, Maxine. Do you know him and have contact info for him? Perhaps give him a heads-up?
- Bora Zivkovic
Yes, I know him - have been involved with his project. Here's the link to him and all about his project/conference. http://www.bl.uk/digital... I'm sure he'd be delighted to come to the conference and/or suggest appropriate speakers for specific aspects of this rather large subject, if you want to "drill down" into one particular specialism. (See digital lives conf programme - http://www.bl.uk/digital...)
- Maxine
Fixed a bunch of my Mendeley references last night by looking up the Pub Med ID...if someone else uploads the same PDF, is their reference data going to be correct because of my entering of the PMID?
suelibrarian and Mr. Gunn liked this
I wish there were such cross-comparisons - this would be very powerful!
- Björn Brembs
When I first noticed Mendeley six months ago, for some reason I thought that was a major point of the service...but now I'm realizing it doesn't do that?
- Steve Koch
Steve - we did have this feature enabled in the beginning, but it needed a lot more tweaks, so we switched it off. Will be available again later this year!
- Victor / Mendeley Team
Cool, Thanks, Victor
- Steve Koch
it's hard to make sure that good data propagates while preventing bad data from propagating
- Richard Akerman
well, the fact that Pub Med is "correct" makes it a lot easier. currently you have to go find out what the Pub Med ID is, cut and paste it in, and then click the "lookup" icon. I'd think if the PDFs are almost identical in the first few pages, then it'd be almost always correct to assign the known pub med ID. If not automated, the process could be 10x easier by suggesting "is this the correct title from Pub Med ID" to the user. This would prevent having to go look stuff up and cut and paste.
- Steve Koch
or, I suppose embedding a pub med search feature in the mendeley window would be another good time-saving step
- Steve Koch
Yes, I agree :-) Also, since the 0.9.1 release, Mendeley Desktop should automatically query PubMed for each new PDF so as to retrieve the PMID and associated information. Please let support@mendeley.com know if there are PDFs where it doesn't work!
- Victor / Mendeley Team
I really liked that feature, too, but with the automatic lookup it makes it something that helps Mendeley internally more than the end user.
- Mr. Gunn
I actually didn't know that newly added PDFs had the PubMed lookup. I was looking through the 100's I'd uploaded long ago. I agree that it's more unnecessary with the auto-lookup feature.
- Steve Koch
afraid I'm locked into Endnote, you can import citations easily to zotero but what about the attached pdfs (almost 100+ of them).
suelibrarian liked this
Add citation; click Attachments; Add -> Take Snapshot of current page (copy of PDF is saved).
- Susan Nelson
Thanks but I don't really feel like doing that over 100 times just to export to zotero
- aarontay
The PDF files are stored in a folder on your disk, right? Does Mendeley not read them properly?
- Mr. Gunn
what's the point of the web version of mendeley,u can't view full text of papers you have in desktop version?
- aarontay
That's planned. Long term, the web will mirror the desktop version. Atm it's for online mgmt/sync across PCs.
- Victor / Mendeley Team
Currently fixated on Mendeley. How have I not previously known the wonder that is Mendeley? I'm still waiting to be disillusioned. Might teach it to a comps seminar this fall.
Hmmm... Maybe I should introduce myself to this wonder of the Internet.
- lris
Hi Kristin - delighted that you're enjoying our software! In case you ever get disillusioned, please just let our support team know (support@mendeley.com) and we'll try to help you out. Also, drop me a line (victor.henning@mendeley.com) if you need any teaching material - we've prepared a bit. Greetings from London!
- Victor / Mendeley Team
new to me - how does it compare to Zotero? We have RefWorks but I am beginning to hate it; only make a point of teaching it for classes using a CSA database heavily.
- barbara fister
I've got a huge directory with PDFs of papers. Any idea how I can get those into CiteULike (both the reference and the PDF)?
