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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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By Joeran Beel, ago

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, here, here, 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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By Joeran Beel, ago

New paper: “A Comparative Analysis of Offline and Online Evaluations and Discussion of Research Paper Recommender System Evaluation”

Yesterday, we published a pre-print on the shortcomings of current research-paper recommender system evaluations. One of the findings was that results of offline and online experiments sometimes contradict each other. We did a more detailed analysis on this issue and wrote a new paper about it. More specifically, we conducted a comprehensive evaluation of a set of recommendation algorithms using (a) an offline evaluation and (b) an online evaluation. Results of the two evaluation methods were compared to determine whether and when results of the two methods contradicted each other. