Archived thread 1067681 from Education & Science. Markdown source: Education_&_Science/thread_1067681_Mendeley_for_scientific_papers_management.md
I found this wonderful software as a very good solution to the problem that was bothering me from a loooonnnnggg time....how to manage the existing (hundreds, thousands..?) scientific papers on my computer....?
Finally, something has happened...!!!!!
Mendeley desktop was was able to fetch metadata from most of my pdf files. I am yet to explore all its features. It gets better if more people use it.
Thanks, looks interesting. Importing my references now.
This does look like good software. Thank you for pointing it out.
Edit: I want to play with it more before I make a final decision, but it seems like this may be able to address some of the problems I always had with Zotero. I like Zotero, but having my citation management built into a web-browser never did work for me very well. These guys really need to come out with a plug-in for OpenOffice.org, which is currently the one thing they are lacking.
If you haven't seen it, check out jabref too, especially (although not only) if you are a LaTeX user. Its my favourite app for day to day use.
FYI
This software is proprietary. See the EULA information @ http://www.mendeley.com/terms/
Although the terms and conditions are very reasonable, by proprietary standards, it's not FOSS.
Just thought everyone should know.
I did read the terms prior to downloading, I have no qualms with using something proprietary if it works and works well for me.
This does work VERY nicely I think. I don't think I'd compare it to Jabref though, yes, I've used it too. No, I still don't think they're the same. This has a different focus to it. Jabref is a bibilography manager first. This is a reference file manager first. Two different focuses. Jabref works ok but just lacks something for me that this addresses, maybe in the interface, definitely the community integration.
This is what I was wanting for quite a while. Definitely handles metadata better and if I can figure out the community aspect of things then it's a great resource for references that I might like.
Am I missing it or Mendeley doesn't have any LaTeX related stuff? I tried JabRef too (which is nice) and at the end (at least for now) stick with Referencer
meho_r said: Am I missing it or Mendeley doesn't have any LaTeX related stuff? I tried JabRef too (which is nice) and at the end (at least for now) stick with Referencer
LaTex related how? It exports Bib, RIS, and Endnote files.
earlycj5 said: LaTex related how? It exports Bib, RIS, and Endnote files.
Yes, BibTeX export will be it. But, I see only import :-k
You can both import and export bibtex files.
To export, select the item you want : file > export and then select the format you want to export to.
To import, click the add document icon, choose library file import and then the .bib file you want inported.
But there is another problem. Sometimes, medneley desktop complains the following
Mendeley Web gave a response that Mendeley Desktop could not understand.Is anyone else also seeing this problem..?
meho_r said: Yes, BibTeX export will be it. But, I see only import :-k
Like I said, it exports bib, RIS, and EndNote. It's under the File menu. :)
meho_r said: Am I missing it or Mendeley doesn't have any LaTeX related stuff? I tried JabRef too (which is nice) and at the end (at least for now) stick with Referencer
I'd stick with referencer too if it doesn't crash on my system with Intrepid Ibex. It worked pretty well with Hardy though ... I'm trying Mendeley now. Its look and feel is quite good. However, it's still a little unstable on my system too. Bad luck ? I look forward the stable version.
Mendeley seems stabile enough to me on my Ibex system at work.:-k
Little slow to import all the PDFs I had but once it did I haven't had any problems with it yet.
stumbleUpon said: But there is another problem. Sometimes, medneley desktop complains the following
Mendeley Web gave a response that Mendeley Desktop could not understand.Is anyone else also seeing this problem..?
Yes! I use Arch Linux and downloaded the generic x86_64 version -- it gives me this error every time I try to sync. Any luck figuring this out?
among others:
4.3. If you choose to download and install our Software, our Software collects (even if you are not online) certain data which is uploaded to our servers with your explicit permission. We collect data relating to your:...
would rather send this data to any forum than them
I installed Mendeley on my laptop with Ubuntu 8.10. It worked well for a while but now it crashes when it starts and it uses my hard drive like crazy. I think it will break my hard drive because I can hear some bad noise. I tried to uninstall and reinstall it and it does exactly the same thing over and over. It probably keeps the setting somewhere and after reinstallation remembers them. Do you know how to completely unistall Mendeley with all its settings?
I've been using Zotero 1.5 for a while now, and it does the same thing as this program. You can drag your pdf files (my max is 30 pdfs) into Zotero and then right-click and select "Get Data from pdf". This extracts all meta-data, creates a biblio reference and attaches the paper within the datum. It works perfectly for all pdf's with text search capabilities.