Michael Habib, Alexey, Mitchell J Stanton-Cook and 11 other people liked this
Jan, have you tried Mendeley? http://www.mendeley.com/
- Graham Steel
Yes. But our department has a group on CiteULike, so we're stuck with that at the moment. Also, I seem to remember that Mendeley was not polished enough yet to start recommending it to my not-all-of-them tech-savvy colleagues.
- Jan Aerts
Noted. Thank you.
- Graham Steel
I just saw something about integration between Mendeley and CiteULike. I wonder if I can load my PDFs into Mendeley and then synchronize them with CiteULike.
- Jan Aerts
Graham's idea was probably to feed your PDFs to Mendeley, which would extract the reference details, and then export them as a standard BibTeX format to import in CiteULike. To attach your PDF files, however, I would say that you are stuck — CiteULike doesn't allow bulk or scripted upload, does it?
- Enro
Mendeley's PDF information extraction is very bad, very. In my case for around 1000 files it missed about 40%, especially if you have some old papers and papers with malformed markup. I can't tell you about the integration between both services, but it might be your best bet.
- Paulo Nuin
How huge is huge? I think the general experience is that Mendeley isn't bad for small numbers but if you are talking hundreds or thousands you'll have trouble. Also not sure that you can push from Mendeley to Citeulike yet? It's on the roadmap but not there yet as far as I know. I think there is a citeulike API but I couldn't find up to date information on it.
- Cameron Neylon
citeulike plugin documentation: http://svn.citeulike.org/svn...
- Cameron Neylon
if you have a Mac, you can try to import into Mekentosj Papers, and then export to bibtex and import this in CiteULike. Papers will try to extract the citation, but to be sure, you will need to match against PubMed. If the PDF has a doi embedded, this takes two clicks per PDF. If not, a few more.
- Michael Kuhn
First option could be to send a POST request to www.citeulike.org/personal_pdf_upload with article_id, username, file, and submit fields.
- Michael Barton
Second option would be to use ruby Mechanize to automate going through each web page and clicking relevent buttons and form fields.
- Michael Barton
Those above two options were aimed at getting the PDFs uploaded
- Michael Barton
This doesn't really solve your problem, but just FYI - SyncUThink - http://www.andrewberman.org/project.... The code might give some insight into automating PDF upload to CUL.
- Neil Saunders
Hire a grad student to do it. They are poor and expecting continued poverty, so they work cheap. :-)
- Bill Hooker
We are still working on a two-way sync with CiteULike. Cameron is right, at the moment you can't push your data from Mendeley to CiteULike, unfortunately. We are also trying to improve the quality of the metadata extraction (e.g. via DOI's or ID's from PubMed and Arxiv, which however is a hard thing to do for scanned PDF's), as well as the stability of Mendeley when handling larger numbers of PDF documents (>3000).
- Jan / Mendeley.com
I think SyncUThink will do it for you, but I think you'd have to rename your files to match CiteULike's convention. Should be pretty quick to give it a try for 1 or 2.
- Fergus Gallagher
Sign up for Labmeeting and you can upload all your PDFs right away... it will autodetect the reference (most of the time)
- David Caplan
Hmmm "Thousands of researchers around the world already rely on Labmeeting...." http://www.labmeeting.com/signup
- Graham Steel
... and I'm not one of them!
- Paulo Nuin
Jan: For those scanned PDFs where DOI extraction is tricky, have you considered calculating a hash (ie SHA1) of the PDF file, or maybe some image fingerprinting (to deal with self-scanned papers and publisher watermarks) ? If you keep a shared database of hashes + user contributed reference metadata, eventually you may find that once one user has manually entered the metadata for an...
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- Andrew Perry
Hi Andrew - exactly what you're suggesting is on the roadmap! :-)
- Victor / Mendeley Team
Is there a lime juice crisis? Can't find any in the shops. All I have left is this lime-green foam ball http://twitpic.com/cvv9q
 |
Victor. I can report a (fresh) Lime drought up 'ere in Glasgow a few months ago, but we're sorted now. Someone is clearly buying 'em all up. Surely, surely, it can't be that fella from Del Monte ??
