Docear 1.0.3 Beta: rate recommendation, new web interface, bug fixes, …

Update: February 18, 2014: No bugs were reported, as such we declare Docear 1.03 with its recommender system as stable. It can be downloaded on the normal download page.


With Docear 1.0.3 beta we have improved PDF handling, the recommender system, provided some help for new users and enhanced the way how you can access your mind maps online.

PDF Handling

We fixed several minor bugs with regard to PDF handling. In previous versions of Docear, nested PDF bookmarks were imported twice when you drag & dropped a PDF file to the mind map. Renaming PDF files from within Docear changed the file links in your mind maps but did not change them in your BibTeX file. Both issues are fixed now. To rename a PDF file from within Docear you just have to right-click it in Docear’s workspace panel on the left hand side and it is important that the mind maps you have linked the file in, are opened. We know, this is still not ideal, and will improve this in future versions of Docear.

Rate Your Recommendations

You already know about our recommender system for academic literature. If you want to help us improving it, you can now rate how good a specific set of recommendations reflects your personal field of interest. Btw. it would be nice if you do not rate a set of recommendations negatively only because it contains some recommendations you received previously. Currently, we have no mechanism to detect duplicate recommendations.

rate a literature recommendation set

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Docear 2013 in review and our plans for 2014

It’s almost a bit late to review 2013 but better late than never. 2013 doubtlessly was the most active and most successful year for Docear, so far. First and foremost, we finally released Docear 1.0, after releasing many Beta and Release Candidates. Of course, Docear 1.0 is far from being perfect, but we are really proud of it and we think it’s an awesome piece of software to manage references, PDFs, and much more. But there were many noteworthy events more, some of which we took pictures of:

We presented several research papers at the JCDL in Chicago, TPDL on Malta, and RecSys/RepSys in Hong Kong. It is always a pleasure to attend such conferences. Not only because they take place at really nice locations, but because you meet really interesting people (for instance Kris Jack from Mendeley, a really enthusiastic and smart guy who develops Mendeley’s recommender system, or Joseph A. Konstan, who is a true pioneer in the field of recommender systems).

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TPDL on Malta

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JCDL in Chicago

2013 hong kong

RecSys in Hong Kong

Almost every year, our mentor Prof. Andreas Nürnberger is inviting his team members to a sailing turn, and so he did 2013. For several days we were sailing the Baltic Sea, learned a lot about team work and had a lot of fun.

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Sailing turn with our mentor Prof. Nürnberger, the Docear team, and some PhD students of his working group

We had the honour to supervise an excellent student team at HTW Berlin thanks to Prof. Weber-Wulff. The students did a great job in developing the Docear Web prototype. It’s a pity that the prototype has not yet found its way into our live system, but we have not had the time to give the prototype the last bug fixes and features it needs. However, this is very high on our todo list.

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Four of the five students at HTW Berlin who developed a prototype of “Docear Web”

Docear is primarily located in Magdeburg, Germany, which is close to Berlin. Therefore, we didn’t think twice when Researchgate hosted the 10th “Recommender Stammtisch” (regulars’ table) in Berlin. There, we could listened to an enlightening talk of Andreas Lommatzsch, and an entertaining introduction of Researchgate’s CEO Ijad Madisch.

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Docear 1.0 (stable), a new video, new manual, new homepage, new details page, …

Today, Docear 1.0 (stable) is finally available for Windows, Mac, and Linux to ico16download. It’s been almost two years since we released the first private Alpha of Docear and we are really proud of what we accomplished since then. Docear is better than ever, and in addition to all the enhancements we made during the past years, we completely rewrote the manual with step-by-step instructions including an overview of supported PDF viewers, we changed the homepage, we created a new video, and we made the features & details page much more comprehensive. For those who already use Docear 1.0 RC4, there are not many changes (just a few bug fixes). For new users, we would like to explain what Docear is and what makes it so special.

Docear is a unique solution to academic literature management that helps you to organize, create, and discover academic literature. The three most distinct features of Docear are:

  1. A single-section user-interface that differs significantly from the interfaces you know from Zotero, JabRef, Mendeley, Endnote, … and that allows a more comprehensive organization of your electronic literature (PDFs) and the annotations you created (i.e highlighted text, comments, and bookmarks).
  2. A ‘literature suite concept’  that allows you to draft and write your own assignments, papers, theses, books, etc. based on the annotations you previously created.
  3. A research paper recommender system that allows you to discover new academic literature.

Aside from Docear’s unique approach, Docear offers many features more. In particular, we would like to point out that Docear is free, open source, not evil, and Docear gives you full control over your data. Docear works with standard PDF annotations, so you can use your favorite PDF viewer. Your reference data is directly stored as BibTeX (a text-based format that can be read by almost any other reference manager). Your drafts and folders are stored in Freeplane’s XML format, again a text-based format that is easy to process and understood by several other applications. And although we offer several online services such as PDF metadata retrieval, backup space, and online viewer, we do not force you to register. You can just install Docear on your computer, without any registration, and use 99% of Docear’s functionality.

But let’s get back to Docear’s unique approach for literature management…

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What makes a bad reference manager?

Update 2013-11-11: For some statistical data read On the popularity of reference managers, and their rise and fall
Update 2014-01-15: For a detailed review of Docear and other tools, read Comprehensive Comparison of Reference Managers: Mendeley vs. Zotero vs. Docear

At time of writing these lines, there are 31 reference management tools listed on Wikipedia and there are many attempts to identify the best ones, or even the best one (e.g. here, herehere, here, here, here, here, here, … [1]). Typically, reviewers gather a list of features and analyze which reference managers offer most of these features, and hence are the best ones. Unfortunately, each reviewer has its own preferences about which features are important, and so have you: Are many export formats more important than a mobile version? Is it more important to have metadata extraction for PDF files than an import for bibliographic data from academic search engines? Would a thorough manual be more important than free support? How important is a large number of citation styles? Do you need a Search & Replace function? Do you want to create synonyms for term lists (whatever that means)? …?

Let’s face the truth: it’s impossible to determine which of the hundred potential features you really need.

So how can you find the best reference manager? Recently we had an ironic look at the question what the best reference managers are. Today we want to have a more serious analysis, and propose to first identify the bad reference managers, instead of looking for the very best ones. Then, if the bad references managers are found, it should be easier to identify the best one(s) from the few remaining.

What makes a bad – or evil –  reference manager? We believe that there are three no-go ‘features’ that make a reference manager so bad (i.e. so harming in the long run) that you should not use it, even if it possesses all the other features you might need.

1. A “lock-in feature” that prevents you from ever switching to a competitor tool 

A reference manager might offer exactly the features you need, but how about in a few years? Maybe your needs are changing, other reference managers are just becoming better than your current tool, or your boss is telling you that you have to use a specific tool. In this case it is crucial that your current reference manager doesn’t lock you in and allows switching to your new favorite reference managers. Otherwise, you will have a serious problem. You might have had the perfect reference manager for the past one or two years. But then you are bound to the now not-so-perfect tool for the rest of your academic life. To being able to switch to another reference manager, your reference manager should be offering at least one of the following three functions (ideally the first one).

  1. Your data should be stored in a standard format that other reference managers can read
  2. Your reference manager should be able to export your data in a standard format
  3. Your reference manager allows direct access to your data, so other developers can write import filters for it.

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Which one is the best reference management software?

Update 2013-10-14: For a more serious analysis read What makes a bad reference manager?
Update 2013-11-11: For some statistical data read On the popularity of reference managers, and their rise and fall
Update 2014-01-15: For a detailed review, read Comprehensive Comparison of Reference Managers: Mendeley vs. Zotero vs. Docear

<irony>Have you ever wondered what the best reference management software is? Well, today I found the answer on RefWorks’ web site: The best reference manager is RefWorks! Look at the picture below. It might be a little bit confusing but we did the math: Refworks is best and beats EndNote, EndNote Web, Reference Manager, Zotero, and Mendeley in virtually all categories.

Comparison of reference management software - Refworks is the best reference manager

Source: RefWorks

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Docear4Word 1.1: Support of “Suppress Author”, “Author only” and some other nice options

Docear4Word 1.1 is available for download and it offers two new features that will improve your work with references in Microsoft Word a lot. Actually, we added two new elements to the “Add References” dialog.

The first one is a “Docear->Docear4Word” button. It’s intended for adding several references at once when you have multiple BibTeX keys in our clipboard. And here is how it works: Most references managers (e.g. JabRef and Docear) allow you to select several reference entries from the database and copy their BibTeX keys to the clipboard. That means you have a string like “Cohen05,ritchie2008,Eto12” in your clipboard. Now, when you press the “Docear->Docear4Word” button, Docear4Word will automatically get that string from the clipboard, identify the BibTeX keys and select the references belonging to the keys. This will make inserting several references at once much easier.

New Docear4Word Features

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How to write a thesis (Bachelor, Master, or PhD) and which software tools to use

Available translations: Chinese (thanks to Chen Feng) | Portuguese (thanks to Marcelo Cruz dos Santos) | Russian (thanks to Sergey Loy) send us your translation Writing a thesis is a complex task. You need to find related literature, take notes, draft the thesis, and eventually write the final document and create the bibliography. Many books explain how to Read more…