See: http://www.zotero.org/support/pdf_fulltext_indexing
And it is OpenSource, you can back-up your whole library to the clouds and it integrates with OO and MS-Word. it's also very quick and works on everyplataform that supports FF 3.0.
Camp
Campitor said: I've been using Zotero 1.5 for a while now, and it does the same thing as this program. You can drag your pdf files (my max is 30 pdfs) into Zotero and then right-click and select "Get Data from pdf". This extracts all meta-data, creates a biblio reference and attaches the paper within the datum. It works perfectly for all pdf's with text search capabilities.
See: http://www.zotero.org/support/pdf_fulltext_indexing
And it is OpenSource, you can back-up your whole library to the clouds and it integrates with OO and MS-Word. it's also very quick and works on everyplataform that supports FF 3.0.
Camp
Yeah, it's supposed to do all that. It wasn't as efficient as Mendeley and the interface is more cramped.
Not to mention that when I tried to use Zotero web-of-science gave me an error 404, when I disabled it, it was back.
But then I thought this thread was about Mendeley, I know I started a thread about Zotero 1.5 beta here...
Mendeley has released another version. 0.6.3.
Startup is much faster, PDF storage is avaialble now, I don't think it was before.
Still having a few bugs, sometimes while uploading PDFs it gives and error message. Still, it's in beta so I can't complain.
I'd stick with Referencer. I tried Mendeley on my XP partition and it was awful. It was atrociously slow, thrashed away at the hdd for ages, was not very good at retrieving correct metadata, and worse, crashed every time I used it. In theory it's nice, but in reality is awful. It would be greatly improved if you could just DISABLE the automatic metadata retrieval, but you can't. I estimate that it would've taken 24hrs of hardcore hdd thrasing before it finished indexing my 1000+ pdfs.
I wish someone would come out with something like Papers for the Mac. Something with a simple interface that allows simple access to basic things like metadata, tagging, bibtex export/import and leaves out buggy "features" like metadata retrieval.
Hi everyone,
A short introduction about me, I work at Mendeley, as a member of their QA and support team, so seeing forum posts like this is always an item of interest to me. : )
With regards to the errors and crashes that you may be experiencing, I would like to mention that we have plans to release version 0.6.4 very soon, which will feature a number of bug fixes and stabilisation improvements, amongst several other enhancements.
We're constantly working on trying to improve the stability of our software, and in order for us to do this, your feedback is really appreciated and we welcome any and all that you may have.
If you experience further crashes once this update is released or have any other feedback, we do ask that you take a second to forward it to us either via e-mail or on our Uservoice page, both of which are accessible at http://feedback.mendeley.com.
This way, your comments should reach us in a more effective manner, and we'll do our best to act upon them acccordingly.
Thanks.
Anyone got the bookmarklet working with Hardy + firefox? This is _the_ killer feature (at least when it supports ISI) because it allows you to inject biblio metadata from the currently visited web page. I do almost all of my reference searching and reading online rather than maintaining a PDF collection. Its easier simply to re-search than to keep a bunch of PDF's around. (Mendeley certainly makes keeping PDF's easier, but all I really need is the URI to find it again, not the actual PDF.)
Anyway, I cannot get the bookmarklet to work.
Mendeley folks if you are reading -- _please_ do your best to support LTS releases for the duration. Some of us have gotten off the 6 month upgrade treadmill for the sake of better productivity.
thk said: Anyone got the bookmarklet working with Hardy + firefox? This is _the_ killer feature (at least when it supports ISI) because it allows you to inject biblio metadata from the currently visited web page. I do almost all of my reference searching and reading online rather than maintaining a PDF collection. Its easier simply to re-search than to keep a bunch of PDF's around. (Mendeley certainly makes keeping PDF's easier, but all I really need is the URI to find it again, not the actual PDF.)
Anyway, I cannot get the bookmarklet to work.
Mendeley folks if you are reading -- _please_ do your best to support LTS releases for the duration. Some of us have gotten off the 6 month upgrade treadmill for the sake of better productivity. Hi,
Our bookmarklet should be working fine with Firefox, regardless of your operating system. Just as long as Firefox is up to date, and you have Javascript enabled.
This said, we currently only support importing documents from a select number of sites, as per our Import page. If the site you're trying to import from isn't currently listed, drop us a suggestion on our Feedback forum and we'll do our best into looking into adding support for this site.
Out of curiousity, what site are you trying to import from, and what errors, or behaviour, do you see exhibited?
Regards, Mustaqil
I migrated from W$ to Ubuntu for many reasons but one the main contribution to my migration is that all software there is not compatible with itself. I mean this between diferent versions. If someone in your workgroup upgrade the version of any software then the rest of the group cannot open the file saved by the upgrade-obsessive guy (everyone got one...) Presentations or posters in powerpoint, SigmaPlot files, word files are good examples of this uncompatibility. However some of the software works pretty good and was not replaced at all. Up to now I think the reference managers are one of these cases. The best think Ive found is Bibus. Bibus uses standard sql database format through sqlite or mysql, and connect with OpenOffice (OO) through UNO connection. But to configure this UNO connection is not so easy and, despite the procedure is well described in the bibus web on sourceforge, you have to repeat that procedure more than one time, restarting the OO and so on. Fortunately I could export my 500 references from endnote 7 to Refer/RIS and then import them into Bibus, but was not easy. Anyway, every 6 months I upgrade the SO to the last version (vices...), but then I ve to configure Bibus again and this take a little work. To configure the citation format and the in-text references to make it to do what you want is really difficult.
I tried twice with zotero (which actually has a OO plugin to insert the references into any .odt). The first time I really didn't realize how to use it and I didn go far. The second time I could import few references with abstracts, but I couldnt import my the SQL library with my 500 references neither the Endnote database.
Another person from my University tried with Mendeley and is quite satisfied with how does it work. The problems of this soft are -1- the delay to give support to the latest version of Ubuntu and -2- IS NOT OPEN SOFTWARE and has a PROPIETARY LICENCE
There is a OpenOffice project working on this aim of reference managing but there is no news about it.
Pybliography is free and connects with OO and M$Word, but I didnt try. Sounds nice but I didnt see any opinion.
Mendeley 0.9.0 is out with some new features but, I am having difficulties with synchronization, I just want to know whether it is unique to my machine. This is the case:
The recent collections that I create within the client is reset when Mendeley syncs itself with the web. It may be my fault, also so I would like to know.
Thanks, Mali
Mendeley 0.9.0 seems to be a (quantum:) leap towards a better software for scientific (including "social science") on all platforms. I have been busy tinkering with it for the last few days and writing to to people I know and elsewhere on its new features.
Metadata extraction simply got better compared to earlier releases, and pdf viewing with annotation capabilities is a long-sought-after feature for me on linux, which is another matter.
Right now the search option still doesn't work on ubuntu / windows even if I logged in. But I believe this issue will be solved in a near future. And, like a number of people (see Mendeley and Zotero forums) I'd like to see a way to integrate Zotero and Mendeley -and, the ability to embed the metadata into the pdf file itself; still couldn't find a feasible solution for this.
Nevertheless, Mendeley becomes better and better -kudos for that. And I don't think it is mutually exclusive with Zotero (my ever-favourite) and I appreciate their efforts in implementing user feature requests, including those regarding some kind of interaction with open source software (Zotero being the most wanted, followed by latex editors as well as LyX). Especially when the lawsuit against Zotero by endnote is considered, Mendeley as a commercial software, plays it fair in my opinion. So it is certainly a software to be followed closely, I think.
Ya, the latest version of Mendeley totally rocks. It actually works with OOffice. The bookmarklet works now most of the time (occasionally it takes 3-4 tries, but then works). I'm hugely impressed with the whole project.
My only gripe with the bookmarklet is that it resizes my firefox window! I have new windows set to popup as a new tab which means my whole session get resized to a tiny window. I have to remember to right-click the bookmarklet and choose "open link in new window" to avoid it opening in a tab.
thk said:
My only gripe with the bookmarklet is that it resizes my firefox window! I have new windows set to popup as a new tab which means my whole session get resized to a tiny window. I have to remember to right-click the bookmarklet and choose "open link in new window" to avoid it opening in a tab.
Try Edit> Preferences> Content and select the "Exceptions" button just across "block popup windows" option there (I guess it is already ticked). In the "Exceptions" add "www.mendeley.com" and click "Allow".
Has anybody managed to get the search function right from the desktop application? I cant "Search" the article, etc. even though I am logged in, it is disabled.
Update: They raised the version beta 0.9.1; the search function seems to work now.