- Graham Steel
A picture is emerging from the fog, then! Some supervillain residing in the highlands of the north clearly needs lime for his evil plans. He first bought all the fresh limes up in Glasgow, then realized that buying juice is more effective, hence started to buy his way down south as supplies in the north ran out. Oh, what he is planning with the limes I cannot fathom, but surely it must involve that sweet, warm, delicious lime fragrance!
- Victor / Mendeley Team
Thanks, Victor. Lime Scale level 2. Some reports just in from Manchester, The Isle of Barra and Cromer of similar lime related disappearances. The latest twist. My sources at the BBC tell me that tonight's Crimewatch has been nenamed Limewatch in light of the seriousness of the issue. Concerned members of the UK public have been advised to call the Lime-Stoppers hotline. The man from Del Monte has been ruled out of enquiries however http://www.youtube.com/watch...
- Graham Steel
:-))) Brilliant! Ooooh, and if you understand German, the Del Monte man is even more hilarious!
- Victor / Mendeley Team
Dramatic new twist. Less than an hour ago, when I was entering Glasgow Central Station, I spotted not 1, not 2, but 3 BOXES brimming with fresh limes. The limes were being given away for free to (unsuspecting) members of the general public along with a 16 page copy of "The Friday" by The Daily Torygraph by 4 reps working on behalf of Gordon's Gin. I didn't have a camera with me, but...
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- Graham Steel
Gordon Ramsay does have a good charismatic supervillain face!
- Victor / Mendeley Team
If you wanted to scan a thousand books, how would you do it? I'm looking into digitizing my library.
Christopher Granade, Fiacre O'Duinn, Brian Ahier and 5 other people liked this
Maybe look up how Google is doing it?
- Meryn Stol
If you bought any of those books from amazon, then some of them may be searchable through your "amazon library". Having said that, it's spotty coverage (in terms of which books are indexed). Same thing for google.
- Ilya Grigorik
I would first look on certain websites (which I would obviously never use myself and certainly don't know the URLs of) to check whether somebody has already scanned them.
- Matt Leifer
Meryn - Done that. Not much help...
- Michael Nielsen
Ilya - I probably bought a couple hundred (or more) from Amazon. SO that's a great idea.
- Michael Nielsen
Incidentally, I found http://sealedabstract.com/... very helpful on this subject. But it'd still be hundreds of hours of work, minimum.
- Michael Nielsen
I never realized I could search through my Amazon purchases. Interesting. Quite a value-add from Amazon!
- Meryn Stol
Looks like Google will give you full access if you scan the barcodes: http://booksearch.blogspot.com/2009... Not clear if this is useful for re-reading, or if it's possible to download...
- Michael Nielsen
I tried that.. no dice. It only works for books that have been "open sourced" by publisher or are not under copyright, which is to say, basically nothing. Ok, not entirely true, but of limited value..
- Ilya Grigorik
Thanks, Ilya. That's one weird Google blog post, then. ("It works for all the books except the ones it doesn't work for. That is, most of them.")
- Michael Nielsen
the way I understood the Google barcode scan was that since it appears you own a physical copy of the book, you can have access to a digital copy. Am I wrong in this, because I was going to do it for my books.
- Kimber Scott
from BuddyFeed
Kimber, yes, but the amount of digitized books on Google Books is limited. Actually, the bar code does not constitute proof of ownership. You can do fulltext search through all books on Google Books. But with "my library" you can limit your search to a group of books. (Pedro, yeah exactly)
- Meryn Stol
I just gave it a try. I scanned a couple of barcodes but its really just a faster way to create a list. I don't think the access rights changes at all.
- Pedro Beltrao
That's the thing.. The scan just gives you the ISBN, which you can find anywhere anyway - it doesn't prove that you own the book in any way, shape or form. For this reason, only books that are not copyrighted are available for search.
- Ilya Grigorik
Ilya, there are copyrighted books searchable on Google Book search. Just not all of them because not all publishers have signed up for the program, or have not committed their whole library. Full search does not mean you can read it in full though!
- Meryn Stol
Ah, well that's good news! Now we just need to get all the other publishers on the same bandwagon. ;-)
- Ilya Grigorik
Major project! I guess ideally, there'd be a way to prove that you own a legitimate copy of a book which would then grant you access to a digital version. Something like scan and upload one page.
- Neil Saunders
Neil - Yeah, that'd be very nice. Sadly, I haven't found anything like that.
- Michael Nielsen
yeah, but that's not going to happen either - publishers are more than happy to charge you twice for the same material - once for print and once for e. Related, Springer now has a $25 print on demand service available to patrons of libraries that buy the big ebook packages - we only have it for medical books right now, or i'd try it
- Christina Pikas
Maybe a pragmatic 80/20 split - re-buy the most important books (those that are not from Amazon) as e-books; then decide if you want to cut off the binding on the remaining books and have em scanned (as suggested in article), or make do with a semi good scan without damaging the book (pay a student to run them through a copy/scanning machine).
- Christof TD
Please try to save the integrity of the book. You may find that they will be quite valuable. Were some of them gifts? Do they have inscriptions you want to keep? Some things to consider.
- Melanie Reed
On 2nd thought you'd better wait a little (machines like the Google book scanner should become more readily available soon) - reading about the Google Book Scanning Machine: http://www.npr.org/blogs...
- Christof TD
Here we go - Book Drive Pro (looks quite industrial; but still doesn't solve the page-turning problem) - http://pro.atiz.com/ or http://mini.atiz.com/ (video on the pro version site shows the scanning workflow); ~several hundred hours for 1000 books... at least it gives you a high-quality outcome without damaging books
- Christof TD
Hmm - you could build this thing yourself (Atiz Book Drive Pro): make a V-shape cradle, including a plastic V-shape that comes down on the book (like in the video), several mounts for two DSLR cameras and a little black tent with lights -> then run an edge-detection algorithm on the pictures taken using the Python Imaging Library; this leaves only finding an open-source OCR library.
- Christof TD
Christof - For all but a tiny fraction of the books (which I'll probably keep), I'm not worried about destroying them as part of the scanning process. Your 80/20 suggestion is a really interesting one...
- Michael Nielsen
You could donate the destroyed books to a local school science library; maybe the library will find the resources to glue them back together again :-)
- Christof TD
More likely the library will waste valuable staff time and resources evaluating and then discarding a book the school cannot use. Please don't use libraries as a dumping ground! Thank you.
- D0r0th34
If you are a DIY person check out http://www.geocities.jp/takasci... and http://www.instructables.com/id... . My personal solution (I got of most my books some years ago - some I kept and scanned them manually) is a change of mindset. Most books are just dead trees that catch dust and are need much to rarely to excuse...
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- Konrad Förstner
Thanks for the link: http://www.instructables.com/id... ...this was exactly what I was thinking (see video at that link for workflow); 20 min. for each book is not too bad. Update: their open source software takes 3 hours to process a book into a PDF.
- Christof TD
Here's my stupid idea: 1) The most difficult part: Build a little stand that automatically flips through the pages - probably doesn't need to be as sophisticated as in the Instructables link above. 2) Take a HD video cam and make a video of the pages being flipped. 3) Write a little script that takes screencaps from the video every other second, after the pages have been flipped. 4) Send all the screencaps to Evernote to use their OCR and search.
- Victor / Mendeley Team
But then again, it would probably be easier to just sync a photo camera with the page flipping :-) Like I said, stupid idea!
- Victor / Mendeley Team
Here are the heavyweights: Treventus Book Scanner Robot (at Bavarian State Library, Munich) - http://www.treventus.com/booksca... and Google/ Microsoft supposedly use Kirtas high-performance scanners - http://content.zdnet.com/2346-95... ... ah, the page-flipper uses suction: http://www.kirtas.com/
- Christof TD
Video of Treventus ScanRobot in action: http://www.youtube.com/watch...
- Christof TD
Ah, sweet.. Now i just need one of those for my house! :-)
- Ilya Grigorik
buy a high speed scanner
- abuzarhamza
abuzarhamza - Even at 20 pages per minute, with roughly 300,000 pages that's roughly 300 hours of scanning...
- Michael Nielsen
How about this: (1) create a new organization called the Nielsen University library (2) offer your library's collection to google to become part of their scanned collection (3) make the one condition of the offer to google be that you get the scans for private use
- Jonathan Eisen
I suppose that this would not be a good time to point out to you that ownership of the physical volume doesn't entitle you to scan the content and create a digital version; that's what got Google into trouble in the first place. You, as an individual, haven't the right to create (even for personal, private use) digital versions of content where other entities hold the rights.
- Jill O'Neill
Don't forget that Michael is covered by Canadian law, which is significantly more lenient on copyright than US law. That's why I suggested finding pirate copies on the net. I believe that under Canadian law might not be liable for downloading them, but only for uploading. However, the situation is complicated so don't quote me on that. After downloading, you are in no better or worse shape than if you had scanned the books yourself.
- Matt Leifer
I note - I had my tongue planted deeply in my cheek when I said he should get google to do the scanning - just in case people cannot see where my tongue was
- Jonathan Eisen
Jonathan: Your original comment gave me, at least, quite a smile :-). Sadly, I can't imagine Google would find much in my library that they don't already have. Maybe the classic "Venus on the Half Shell"...
- Michael Nielsen
Jill - Is it true in Canada that you can't legally transfer between media in this way? I know I've been told that in some jurisdictions this definitely _is_ allowed, but I don't recall in which jurisdictions.
- Michael Nielsen
Michael: I was speaking from a US-centric view. That said, I would be surprised if -- to pick a publisher at random -- HarperCollins (whether US or Canada) would look favorably on such scanning activity. Libraries are permitted to scan for purposes of preservation under specific conditions, but I am not sure that the same permission has ever legislatively been extended to private...
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- Jill O'Neill
Have you read Victor Vinge's Rainbows End? ok it's a bit extreme but it works for gene sequencing :)
- Alexei
the fujitsu snapscan is reasonably good but v manual and destructive, I've taken to guillotining spines and feeding pages while watching tv .. ~ couple hrs / book. End result not that good, big bulky pdfs. Getting eprints would be much better.
- Alexei
Thankyou, by the way, to everyone who's been commenting on this!
- Michael Nielsen
If you want to use all free and open source tools, read this blog post: http://philikon.wordpress.com/2009...
- Nate Aune
Mendeley: an extremely short review (sort of) - http://blindscientist.genedrift.org/2009...
Ricardo Vidal, Steve Koch, suelibrarian and 3 other people liked this
Yeah, I wasn't so impressed with their PDF meta-data extraction, and gave up.
- Bosco Ho
That makes three of us (another one is a commenter on Blind.Scientist)
- Paulo Nuin
Well, I apologized to two of you already - Bosco, sorry if it didn't meet your expectations. Please keep in mind that we're still only in beta 0.6.3 - we're working on both speed and extraction quality. Beta 0.6.4 (next week) should almost double the extraction speed, beta 0.7.0 (in roughly six weeks) will use more external databases (e.g. PubMed) to improve extraction.
- Victor / Mendeley Team
No apology needed. Just keep working on it. One disappointed "customer" is not the end of the world.
- Paulo Nuin
I've been pretty harsh on some bookmarking services over the past years myself, so I understand how hard it is to please early adopters like us.
- Mr. Gunn
I was testing two versions and both constantly crashed during indexing (in random places, so it's not the matter of a single pdf with errors). As Paulo says, maybe one day.
- Pawel Szczesny
Well, I must have realy low expectations then, because I like Mendeley :-)
- Björn Brembs
To be fair, mendeley is competing against endnote citeulike zotero and papers. The only way for mendeley to steal users is to provide the killer feature the others don't have and that is afaik pdf meta-data extraction.
