Qiqqa provides more functionality. In particular it finds themes by autotagging.

In terms of nice usability & GUI, open access, good integration with Word, web importer, Zotero is comparable to Mendeley. The difference is that Zotero does not provide users with the latest papers related to our collections as Mendeley does.

In terms of Word connection, I believe that EndNote and Docear also provide similar functionality, although they differ in other aspects.

if you care about seamless and intuitive word integration, try Zotero:

https://www.zotero.org/support/word_processor_integration

You also try Cite4Me or citation machine.

The choice depends on the specific needs, because the basic functions of these programs are quite similar. I presently use JabRef which is TRULY free and opensource.

Try endnote

Qiqqa has been largely abandoned by its creator, and still has some outstanding issues. It's not a bad piece of software, though.

Kierin Jeffrey Mackenzie : What outstanding issues do you have that you feel you would like to be fixed?

I have been using ENDNOTE program since 10 years without any problems.

It can organize references accurately and according to the style of journals you required.

Besides it imports from Google scholar effectively

End Note

Nice and interesting query!

EndNote

A note about EndNote: I'm not using EndNote myself, but I often receive documents from colleagues and students who have been using EndNote, and unfortunately I have often discovered various errors this "automatic" software and collecting from the web have introduced, where some typical errors are related to the author names, e.g. special country specific letters not among the 26 ones in the English alphabet (e.g. æ, ø and å and their capital ones in Norwegian) may end up in many strange (and wrong) letters or combinations of letters, and even characters used in articles for marking the author affiliations (e.g. a, b, c, ..., *, other special characters) at the end of the surnames have ended up being wrongly part of the author surnames. So care should be taken.

End note or Zotero. Any of them would be a good replacement for Mendeley which as you indicated, is currently fraught with numerous challenges.

I agree with my colleagues! Zetero is worth a try.

Ian Kennedy, much of the functionality falls apart with larger libraries containing more than about 8 GB or so. The workaround is to create smaller libraries, and then use the tools on those.

I have been a big fan of Citavi due to its easy UI and powerful functions for knowledge management. In the latest version, you'll find decent group functionality as well.

Not OpenSource but a good (the best in my opinion) alternative is Biblioscape. It is licensed , but the price is worth its robustness and quality. I have been a happy user for about 15 years. Zotero is definitely not a good option, you will experiment even more problems than using Mendeley.

Endnote is good!

I have been searching for alternatives to Mendeley too. One option that I'm considering now, is to use a PDF reader with good annotation capabilities such as FoxIt reader (https://www.foxitsoftware.com/pdf-reader/), combined with a desktop search system (there are many, both free and commercial), or using the search feature in some online storage service like Dropbox or Google Drive.

This would cover the search and annotation features, which are the ones I'm mostly after anyway. For the reference management, I find that Mendeley ends up generating too many errors anyway, that I still go out to fetch the original BibTex strings directly from the respective journals online, when I'm citing stuff.

I was a bit tired of Endnote and Mendeley. I have just downloaded F1000Workspace. It looks perfect for what I need. I will try it out for 30 days and let you know.

Thomas Brudermann

Milena Gurgel Teles any news on F1000Workspace? Would really like to know how it works!

Dear colleagues:

As an alternative to Mendeley you can try "citationsy" (https://citationsy.com/) or option "Cite (")" in the entry My library of scholar.google** best regards

*** https://scholar.google.cl/scholar?oi=bibs&hl=es&scilib=1

My 2 cents on the current state-of-the-art regarding reference managers and why Zotero seems like the only alternative for somebody looking for a desktop reference manager.

https://medium.com/swlh/fantastic-reference-managers-and-where-to-find-them-a412621eb4ba

Thanks, Niccolò Granieri , ZotFile seems to be very useful to avoid paying Zotero subscription. I am looking for a better .pdf reader to use together with Zotero, any suggestions? I am using Mac's 'Preview' but if often crushes and has not many updates in functionalities, any idea on what good open-source software is available out there?

Matias Milia I went back to using Preview, it wasn't working that well but with Catalina's update they seem to have fixed a lot of issues. There is PDF Expert, even though I am not willing to pay £80 for a PDF viewer.

Thanks Niccolò Granieri , I haven't updated to Catalina since I've heard it has some troubles with TexShop which I use a lot to write most of my work. Any clues on that? some insight you might want to share?

Matias Milia I use TexPad to write my LaTeX documents and it works perfectly on Catalina.