Hi,
The last few days I've been giving mendeley a go. Here are my impressions:
Overall it is much improved from the last version I tried. It is a great idea to be able to sync with an online account as I use multiple computers with multiple operating systems; a mac in the lab, a desktop with ubuntu at home and an old ibook. That said, the syncing feature seems to sometimes create duplicates, maybe I'm not using it correctly? vaguely thought the "watch folder" feature might be messing with things?
I realize this is the ubuntu forums but...on my mac at work mendeley is incredibly unstable and crashes frequently, much less frequently on ubuntu. Has anyone else found this? I'm running Leopard.
The pulling of metadata is ok but can be quite dodgy, often it seems to think I am studying bacteria/genetics and inputs that. Satisfied with a job well done, it no longer gives the option to search by title, and there is no option to clear metadata (at least that I can find).
Think I'll persevere for a bit longer. m
Hi,
Just a heads up, I'm part of the QA and Support team at Mendeley, so it's definitely of interest to see feedback like this. :)
mathyou said:
Overall it is much improved from the last version I tried. It is a great idea to be able to sync with an online account as I use multiple computers with multiple operating systems; a mac in the lab, a desktop with ubuntu at home and an old ibook. That said, the syncing feature seems to sometimes create duplicates, maybe I'm not using it correctly? vaguely thought the "watch folder" feature might be messing with things? When you mention that you're using it across multiple operating systems, do you have the same PDFs stored on each of your machines, with the Watch Folder option turned on for each? If so, what you can do is set Mendeley Desktop to upload the attached files, and then it should be able to automatically detect when a file was imported on a different machine much more accurately and prevent duplicates from entering your library.
You can enable the file uploading option by selecting "All Documents" in the collections list on the left hand side, and then clicking "Edit Settings" towards the top of the centre pane. We will be working on improving this automatic duplicate detection of ours, so hopefully issues like this will be ironed out with future releases.
I realize this is the ubuntu forums but...on my mac at work mendeley is incredibly unstable and crashes frequently, much less frequently on ubuntu. Has anyone else found this? I'm running Leopard.
Do you find that doing any specific actions causes Mendeley to crash? Also, when it crashes, does the application actually close down completely, or does it simply freeze up/beachball and become unresponsive? Similarly if you have any error messages generated, it'd be great if we could get a copy of them so that we can look into it. Our contact address is [email]support@mendeley.com[/email]
The pulling of metadata is ok but can be quite dodgy, often it seems to think I am studying bacteria/genetics and inputs that. Satisfied with a job well done, it no longer gives the option to search by title, and there is no option to clear metadata (at least that I can find).
We are planning on changing how we extract metadata from PDFs in a coming upgrade with the hopes of making the entire process much more accurate.
We've also got some improvements planned for the automatic data retrieval from title lookups from places such as PubMed, DOIs, Arxiv and Google Scholar. For now though, if you have an unverified document, you can drag any item into the "Needs Review" collection to reenable the "Search by title" option.
There isn't currently an option to wipe the details of a document completely, but given that there appears to be some sort of demand for this I'll pass this feedback onto the rest of the team so that we can keep it in mind for one of future releases.
If you've got any other feedback, further questions, or suggestions, please don't hesitate to drop us an email at [email]support@mendeley.com[/email] and we'll do our best to address your concerns as best we can.
Thanks for trying Mendeley! :)
mustaqil.ali said:
When you mention that you're using it across multiple operating systems, do you have the same PDFs stored on each of your machines, with the Watch Folder option turned on for each? If so, what you can do is set Mendeley Desktop to upload the attached files, and then it should be able to automatically detect when a file was imported on a different machine much more accurately and prevent duplicates from entering your library.
I think this is maybe a case of me being disorganized and having different machines watching different folders. Now that I've imported all my pdfs and weeded out the duplicates it's not being a problem. The watch folder is working well for those papers from sites where I can't use the bookmarklet (which is awesome btw).
Do you find that doing any specific actions causes Mendeley to crash? Also, when it crashes, does the application actually close down completely, or does it simply freeze up/beachball and become unresponsive? Similarly if you have any error messages generated, it'd be great if we could get a copy of them so that we can look into it. Our contact address is [email]support@mendeley.com[/email]
It tended to be when I was correcting metadata and the program attempted to sync. The application "unexpectedly quit" and I would just relaunch, fortunately didn't seem to lose any changes.
For now though, if you have an unverified document, you can drag any item into the "Needs Review" collection to reenable the "Search by title" option.
Thanks, hadn't noticed that. Maybe an additional button at the bottom of the Document details tab would be good.
There isn't currently an option to wipe the details of a document completely, but given that there appears to be some sort of demand for this I'll pass this feedback onto the rest of the team so that we can keep it in mind for one of future releases.
Sounds like a good idea to me, and not too hard to implement I would imagine?
If you've got any other feedback,
I guess another thing might be the pdf viewer seems to struggle a bit and you have to wait for it to 'depixelate'
Thanks for trying Mendeley! :) Thank you, really useful and promising.
I tried this and was impressed in the beginning. But it seems to be unstable and removed all the pdfs I had added following a crash. It crashed several times and not sure I could depend on it.
I tell you that this is one of the best as it is.
In the latest version, metadata extraction is still very slow, inaccurate, and buggy (crashes A LOT). I've forgone adding pdfs to the library and instead stick to just my citeulike entries and attach pdfs to those when needed.
I like the tagging, notes, pdf annotation (with export feature to embed the annotations to the pdf itself), and integration with citeulike.
I don't like the slowness of the pdf viewer, and the fact that it doesn't view annotations (e.g. comments created in acrobat pro or foxit reader). It does display highlighting at least (unlike evince in Jaunty). There should also be more navigation buttons, like go to first/last/specific page. Did I mentioned rendering is slow as hell (on my Core Solo 1.04Ghz ULV)?
This looks pretty good, although I think Google Desktop already does a good enough job of indexing all my papers, and I can use Google Scholar for generating BibTeX references :)
Looks quite good, but I prefer something that manages a BibTeX file for use with LaTeX. I've heard a few whispers about KBibTeX moving to QT4, and possibly implementing a new interface more like Papers for Mac, so that will be interesting if that happens.
ad_267 said: Looks quite good, but I prefer something that manages a BibTeX file for use with LaTeX.
You can export to .bib with mendeley. Just select the papers you want and click file>export.
mathyou said: You can export to .bib with mendeley. Just select the papers you want and click file>export.
Yeah, I like not having to export though. I like using an application that uses the BibTeX file as its native format so I can just hit Ctrl+S and not have to keep two separate files up to date. That's one thing that put me off Referencer too. The option to manage a BibTeX file seemed a bit buggy when I used it.
If there was an option to automatically keep a BibTeX file synchronised with the Mendeley database then I might give it a go.
I see what you mean, that would be quite useful. I haven't written anything that long and at the moment I tend to just leave doing my references to the end. When I come to doing my thesis that probably won't be a good idea. It probably wouldn't be too hard for them to implement.
Hi again,
Regarding the crashes and instability that has been reported, we are coming incredibly close to releasing a development preview of our next version. This update has the sole focus of stabilising Mendeley, and optimising the codebase to allow for faster performance speeds.
Following us releasing this development preview, we will release the next stable version that will incorporate fixes for additional bugs, a few new features and other changes based on feedback we recieve. You can keep up to date with these updates on our blog at http://www.mendeley.com/blog/.
As for the suggestion about continuous BibTex exporting, this would be a killer feature to have and we think it's a brilliant idea. So much so, we're going to incorporate this in one of our next stable features. :) For now though, the suggestion to export things is pretty spot-on, but we will work on automating this and making your work process as effortless as possible.
Regards, Mustaqil
Hello,
I have just read the thread and I am very interested with Medeley. Actually, I am using Bibus to manage my references/citations and it works well for me. However, I will try Medeley and I will soon give a report of my experience.
Incredible program! PDF annotating is wonderful. Works especially well with a shared PDF file repository that can be created with Ubuntuone. The bibliography creation is a snap, too. I'm glad I didn't waste more time trying to get gPapers to work.
Hellow,
I am using Ubuntu 9.04 NR and OpenOffice 3.1.1. Installation of Mendeley's plugin for OO going with error: ERROR: python-loader: <type 'exceptions.ImportError'>: No module named pythonloader, traceback follow no traceback available unopkg failed
Do anybody have got the same error? And how to fix this bug?
P.S. Mendeley's team avoid discussion of this bug http://feedback.mendeley.com/pages/4941-mendeley-feedback/suggestions/80934-openoffice-plugin-for-citations-bibliographies
Thanks.