- Bosco Ho
I don't understand why they try to rely so much on the metadata extraction from the PDF itself (I might be wrong). It would be much easier, maybe slower but easier, to extract the DOI from the PDF and then get the metadata and PDF text online. The program already spends a good amount of time computing things, why not do it by accessing the data online? In my case I tested with 500+ files, I wouldn't mind if it took a couple of hours getting the data online, but eventually getting the information correctly.
- Paulo Nuin
The Zotero v1.5 beta does have a PDF metadata detection feature, although I haven't used it myself yet so I don't know how well it works: http://www.zotero.org/blog...
- John Dupuis
Paulo, I believe that's what Victor was talking about doing in his comment above. Bosco, I don't think it's a Zotero or citeulike vs. Mendeley situation. Mendeley tries to work more like an "itunes for PDFs". When you've already got an existing collection of PDFs on the desktop, it's not easy to convert that into a library in a online reference manager. It's also nice to be able to do a full-text search across your library and share files instead of just links.
- Mr. Gunn
In that respect, Mendeley stands to get more converts from Endnote than from citeulike or Zotero, and that's something that I think we can all support, right? That's my motivation for working with these guys. I sought them out, they didn't approach me, and I did so because, although they didn't even have the bookmarklet out yet, I think they're closest to having the total package.
- Mr. Gunn
I love Zotero and they've really done a great deal to force innovation on the rather stagnant field of academic reference management, but I just have a better feel for the direction in which Mendeley's heading with the recommendation and sharing features, and they're moving fast. Also, I guess I just prefer a desktop app for some things. I don't like a web service or firefox addin for...
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- Mr. Gunn
Apologies for re-hashing this thread, but FWIW, Zotero stores everything locally, too, and by default nothing remotely. I like it because I can use it offline (even though it's in a web browser). Also, since I search for papers using a browser, and Firefox, specifically, I've accepted that it's a browser plugin.
- Chris Lasher
Chris, there's a browser bookmarklet that allows you to easily import papers from a growing number of sites directly into your Mendeley web account. You can then just sync up your desktop app and you're good to go, on or offline.
- Ricardo Vidal
Mendeley team will find it interesting - I've stumbled across forum thread where Polish grad students are recommending Mendeley instead of Endnote :).
Mr. Gunn, Björn Brembs and Victor / Mendeley Team liked this
Thanks for sharing this find, Pawel! :-)
- Victor / Mendeley Team
Care to share a link?
- Jennifer Melinn
Jennifer, it's a closed forum - the thread is not available without registration.
- Pawel Szczesny
Bug when upgrading Mendeley desktop: needed to rename install folder to "Mendeley Desktop2" to upgrade to latest version.
Not sure, I think my previous version was 0.6 something. First tried to find "update" but couldn't. Next downloaded latest and tried to install, but got error message. Then uninstalled current version. Retried install with same error. Next time I renamed the install folder and it seemed to work.
- Steve Koch
Hi Steve, thanks for reporting. It's a little odd - usually you should just be able to install into the same directory, over the old installation. I'll forward this to our developers.
- Victor / Mendeley Team
Thanks, Victor. Yeah it is odd. I notice now that the old directory still has info in it, even after trying to uninstall. See: http://openwetware.org/wiki...
- Steve Koch
Also, here is the error message screenshot: http://openwetware.org/wiki...
- Steve Koch
Was updating because I'm interested in trying out the PDF annotation and whether it can be shared amongst group members. May try it out soon.
- Steve Koch
Hi Steve - the current version does not yet allow sharing PDF annotations (we needed to do more backend work). The next major release (a couple of weeks away at most) will allow sharing these annotations.
- Victor / Mendeley Team
Mendeley ou les chercheurs reprennent le web d’assaut: http://intruders.tv/fr-tech...
Victor / Mendeley Team liked this
Great video, thank you very much!
- Victor / Mendeley Team
Mendeley Desktop v0.9.0 released - http://www.mendeley.com/blog...
Michael Habib, Dahaniel, Björn Brembs and Euan liked this
Wheee! Lots of new features - internal PDF viewer with annotations, embeddable public collections, completely revamped interface for Mac...
