EndNote is a good program to manage references. You can create separate libraries and organize your PDF's. It also helps to immediately update your citation styles to any Journal.

The two leading alternatives to Endnote (in some features), Mendeley and Zotero, are (essentially) freeware, although you can give Mendeley money for online storage facilities.

Endnote can afford to employ a large enough team to design and constantly improve their software, but that comes at the cost of a licence fee, although this is often covered in some institution. The question is: are the freeware alternatives suitable?

Hi Anna,

Have you tried Mendeley? it has both online (including mobile ) and desktop versions. http://www.mendeley.com/

From the website: Mendeley is a free reference manager and academic social network that can help you organize your research, collaborate with others online, and discover the latest research.

Automatically generate bibliographiesCollaborate easily with other researchers onlineEasily import papers from other research softwareFind relevant papers based on what you’re readingAccess your papers from anywhere onlineRead papers on the go, with our new iPhone app

The same for Endnote: http://www.endnote.com/

Bests,

Rolando

Mendeley is certainly the best available reference manager - and it's free!

We know two programs: EndNoteX4 for Windows and Papers for Mac. They manage references even from online databases

Mendeley (http://www.mendeley.com) allows you to organize your papers and access them from different comupter, Iphone,...

Hi, You can try Copernic Desktop Search, the home version is free. I index all parts of my computer by it, then i would see all the words in any file including PDFs, Words, etc. you should index all the part of your computer after installation and before searching.

Endnote it's a good one.

The free pdf reader from Adobe.com includes an excellent search tool. You can search single pdfs or groups in a folder.

I use Zotero (www.zotero.org) and/or JabREF (http://jabref.sourceforge.net/). They both are opensource managers with great functionality. Zotero integrates very good with OpenOffice (Libero) and MS Office. JabREF on the other hand supports Latex. Both can link local and online documents to the database and can export the database in any format you like for increased compaibility.

EndNote X5 would be the best choice. You can organize all your papers (Abstracts and Full Text articles) in a user friendly way. You can also read these papers inside the software using its built in PDF viewer. In my opinion EndNote is the best citation tool.

you can read more about it and download it here: http://www.endnote.com/

I also advice EndNote...And it's easy to use (and fully compatible with Microsoft Word, if you want to create your bibliography for the THESIS).

But, if you want only to organize and search into PDF files...Mendeley is the best choice...(even if EndNote do it too...but not for free)

Buy EndNote, One of the best way to solve the problem. You have to make a folder/s (called Library) of all pdfs relevant to your work based on the key words. It is an user friendly software, if you have any questions, contact customer service, they will help you modify or create new styles while formatting your thesis, manuscript, reviews or commentaries.

Good Luck.

I can only agree with Stoyan Pavlov. To do a HDD wide search for pdfs I recommend you to install Google Desktop. It will index EVERY word of any File on your HDD. It doesn't matter if you are searching key words, authors or just a number. The best thing is, you don't have to care about the file name. No more clicking through your filesystem, its just a matter of seconds to find your desired paper/file.

Hi Anna,

I was in your situation. but now i m enjoying Mendeley (desktop versions. http://www.mendeley.com/). it is really nice.

I use Papers2, the new version. If you are using Mac, I think that it is the best. I tried EndNote X4. Endnote allows you to customize different reference styles, but I don't know if it can retrieve all the fields data (authors, year, journal, etc...). I don't know if EndNote implemented any kind of DOI recognition either, so it can download the article information in the computer. I have to say that I had some issues with the abbreviations too.

In summary, I prefere Papers2 for its simplicity, ease of use and compatibility with Word and Pages. Endnote crashes sometimes with word.

There are so many options that's are really amazing to work within a minute.

Need your vote to prioritize, which one is the best and quickest............?

There's also another reference management tool called "Citavi" (http://www.citavi.com/). More or less, it's quite similar to Endnote when you look for functionality but it's a little more eye candy.

I vote for papers2. If you have a Mac.

But, in the other hand, I have to acknowledge that EndNote is very powerful because it lets you edit the reference style you want to use for your documents. Moreover, it supports grouped references, papers2 still doesn't support it.