P.S. I have the last version of python-uno.
python-uno full-featured office productivity suite -- Python interface version: 1:3.1.1-1ubuntu1~jauntry
Alasheev said: Hellow,
I am using Ubuntu 9.04 NR and OpenOffice 3.1.1. Installation of Mendeley's plugin for OO going with error: ERROR: python-loader: <type 'exceptions.ImportError'>: No module named pythonloader, traceback follow no traceback available unopkg failed
Do anybody have got the same error? And how to fix this bug?
Have you tried uninstalling mendeley's openoffice plugin and reinstalling it after restarting openoffice?
I've the same problem, and I did uninstall the plugin. When I tried to reinstall, I get a similar error:
The OpenOffice unopkg utility gave the following output: ERROR: python object raised an unknown exception ('No module named uno', traceback follows <NULL> unopkg failed.
Thanks for your help.
Thank you. But it does not help. I get Window 7 and all is fine working now on my netbook (Aspire One 110, RAM 1.5Gb, HDD SSD 8Gb).
krgp said: I've the same problem, and I did uninstall the plugin. When I tried to reinstall, I get a similar error:
The OpenOffice unopkg utility gave the following output: ERROR: python object raised an unknown exception ('No module named uno', traceback follows <NULL> unopkg failed.
Not sure whether this works, but try uninstalling mendeley OOo plugin, close openoffice completely, and then find out the uno packages folder - the extensions folder. Find mendeley folder there and delete it completely - in windows xp, the path I am trying to explain is as follows (I am sorry, my ubuntu broke, couldn't fix it yet):
C:\Documents and Settings\user\Application Data\OpenOffice.org\3\UserName\uno_packages\cache\uno_packages\145.tmp_\Mendeley-0.0.15.oxt\Mendeley
so in ubuntu it might be in the openoffice installation folder or in the user home directory in the hidden ~/.openoffice (or something similar) folder (a tracker search for mendeley might be helpful)
after removing the old extension installation folder, start Mnendeley try reinstalling the OOo extension. Then, start opnoffice again and see whether it works (without closing Mendeley).
I did this already (I #'d it) because the uninstall option didn't work.
Now, with a clean slate (so to speak), when I try to install openoffice plugin from mendeley, mend. says that python-uno is missing (the error I posted above).
I have OOo 3.1.1, python 2.6 (altho I got the same error with python 3). Python-uno is the latest (of course, since it was loaded with OOo last week).
Anyways, I'm trying to write a book here, and having a citation software that work would be great. No joy over on the Mendeley site.
Thanks.
Sorry for that, my limited help options for mendeley are exhausted (for now:).
If you are looking for a good citation management option though, try Zotero firefox extension, which is both opensource and already more powerful than Mendeley:P
If you have not heard it before , here is the link: http://www.zotero.org/
and here is the link for the open office integration plugin: http://www.zotero.org/support/word_processor_plugin_installation#openoffice_neooffice
I would suggest you use the beta version, which seems almost complete.
The new version of Mendeley beta (9.4.0 by now) began supporting zotero databases as well (which is not that complete but anyways a good start); so until this support is developed and your problem is solved, in the meantime you can enjoy grabbing citations and using them in OOo with Zotero (and chances are you will appreciate Zotero more for both its stability and strength)
Hope this helps:)
They're on the right track and LaTeX/BibTeX support is improving, but it's as if the developers have never used LaTeX before. When importing and exporting, BibTeX's "number" field should be mapped to Mendeley's "issue" field, but it's not. The title is also put in double curly brackets which is just plain annoying because it prevents LaTeX from correctly capitalising the reference according to your reference style. This has all been mentioned on the Mendeley feedback page but the developers don't seem to have taken any notice.
My version of Mendeley handles the number-to-issue "issue" perfectly when importing. With the new OOffice plugin, I no longer use latex, so I can't speak to the exporting of bibtex files.
thk said: My version of Mendeley handles the number-to-issue "issue" perfectly when importing. With the new OOffice plugin, I no longer use latex, so I can't speak to the exporting of bibtex files.
Hmm what version is that? I tried the 0.9.5 preview version and it still didn't seem to work.
I just started using Mendeley a few weeks ago, when I switched all of my systems from Win XP Pro to Ubuntu 9.10. Mendeley is a great program but it. crashes. all. the. time. I get a complete shutdown of the app when I click certain pdf's to open. I also find duplicates keep sneaking in, although this may be a symptom of the crashes, which removes the 'watch folder' on restart, which I then have to re-enable, which then re-indexes all the files in my watch file, which wastes a ton of my time waiting for this to finish. I hope the Mendeley people can clean the program up a bit.
I have never used Papers but know lots of people that rave about it. I briefly toyed with using Zotero, but the main reason I chose Mendeley is because Foxit in Ubuntu no longer lets me highlight and save pdf's, and Mendeley's built-in pdf reader does, so I really have no choice but to tough it out until Foxit upgrades their Ubuntu pdf reader. Hopefully Mendeley will fix their program first since I have put a lot of time into re-organizing my pdfs in it and like the program overall.
Greg
Before converting to Ubuntu I was using EndNote and it was rl nice. Now I am trying Mendeley. It crushes sometimes but in general works fine. Does anyone know if it is possible to import or add specific journal citation style?
Is there a way we can export A collection as a bibtex file... What I want to be able to do is this
I have created a collection in Mendeley. What i now want to do is export the collection as a bibtex file so that I can include it in say Lyx For eg.
I know I can highlight all the relevant papers and choose "Export..." but what i was wondering was if there was a shorter way to do this.. like export a collection.
samgurung said: Is there a way we can export A collection as a bibtex file... What I want to be able to do is this
I have created a collection in Mendeley. What i now want to do is export the collection as a bibtex file so that I can include it in say Lyx For eg.
I know I can highlight all the relevant papers and choose "Export..." but what i was wondering was if there was a shorter way to do this.. like export a collection.
Go to Tools > Options > BibTeX
You should find what you need there.
This is great; thanks for the link. I'll get a lot of use out of this.
This software is proprietary. Although the terms and conditions are very reasonable, it's not FOSS. Just thought everyone should know.
gunksta said: FYI
This software is proprietary. See the EULA information @ http://www.mendeley.com/terms/
Although the terms and conditions are very reasonable, by proprietary standards, it's not FOSS.
Just thought everyone should know.
nevaeh.aaric said: This software is proprietary.
Although the terms and conditions are very reasonable, it's not FOSS. Just thought everyone should know.
Already been covered, probably more than once in this thread.
As I already said, it's free, it works well, it does what I want. Yes, I'd like it to be OS, but if the tool works, use it!
<sarcasm>I think nevaeh.aaric is just trying to plagarize my brilliant comments.</sarcasm>[FONT=Arial][/FONT]
I use Mendeley and really like it's features such as OO integration, pdf highlight (which I've found to be a major trouble in ubuntu), etc. However, it has more than once messed up my collections so that pdf in some collections got mixed up, etc.
I would be happy moving to a totally FOSS thing (I've tried Zotero but it wasn't as intuitive for me and I also didn't like that it was a in-the-browser app). But the problem is none of the other options (as far as I've seen from their webpages) seem to be able to highlight PDFs. Does anybody know about this?
I also eventually want to move to LaTeX but for now I'm OO.
AFAIK the only way to annotate PDFs on Linux is with PDF-XChange Viewer. It is not a native Linux application, but they claim they are almost entirely Wine compatible.
bubblehead74 said: AFAIK the only way to annotate PDFs on Linux is with PDF-XChange Viewer. It is not a native Linux application, but they claim they are almost entirely Wine compatible.
I just came into forums to mention PDF-XChange Viewer and missed it by 4-hours :) PDF_XChange viewer is an excellent software, works almost perfect under wine, and keeps free options free - all sorts of annotations without any 'PRO' marks, and can even export annotations to .rtf ;)
There is only one open source program for linux that that can do annotations as far as I know: Okular; which is kde based but also works nicely in gnome (if you don't mind the dependencies). So, you can also use it if you are not satisfied wit somewhat crash-prone nature of the PDF viewer in Mendeley (nevertheless, still a good software although it's beta).
I tried Okular and it was mostly fine but everytime I wanted to highlight I had to click on some buttons and select the highlight tool, yes every single time. I don't know if it was me... So I had to stop using it.
I'm new to ubuntu and scared of wine, so I prefer native linux software.
I recently tried to download Mendeley from the website, but was unable to do so. In fact, when I click on the direct link, I get a page citing permissions errors.
Am I the only one with this problem?
gunksta said: I recently tried to download Mendeley from the website, but was unable to do so. In fact, when I click on the direct link, I get a page citing permissions errors.
Am I the only one with this problem?