Great, I think ZotFile will give me just what I was looking for. It extracts annotations from .pdf and export them to zotero. It will help to share files with tablets and phones. Will give it a try!

http://zotfile.com/

https://en.wikipedia.org/wiki/Comparison_of_reference_management_software

Citavi is very userfriendly along with its chrome plugins (reference picker)..the only drawback is that the free version has some limited functionality. https://www.citavi.com/en

I have wasted half a day struggling with Mendeley and am so frustrated that I don't have enough words. All my documents suddenly vanished from the offline version. Then I checked offline and attempted to sync and then documents vanished from the online version as well. All I got was a message "Access denied"

Anyone tried https://www.readcube.com/home

Yeshasvi Tirupachuri I had high hopes for ReadCube but they've been pretty flaky with their online presence, they've been promising a desktop app for ages without actually releasing anything and overall the experience I had with them was not good. I used to love and own Papers 2, and that was a great piece of software!

Qiqqa looks promising, especially after it was open sourced in July 2019.

https://github.com/jimmejardine/qiqqa-open-source

Useful features:

• PDF annotations and annotation report
• full text search
• OCR

Hello Thomas,

I have been a Mendeley user since 2011. Startig from 2018-19 I moved to Zotero as it seems more flexible option. Two main reasons I switched to Zotero are:

a) Zotero supports Linux and Libreoffice.

b) Zotero support GoogleDocs.

another important feature of Zotero is an open access to bibliography catalogue (folder), which Zotero creates in you home folder (In Mendeley this is an encrypted single file (archive) since some of 19.x version).

Regards,

Vjaceslavs

Dear All, I am a Mendeley user since 2011, an official adviser and reding lectures about it. During these years I see constant improvements and de-bugging. I see no problem using it. YES, I met some issues with sharing a common folder, BUT just need to carefully read rules and instructions (!),. In my case (with many years of teaching Mendeley (!)) I made a simple mistake - shareed not PRIVATE, but invite-only folders. That's all! when I share "Private-only" my colleagues could see a full-text pdfs. Working on-line with Science Direct is possible to send source(s) directly to mendeley, but I prefer via downloading file, or if I do not need the whole pdf, just export BibTeX file with bibliographic info for one or multiple sources. ONE limitation I really met, this is what about mention Vjaceslavs Lapkovskis - no possible to use Mendeley in Google-doc, that YES! But I can't find other drawbacks for the moment. If YOU have some questions or issues - please ask me I will be ready to help. Before choosing the citation software please check first FREE CLOUD STORAGE, In Mendeley case, it is 3.0 Gb.

GOOD LUCK for choosing optimal solution FOR YOU !!!

Andrei,

The one reason I do recommend to my students avoid Mendeley is the final format of references and citations. Cloud options and cloud functions of Mendeley are quite good, but when you create a manuscript, and select a bibliographic style to the final document, Mendeley is a mess. Usually, I carefully proofread each reference and citation, Mendeley always omit elements of the references. One could say it can be due to a not proper registry of the fields for each reference, sometimes it is, but even after fixing the usual errors, the reference format is incomplete or even wrong. Moreover, after fixing carefully the fields for records, Mendeley automatically overwrite the manual work, which is a real weak and a headache. What's wrong here?

I do recommend Biblioscape, a very solid bibliographic manager, it lacks many cloud functions, but it makes perfectly the main task of any software that aspires to be a professional bibliographic manager: reference and citation (amongst others).

Dear Willington,

thank you very much for the interesting software - Biblioscape. I already take a look. Imeetdeatly, one think what I suffering - it is easy-understandable style editor. Regarding the changing style in Mendeley - I do not meet such problem. Actually, if the document has DOI Nr. it is shouldn't be some problem. In manual information addition - it's easy because of it you should strictly follow the rules. I know, that some style look or strange or mistake. for example in IEEE style "Article title," Jour.Chem.Soc. the comma should be after the brackets. But in common I almost happy with Mendeley.

Yes, as you add or delete any ref. or made refresh - the bibliography will be updated and your changes disappear.

Change to Qiqqa. You will never change again.

Zotero is the solution!

Auraticum (https://auratikum.com/) seems to be a good online based product. It's not just a reference manager but also includes note-taking. Check out this comparison blog.

https://auratikum.com/blog/4-best-endnote-alternatives/

https://www.youtube.com/watch?v=YnaTF3bdZMI

https://auratikum.com/

I've been using EndNote for years and I love it. Easy to use, very fast, and good support.

You may try ZOTERO.

You can try qiqqa

Sciwheel simplified import from EndNote and them it is compatible with MS Word and Google docs. Web based, so no problem with compatibility. Freemium version has most functions running except no more than 3 projects and no recommendations.