My Vote is for Zotero combined with Mandeley (there is actually very good compatibility between zotero and mandeley). If LaTEX and BibTex compatibility is needed, than Jab REF is also a must. The advantages of such combination are free software, fast database building and fast search inside the database, a complete compatibility with any text editing and reference management software (citation database can be exported as xml, bibtex database, ris format etc.), enormous amount of citation styles are supported, zotero (and i think mandeley too) uses the citation style language (CSL) and with littlle effort citation styles can be edited to your liking or even new ones can be created.

In addition I use one small but very useful tool that is really helpful. It saved me significant amount of time and allowed me to build my database from scratch using only the reference list in my articles - it's a tool called clipboard to bibtex (cb2bib). If you paste inside a citation information (even if it is partial) it searches several databases and fills the gaps, retrieving the entire citation information and converting it into bibtex format.

Mendeley is very handy but as soon as you start to organize your references to create a reference list for your publications you'll reach its limits quite soon. For everything above just organizing some pdfs on your harddrive you need something like Endnote or Citavi.

But there is a very nice feature in Mendeley which Endnote doesn't have (as far as I know. Please correct me if I'm wrong): Automatic renaming of your pdfs according to their annotations. Depending on how many publications you have to rename it will save you a lot of time.

I'm using Mendeley and find it the best app for this job I've ever come across. Very happy with its search capabilities and built in PDF access.

I don't use a reference database. I Just rename the pdf-files in a scheme like "FirstAuthor_Year_Journal_Title_optional:keywords" and store them in a tree of directories to keep papers on the same subject together. Is quick and easy in daily life and prevents a stack of unorganized papers with ambiguous file names growing, especially, when you use several computers and sometimes exchange papers with colleagues.

I think, it's less work to include the relevant papers then in a reference managing software (if one really needs it) when you know that you'll cite them.

Another option would be to create a simple e.g. SQL database and add keywords, comments etc.

A file system based organization is perfect, but what do you do when it comes to citing and creating reference lists. Until i tried zotero i lost about 5-10 hours while writing a paper only to get the reference list in the correct format and the correct information. And when it turned out that the publication requires some special citation style and I forgot to check in advance, it was really awful then - it took several days for example to change an author-date format into let's say Vancouver style. Now with the zotero i cite as i write and i don't really care for the citation style, misspelled authors or even missed citations - if you want to change the styles it's simple as few cllicks, if you misspelled author name or publication you just need to update it correctly in your zotero database, if you forgot a citation - you just put it in the right place and update your list (two clicks). This really saves me time for actual writing. And the database is build almost by itself as i browse the net and the publications that seem interesting to me.

I have had very good experience with Mendeley. More details here

http://www.mendeley.com/spread-the-word/

Recently nature journals are promoting "readcube". I have used endnote, mendeley and readcube.

I like endnote for reference management, but don't use it for anything else. Mendeley and readcube will read the metadata from your library and will help you to organize your library. Comes pretty handy when you have many, many papers (as an average grad student does). I personally like more the user interface of readcube, and believe that it may be faster than mendeley. Mendeley is quite slow when you ask it to search for specific terms.

'Papers' works well.

http://www.mekentosj.com/papers/

Try Zotero. It is free and made by scientists for scientists. It works with firefox and once installed will appear as a little icon on the bottom right corner of the fire fox browser. I have my entire library of papers from my PhD and postdoctoral work as well as many others as a Zotero library. You can also use it as a reference manager.

http://www.zotero.org/

Endnote is a common Microsoft product which fulfils the same functions as Dayanjan has listed above for Zotero. Although it is not exactly free.

Check out the Papers app for Mac.

Will, here all colleagues talk about the services that facilitate only the references or citation part of the artiles, but is there any software or online service which can also formate the whole document in accordance to a particular journal?