Repository still works for me? http://www.mendeley.com/download-mendeley-desktop/ubuntu
Unless your using Windows? In that case I have no idea, I've not tried to download this program directly via the website in some time now.
Dunno. Weird. I was getting weird errors yesterday. Now everything appears to be fine. Dunno. Thanks.
Anyone got the .svg icon for Mendeley which they could post here?
Mendeley icon (png) should be located at:
/usr/share/icons/hicolor/48x48/apps/mendeleydesktop.png
anatolica said: Mendeley icon (png) should be located at:
/usr/share/icons/hicolor/48x48/apps/mendeleydesktop.png
Thanks, found those but was looking for the .svg for gnome panel.
mathyou said: Thanks, found those but was looking for the .svg for gnome panel.
As far as I know Mendeley hasn't provided an SVG, so you'll have to get out Inkscape and do some tracing.
are mendeley ubuntu reps updated? I just got notification to install new update to mendeley, however sudo apt-get update && sudo apt-get upgrade does not find new version.
slaanco said: are mendeley ubuntu reps updated? I just got notification to install new update to mendeley, however sudo apt-get update && sudo apt-get upgrade does not find new version.
It's there now.
Hi All!
I'm trying update now and the new version is not available. I'm received the notification to update too. On Karmic the update don't go. On Ruindow$ the program was updated automatically, but now it is freezed on "sending new documents and references (86% sent)" because I have many pdfs, I suppose....
Could you help me with this problems?
I tried by synaptic too. Don't go.
cabruca said: I tried by synaptic too. Don't go.
Update is in reps as of yesterday afternoon. Did you add reps from Mendeley page?
It was in the repositories 23 hours ago when I posted. I updated and upgraded here at work. Upgraded at home last night too.
Hi all.
I suppose I have a problem here.
I tried synaptics today and it informs version 0.9.5.2.
I used the command line
sudo apt-get install mendeleydesktop -y --force-yes
suggested in this post http://www.uluga.ubuntuforums.org/showthread.php?t=1332359&highlight=mendeley+script and obtained the same result:
0 pacotes atualizados, 0 pacotes novos instalados, 0 a serem removidos e 0 não atualizados.
Because my curiosity, I do
sudo apt-get update
to see the response of repository and obtained this response from terminal:
Ign http://www.mendeley.com Release.gpg
What this means?
Thanks!!!!
Solution for update: use the Jaunty repository in Karmic. I read this suggestion on some place I dont remeber. Before this I had removed all packages related to Mendeley on synaptic.
But proram continues very slow. Both on linux and windows. In this $ystem its lost the connection with server and crashes. Now tryng on Karmic and waiting contact from support.
Thanks, bye.
for me update went smoothly. I just did sudo apt-get update and sudo apt-get upgrade. I am using this repository deb http://www.mendeley.com/repositories/xUbuntu_9.10 / . It is for 64 bit Ubuntu.
Well, I'm migrating to Ubuntu for good. I want to make this system work in a science environment where everyone else uses either Macs, or M$.
Mendeley 0.9.6.3 works. Its best feature is to watch folders, where it grabs the pdf, and automatically creates a reference, slots the file into the directory structure, which I can then sync with my web account. It also references acceptably with OO.
Awesome.
Bibus seemed pretty decent too, but I think it's Mendeley for me.
Too bad their EULA is restricted. Use Referencer instead and you will not have any problems in the future with all your documents. And if you got any problems, you at least have the sourcecode. :KS
Apparently, to use Bibtex, you don't have to re-export your mendeley collection to .bib file everytime you make a change:
You can also cite and create bibliographies in LaTeX documents. Mendeley Desktop creates a BibTeX file for your entire library, for each collection or per document. The BibTeX file(s) are updated each time you make a change to your personal library in Mendeley Desktop.
The citation keys are automatically generated in the format [AuthorYear]. You may edit citation keys manually by enabling the “Citation Key” field under Options (Document Details tab). Then you can edit citation keys under the Document Details tab in your library.
Haven't tried it yet but it seems promising.
peutch said: Apparently, to use Bibtex, you don't have to re-export your mendeley collection to .bib file everytime you make a change:
Haven't tried it yet but it seems promising.
It works quite nicely. I have "collections" for each manuscript that I'm working on and just add new documents as necessary to the collection, the .bib file is updated.
I was worried that it was not open source but when I compared its effectiveness and flexibility with the others - there was no competition. So I am installing it. Ill see how it goes.