- Victor / Mendeley Team
Nice one. Victor, re: "Please note: As part of the upgrade process, if you have an online account already, Mendeley Desktop will need to perform a full sync when it next starts. This may take some time depending on the size of your library". Tried and failed to do this. Where did I go wrong? Thanks.
- Graham Steel
Hi Graham - did you get an error message? Or no reaction at all? Any info would be appreciated; best to support@mendeley.com so we can track it. Thanks!
- Victor / Mendeley Team
waiting for my validation mail...
- Dahaniel
Hi Dahaniel - can you please mail me at victor.henning@mendeley.com, then I'll send you the verification link!
- Victor / Mendeley Team
I just got it seems I am a bit too impatient :)
- Dahaniel
For some reason, my collections are empty
- pqs
Does the mac client allow you to import a folder with lots of subfolders full of pdfs in one go yet?
- Matt Leifer
Yes, from a functionality perspective. I would however ask you to only add files in batches of ~200 articles or so, instead of adding 1000 PDFs in one go.
- Jan / Mendeley.com
OK, I do want to try out Mendeley, but what I really need is a script that allows me to import my entire library of several thousand articles in one go. Otherwise, the time I would need to invest in switching from my existing reference manager seems like too much. Of course, an "import from Papers" function that also preserves metadata would be even better.
- Matt Leifer
Mendeley 0.9.1 is out today, mostly a bugfix release. Should fix the empty collection issue.
- Mr. Gunn
PQS, can you please send the bug report to support@mendeley.com, including the e-mail address you are using the account with? We can then have a closer look at the problem. Thanks!
- Jan / Mendeley.com
I'm trying to work out if twitter, ff etc are at all useful.
Anthony Leverrier liked this
FF is useful once you get it set up correctly, which takes a while. Twitter is useless aside from the small fact that most of the people are there rather than on FF.
- Matt Leifer
Hmm what do I need to do to set it up correctly? It seems to be working ok so far.
- Sean Barrett
I mean that once you have a lot of subscriptions the Home feed becomes really noisy and difficult to keep up with. You will eventually need to set up several friend lists and saved searches in order to keep track of important things and eliminate some of the noise. Also, if you are interested in using FF as a Twitter client and feed reader as I do then you have to set up a lot of imaginary friends in order to deal with the people/blogs that are not on FF yet.
- Matt Leifer
Matt, do you find that people on here are discussing physics/CS (as in research) in the same way (or as actively) that they are discussing, e.g. science 2.0? If so, where?
- Sean Barrett
Generally no. There are not enough physicists/theoretical CS people on here for that. For example, the Quantum Computing room is pretty dead. We are vastly outnumbered by bioinformatics and chemistry people, who apparently do have some useful research discussions. It's one of the reasons that I pull a lot of blog feeds into FF.
- Matt Leifer
I find that FF is more useful for quantum link discovery rather than for discussion at the moment. For example, someone like Dave Bacon might point out an interesting article that I had ignored (especially experimental stuff). Also, I pull in a feed from Google Alerts about quantum stuff, which occasionally comes up with good stuff that I haven't seen, but mainly lets me know what articles people are blogging about and writing about in the press.
- Matt Leifer
I guess "quantum link discovery" is part of why I'm here. I found myself emailing people a lot about papers I was excited by, it seems to make more sense to make those comments public. I think if we start doing that then the discussion will follow in these comment threads.
- Sean Barrett
Absoultely, but unfortunately we lack the critical mass to make that happen at the moment. You should also look into social bookmarking sites like Delicious, and social reference management like CiteULike, Connotea and 2Collab, which are better for managing papers and can replace a desktop bibtex manager. You can then pull a feed from those services into here. Unfortunately, they also lack critical mass in our field at the moment.
- Matt Leifer
What would be really useful would be if any of those sites could connect to some sort of "scrobbler" plugin, like Last.fm has, which could just quietly collect information on which abstracts/pdfs I was looking at or printing, and building a recommendation engine based on that. I don't know if such things exist but it would certainly harvest more data than having to explicitly link to things on ff or wherever.