EndNote

@Najm ul Hasan: The problem with document formating into a certain style is very old. This is very hard with the usual office text editors, because they are "WYSIWYG" (what you see is what you get") software. If you look hard enough you may find customized templates and/or macros for reformatting in to a certain style but they do not always work as expected. I recently discovered LyX (although it has been out there for a while) . It is described as "WYGIWYM" (what you get is what you mean) and can be considered (although this isn't 100% correct) as a Graphic User Interface to LaTEX, which is a Tagged Markup language for document formatting and processing . The thing is when you write your paper you don't care about formatting. When you are ready however you can export the document into any style or format available, and believe me there is a huge number of them because many serious publishers are using LaTEX for their Document processing (or at least provide styles for others who do). I do not want to sound as though I am advertising for this package, but I was really impressed. Of course it requires a bit of adjustment and learning, but I think it is worth every second of it (and there is huge help database too).

Not everywhere there is license for EndNote. It is a rather expensive piece of software and for example we here in the former Eastern Europe can't afford it. That is why the powerful and cheep open source alternatives are so important to us.

@Stoyan Pavlov, @Jose Carlos Penteado,@Johannes W. Dietrich

Thanks guys for your kind guidance, I really owe you for this act of grace!

Try zotero found at www.zotero.org. And one more thing, you don't have to sweat a dollar cause its free of charge .

you can use EndNote, this is best one , I used

Hi Anna,

In my opinion, Papers (from Mekentosj.com) might be the best solution for your question. It is an 'iTunes-like' library system with very powerful search options. It has lots of very useful and handy features.

You can check it out here: http://www.mekentosj.com/papers/

Endnote

there are some free programs like Mendeley (http://www.mendeley.com/) or qiqqa (http://www.qiqqa.com/)

Endnote

Try mendeley. it is free ! and has a powerful features. yes it is not as good as Endnote But it is free

I use Mendeley!! It´s wonderfull... You can download online and there is a add for Microsoft word for generate references automatically, highlight the most important ideas in your pdf and other things... Look at the link: http://www.mendeley.com/ !!! Hugs!!!

Just buy endnote and relax. There is a new version out.

Hi Juliane, This is really a pain to arrange your .pdf files in computer, specially when you are going to write some papers, its difficult to access in the sea of articles. I too faced the same problem. As many others has suggested you can use EndNote for managing your references, from where you can search and cite your ref directly onto your word doc. Other useful reference manager software I used is "Mendeley". Its a ref manager and you can search, store and cite your pdfs in different styles. This can also store the full paper in pdf format (if available). Its free and i found it very useful. Another free ref manager i have seen recently is the "Readcube". Although i have it but can't tell you ore on it since i used it very rarely, but its too free.

Try Zotero (www.zotero.org). It's free and open-source. There's a standalone version and one that works as a Firefox extension. It will index the text of your papers for searching as well as allow you to organize them by folder and by tag.

It also has plugins for Word and OpenOffice.org/LibreOffice to manage citations in documents.

I recently found a web script which can be installed on an intranet : I,Librarian (http://www.bioinformatics.org/librarian/). You can give it a chance as the man is alone to develop the application and there are for the moment interesting features.

Mendeley is great. May I also suggest as an additional aid, use Utopia Documents (http://utopiadocs.com) to discover more about your papers. It uses web based resources to turn your PDFs into live interactive documents. It is also free.

Vermel,

That's interesting software, but somehow there's a trailing ")" on your link that prevents it from working. If anyone else in interested in an intranet-based solution, be aware that there is an old page for I,Librarian on bioinformatics.org (http://www.bioinformatics.org/groups/?group_id=131) that hasn't been updated since 2004, though Vermel's link shows that it's still under active development.

Zotero also has an online sharing function, but I've never used it.

Yes, sorry for the trailing slash. I,Librarian is still active as the last version (2.9) was published on the 03/09/2012 (or 2012-09-03).

http://www.bioinformatics.org/librarian/

I prefer Mendeley

- multi-platform

- free ( 2go for paper, 2 go for sharing)

- nice website

--> share library for journal club

--> share pdf comment

--> create closed workshop (for shared co-authorship)

- save + update of your library automatically

- tool allowing good exposure of your article via google scholar

- robust integration of reference in several text editor

- small software, could be install on server portable

To my mind, zotero miss a bit of development to be at this level (but I'm confident concerning the open source community to solve them), and end note is way to big and to expensive to recommend it to somebody without an university licence.

readcube will also be better option. It is also having as many options as there in Mendeley...