And besides, a lot of communication functions - sharing of projects, notes, alerts, manuscript, discussions.

anything more, please write to [email protected]

Jabref is a good open source reference management system. The main interface combines a table and a form where you can edit each reference. It can retrieve references from the web. Bibliography files are plain text .bib files. I recommend archiving them with a version control system such as git. That way you can share and merge bibliography files with others.

Switch to EndNote. For me it is perfect but unlike Mendeley it comes with a cost.

Try Zotero

You can try the free personal research assistant, Zotero.

Yes, although Zotero is a little clunky at times, it is the only viable alternative. (If you change your password on some journal that happens to be in the Elsevier stable, then you break everything, including your Mendeley password). Even with Mendeley desktop, Elsevier has the database on your own computer encrypted, and so you break that also (and they can revoke your password any time they wish - and suddenly your research simply stops.)

You can try Endnotes, Zotero, etc.

Switch to Zotero please

Trying to advance my work with Mendeley has been endlessly frustrating. I had to work between devices for some time because it wouldn't work properly on my desktop. Now I cannot log in anywhere, I cannot reset my password, and the deadline for submission of my thesis is looming. I used to use ENDNOTE, Zotero and JabRef. Looks like I'll be going back to the latter two to circumvent the frustrations. Mendeley was great while it lasted, but I think that's it for me.

Matias Milia I also used the Preview on my Mac, but now I'm using Acrobat DC Reader. It's free but doesn't have the functionality of Adobe Pro. Nonetheless, you can add comments and highlight things, and you can also use the table of contents. One more advice: If you want to set it as your default PDF reader, go to 'get Info' (of the PDF file), then to 'open with' and then to 'change all'. This way it will use Acrobat Reader every time. If you just change the App by clicking on 'open with' -> 'other' -> 'always open with', it somehow doesn't work and you will have to change it every time you open a PDF. I don't know if it's the case for everyone but for me that information was very helpful.

Frederik Walter actually I end up with a nice workflow using Skim (https://skim-app.sourceforge.io/) in connection to ZotFile (http://zotfile.com/) to harvest my notes and highlighted passages into my zotero. You can connect both and automatically export these to the notes in the bibliography entry in Zotero. If you want me to expand about it, let me know.

Perhaps the biggest problem with Zotero is the inability to merge citations after they have been placed into the text. This has been requested for years, and the response is usually the same: "What do you want that?" I have seen many work-arounds, and could not get any of them to work consistently.

I use Paperpile. Give a try ir works well with Google Docs and is much better than Zotero

I use a Chromebook and Google Docs. Paperpile works smoothly with this combination. No hiccups till date.

Been using Mendeley for a while, but just came across Paperpile and I have to say it made my day!

Haven't written up a report since coming across it, but apparently it works with google docs, formulates your reference list, allows instant citation, leaving no work for referencing at the end of writing and has a very nice metadata sourcing algorithm - far better than Mendeley's IMO.

Looked to good to be true!

Next add-on I'm hoping to find is a databasing-excel spreadsheet tool that allows tabling of pdf papers in folders in order to group them into various categories, allowing for some better organisation.

Till then!..

Bibdesk at https://bibdesk.sourceforge.io, if you’re using a Mac. Or you can use jabref. Of course these tools ate for latex.

JabRef can collect references from the web using extensions for many web browsers and has variuos citing capabilities:

• Support for Word and LibreOffice/OpenOffice for inserting and formatting citations
• Native BibTeX and BibLaTeX support, perfect for text-based typesetting systems such as LaTeX and Markdown.
• Cite-as-you-write functionality for external applications such as Emacs, Kile, LyX, Texmaker, TeXstudio, Vim and WinEdt.
• Format references in one of the many thousand built-in citation styles or create your style

https://www.jabref.org/

Try Zotero

Mendeley was greatly sync through my devices. Zotero is not available anymore for iphone. Any tool? Paperpile is free only for 30 days ...

Question: "What are decent open access alternatives with good usability and team/multi-user functionality?"

Answer: smaller tools that do one thing and do it great: git + vim + other open source tools to edit and collaborate on your bibliography files under version control.

• Copy plain text citations in bibtex format from journal pages or search sites into a text file ending with ".bib". You can use Jabref if you prefer a GUI, but over time, you'll realise plain text is quicker to work with.
• Archive and edit your article and bibliography collaboratively with git. You can learn git from the pro git book. Just learn a handful of commands to check the status, add, commit, push and pull. Git can be used to archive all pdf articles in your literature review. Use pdfgrep to search text in all pdf articles at once.
• Edit your article in Latex format. You can get good help from tex.stackexchange. Or use Lyx if you prefer a GUI.
• You can embed small (< several Mb) curated datasets and the R or python code for your result tables and plots into the git repository to make a fully reproducible article.