- Sean Barrett
You might try looking at Mendeley http://www.mendeley.com/ It claims to be a "Last.fm for research" and is backed by some of the people behind Last.fm. Personally, I found the desktop client to be very slow on the Mac and I had difficulty importing my library from Papers so I haven't used it too much (it didn't seem to want to import whole directories at once and I wasn't about to add...
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- Matt Leifer
Hi Sean - as Matt points out, what you're saying is exactly the idea behind Mendeley. Matt: We've had a major new release yesterday, with many new features (including PDF annotation: http://www.mendeley.com/blog...) and a much more native interface for Mac. Some speed/stability issues remain, but these will be ironed out as we approach version 1.0. Perhaps you could give it a try and let us know what you think?
- Victor / Mendeley Team
As Matt points out, social reference managers (like 2collab) are meant for this, but lack critical mass. I added my 2collab feed to FF, which at least is a good way to get scholarly citations into FF.
- Michael Habib
Do any of the online reference management sites (e.g. Mendeley, citeulike, Zotero, etc.) has a usable and *well documented* API? I'm want to integrate reference management and sharing into my site and I don't want to reinvent the wheel. Also, how well does bibtex import/export work on these sites?
Mike Chelen, Khader Shameer, Sarah Kendrew and 8 other people liked this
Hi Matt, we don't have a *public* API yet, but we're planning to introduce one. We'll also enable reference management/sharing my simply pasting some code into your side, much like embedding a YouTube video. Apologies if that info doesn't help you much for now!
- Victor / Mendeley Team
I can't really tell you about usable APIs, but the bibtex features (export and import) seem to work really nicely on citeulike. Sorry I can't be of more help!
- Allyson Lister
Zotero is a firefox browser plugin. References are stored in an sqlite db on your hard drive. Their api allows you to create additional Firefox plugins to extend its base functionality. I wrote a plugin to add an extra menu item that allows our users to export to our wiki...took about a day. It exports to bibtex if you want. If you're more advanced, you can just write SQL to read/write from the db, but that's obviously not recommended.
- Fitzgerald Steele
Connotea (http://www.connotea.org/wiki...). Bibsonomy (http://bibsonomy.org/) also has an excellent API.
- Euan
Thanks for the responses!
- Matt Leifer
2Collab has an API, you could try emailing or tweeting them for more info http://twitter.com/2collab
- Richard Akerman
Have you done any more work on this? I got a tweet follow up on this today...I'd love to hear about the approach you've taken..
- Fitzgerald Steele
I will send the 2collab API info. if you are still interested.
- Michael Habib
Citeulike appears to have a rest based API if you can figure out what the necessary URLs are
- Michael Barton
As far as I know, most of the sites/software have decent BibTeX export/import options. In any case, I'd just check the reference management comparison tables at wikipedia (http://en.wikipedia.org/wiki...) or Martin Fenner's Reference Manager Overview graphic (usually up-to-date) (http://network.nature.com/people...)
- Ricardo Vidal
Somehow I missed all the responses after my initial thank you comment. I'm not actively working on this at the moment, but I am still interested in the available APIs. FYI, I would need an API that allows for upload of bibliographic records rather than one that just returns the results of search queries.
- Matt Leifer
References in Zotero 2.0b5 beta can be stored in Zotero's cloud servers and/or on your hard drive: http://bit.ly/N5nxp Bibliographic data can be accessed via Zotero data API or with an external SQLite client. Here's what I found about Zotero's API documentation http://bit.ly/1a51Tl I'm not sure how exactly you want to integrate reference management into your website, but maybe this Zotero doc page - What Do You Want Your Users To Get? - will help explain your option(s): http://bit.ly/3x1vQi
- Ryan Williams
New blog post: Mendeley Desktop v0.9.0 released http://www.mendeley.com/blog...
Wheee! Lots of new features - internal PDF viewer with annotations, embeddable public collections, completely revamped interface for Mac...
- Victor / Mendeley Team
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