This is a problem that we all face nowadays. It was good to see so many replies with different possibilities. Thank you all for the tips that I will pass on to my students!

the best software and a open source software that can be used to manage references would be Mendeley, further info can be obtained from mendeley.com, I am pretty familiar with using most of the reference softwares such as endnote,refworks, mendeley etc.

The best program I have seen ever for finding files is "the Copernic Desktop Search". It is unbelievable in finding documents in your PC. You can find any document by searching only one word in the PDFs. It is a free version (so-called home) that you can download it, then instal, and finally the software will index all the words in your PC at just 1 or 2 days, depending on total files.

Enjoy it.

Wow! This has helped me a lot! Thank you all!

I also started using Mendeley and i am still very satisfied with the program. Only letdown for me is once you reach 1GB they will charge you (But i will do so :) ) and when you prepare a manuscript for a journal it is really hard to create the citation style on your own when its not in the Mendeley library.

I use Mendeley for organizing my PDF files (it works like iTunes)

ENDNOTE seems best when you are writing a paper or thesis. The "Cite while you write" function is very good.

We use Zotero , it is very good. Reference manager can also be used.

Julianes comment showed the one limitation that made me use zotero instead of mendeley. In Zotero you can put the database and your references everywhere on your computer, including synchronization services like dropbox or sugarsync. I now have my whole article collection including all full text pdfs (~700) inside sugarsync. This way I can search and download fulltext articles from the university (which works like a charm in zotero since it runs inside your browser) and read them later at home without further actions needed. The easy downloading is in my opinion the greatest strength of zotero. If i come to a journal article page i simply click on "add reference" and zotero will automatically retrieve the full text pdf if my university has a subscription.

I would recommend you Mendeley http://www.mendeley.com/ ... I've tried ReadCube but Mendeley is better for it has more tools.

I think EndNoteX4 for Windows will be a better option than any other.

Silvia Sato. Thanks for posting Mendeley website, great job.

Thanks, Its awesome :)

EndNote is a good program to manage references. You can create separate libraries and organize your PDF's. It also helps to immediately update your citation styles to any Journal.

The two leading alternatives to Endnote (in some features), Mendeley and Zotero, are (essentially) freeware, although you can give Mendeley money for online storage facilities.

Endnote can afford to employ a large enough team to design and constantly improve their software, but that comes at the cost of a licence fee, although this is often covered in some institution. The question is: are the freeware alternatives suitable?

I tried Endnote 3 years ago and found it nearly as limited in its possibilities as is Reference Manager (did one ever realize that those are sold by the same company - Thomson Reuters?). I just looked up Endnote X6 features and every single feature (uh oh - endnote sync) has been in zotero and mendely since they exist. Collaboration? Was ever since in Zotero. Online storage? In Mendeley and Zotero you have 0.5-1 GB free like in free beer (also since long ago) and can purchase more storage in both programmes; further above I described how to use Dropbox for free online sync. Thompson advertises 5GB free - for 2 years, after which you pay.

And still there is no browser integration?! What is the sense behind browsing for new articles on PubMed or elsewhere, and once you found something worthwile, you have to open another program, search again for that article, save it...? I am searching for everything in the browser, so it is only natural and ergonomic to also store my information from within the same user interface. And here is one big plus for Zotero - it can store everything (offline websites, blog entries,...), not only journal articles.

I actually see no impact of that "large enough team" on the innovative potential of the Thomson Reuters product line (not to mention the Windows 95 look), their only merit is copying the good ideas of the Mendeley and Zotero devs, resting on their laurels earned long ago and selling it off to people to shy or conservative to try something new.

Sorry for probably offending some people, I just felt the need to add some things to the discussion.