Embrace the learning curve.

I've been trying out Paperpile. Unlike Zotero it easily copies all your papers and folder structure from Mendeley, and it interfaces with Google Drive. Might be the best option.

I switched to Zotero last year, after mendeley didn't follow up with updates to MacOs. It's free and it works with MS Word and Google Docs.

I really like Bookends. Just give it a try it runs on all my devices and I like the pdf annotation. Hope they devlop this further.

https://www.sonnysoftware.com

I am also back on Zotero after several years using EndNote, and then, Mendeley. I am advising and training my students to use Zotero. Thanks, Nico Steckhan for the info about Bookends. I also encourage my students to stay flexible, and not get locked into one platform or one way of doing things. Will share this with them in our next lab meeting.

Zotero is an excellent alternative.

I have the same problem here and will try Zotero, thanks for the suggestion. After years of dealing with annoying bugs, the final blow to Mendeley was the new split into Mendeley Reference Manager + Mendeley Cite. They've just stripped the software of its most useful tools!

The same experience I had with using Mendeley as a reference manager program.

So disappointing how things have turned out with Mendeley. Will try Zotero.

BibDesk and JabRef are simple but powerful.

I have been using Zotero for a long time. It is free and works well with Word and OpenOffice, and somewhat well with Google Docs. I recommend using the Add-on zotfile for working with pdf files. Great App.

Any good alternatives just for managing your papers library? (I already use Zotero for citations).

Mendeley is a monumental pile of crap now. It's shocking how many bad design decisions they made these past couple of years. When it's syncing you can't use the search function, it logs out almost every time you close the laptop but it doesn't save the password so you have to type it again, it's poorly synchronised between gadgets/cloud, etc. It's like they deliberately made decisions to make it awful.

> Any good alternatives just for managing your papers library? (I already use Zotero for citations).

Do you mean your own papers? In Zotero, just create a new folder (it's called a collection), and place your papers there. NOTE: They are a copy of what is held in the main area. You may wish to experiment to see what I mean.

https://library.stanford.edu/research/bibliography-management

https://library.si.edu/sites/default/files/tutorial/pdf/endnotezoteromendeleychart-2018sept.pdf

https://libguides.wustl.edu/choose

https://aut.ac.nz.libguides.com/managingreferences

I just switched from Mendeley Desktop and Reference Manager to Zotero. You can transfer all your articles with annotations relatively easy.

Zotero is a good option

EndNote is a better choice.

Manish Agrawal For most people (especially students), EndNote is not a viable option, because it is not free.

Have used many reference managers and been very disappointed with them. Tried to set up a Mendeley account very reluctantly and cautiously. When you log in and try to change your password, you are pushed over to Elsevier and everything stops. Why can't Elsevier let people use this apparently-good software without inserting its own desire to capture our information?

Will John Martin Worse than that: if an Elsevier journal has problems, and your password gets corrupted when you try to log in as author or reviewer, then everything connected to Elsevier is blocked. That means you cannot access Mendeley, and so your research stops. (Yup, happened to me). And, when Elsevier took over Mendeley, they also encrypted your Mendeley database, so you're completely blocked from accessing it any other way.

Yes, I think a large number of people do not realise that: your Mendeley database on your own computer is encrypted, and Elsevier controls the password. Lovely!

Mendeley adds and repeats the same citation everytime I open the word plugin. It keeps asking me to turn on tracking, once I do that, it deletes all references and re-inserts duplicates upto a paragraph of the same citation. Going back to manual reference management.

Dennis Munetsi You really might want to give Zotero a shot. If you like, I can send you the (quite detailed) notes I give to my students. Let me know if you (or anyone else) would like them.

Ken Masters I'm getting very fed up with Mendeley. If you're willing could you please share me your notes for using Zotero?

Nikhil Vasireddi (and anyone else) Sure - please see attached. (Note, these notes are intended for undergraduates straight from school, so might be rather detailed. Please don't feel patronised. If you spot any errors or problems, please let me know).

Thank you @Ken Masters

Following the discussion here, I just found out that the new Zotero 6 (https://www.zotero.org/blog/zotero-6/) has a built-in function that allows exporting highlights and comments to its notes. This new function is available in the 'add notes from annotations' tool. It does what ZotFile used to do in an integrated manner. Then, you can easily extract highlights and comments as notes in the bibliographic entry of each text. This tool is excellent when building courses, building extracts from texts, and keeping annotations orderly archived to connect a text's bibliographic information.

Of course , end note is best software to use for referance , I am using it for several years, it's so easy to use..