Yes, Reference Manager and EndNote are both Thompson Reuters brands. They also bought a competitor of both products and effectively killed it off, called ProCite. It was liked by both Librarians and Medical Researchers. I think the point about Thompson Reuters is that they have pursued a policy of market domination, buying out competitor products. Sadly it worked for a while. They were able to iterate endless versions of EndNote and Reference Manager without moving the software from a pre-Internet model into the Internet age. Although EndNote Web is a nod in that direction. My view is that they have been complacent and caught out by Mendeley and Zotero with their free Basic Versions. Both offer a very credible desktop reference management software for free compared to the paid for EndNote/Reference Manager product. Mendeley's aim is to use it as a tool to get the users to build their database and user base. It's an interesting new model that seems to be working for the moment. It is certainly smart, innovative and forward looking.

Endnote can do these for you. I have been using it for almost 20 years. You can attach the PDFs to the reference records. You should also avoid typing any information into Endnote, and rather import them from public databases (such as PubMed).

When it comes to managing and formatting bibliographies in your word files, I find Endnote the best. It is supported well and almost every reference style is available. The search feature is awesome as its very fast and a number of databases can be searched with category wise search terms. In my experience, Endnote can handle very large number of records very easily, while other programs usually hang/crash and demand more RAM. Endnote can also attach a PDF to a record in the library and the file can be accessed conveniently. Personally, I do not do it because its not possible to attach every record to its PDF, if you have high number of records to keep. I would simply search in readcube and it is found in no time.

For managing your PDF files, readcube/mendeley both are good as they can scan all the pdfs in your system and extract the bibliographical info from them. Old files generally do not have this data embedded, so can not be detected. But both programs are equally good at arranging the files the way you want and finding a PDF you downloaded last year is so easy with these.

I too favor Opensource stuff but in reality, you have to find a combination that works for you. No program can cater to all of the intended users in an identical way.

There are many messages most say endnote. I understand from the question than the matter is organization of pdf references. It is very easy. You do not have to arrange them in any way. Put them in a folder and index with acrobat. Then search them using acrobat. You will be amazed....

I simply love Papers2. It's an all-in-one (managing pdfs, reading, annotating, editing ref lists...). My students use Zotero or Mendeley, which is very similar to Papers, because they're free.

Yeah!!! Endnotes...

This is not what you are looking for but I hope you find this helpful too. There is "find" feature under edit in Adobe and Foxit readers. This Feature makes it possible to search all pdfs on your system for any word. You can access the "Find"feature using the Ctrl+F keys.

The Menu under find offers:Find next in Current pdf;Full reader search;Search of bookmarks and comments.

I would like to revise my answer, because I do not think that not all are aware of this feature in acrobat.

You do not have to care where the pdf files are, let them stay where they are.

Then go to "Tools" on the ribbon on upper right.

Then select document processing,

if document processing not present you could add that through the small botton below SHARE.

Then select "Full text index with catalog"

Then name the index in the coming menu and select whole hard drive (if you want) for pdf indexing, and exclude directories you want. It will find all pdf s and index them. Once you have the index, then you can use that in the find menu, there, select the index you named to search also.

Then you can use different types of "word" searches inside pdf.

For example you can find documents that include "fish density stress" words only.

It is pretty good,

I find Endnote or Refernce Manager are best for writing with, i.e. putting the citations and bibliography in once you know which papers you are going to use. However, I'd also use a program such as Mendeley or Papers to help organise your whole library as they are much more fluid. You can tag and favourite papers and link more easily to the PDFs in your library.

recently, I found a new program called qiqqa http://www.qiqqa.com/

I think it is really good. It finds similar papers to the one you are reading, finds automatically references....

@ Jolanta: Just reading from their web page it looks very similar to Mendeley or Papers, apart from the "discover new papers" tool. Is that tool really good?

@ John: I find Papers also excellent in inserting citations and writing bibliographies. I’ve totally stopped using EndNote.

here is a link to webcast about this function http://www.youtube.com/watch?v=ttg0B1RFuaw

I would recommend you the TaggTool software. You "stick" labels- tags to any of your files, including PDF files, with a meta-data - keywords, that are important for YOU.

I find this very useful, because many times I keep one full-text PDF for several reasons - interesting design, new RNA extraction method, interesting graphical representation of data, etc. Making a system of folders is practically impossible when handling with so many PDFs...

Try also reacube very easy to use, free

I highly recommend Zotero. It is suitable for both mac and windows. Very easy to use when you cite for papers.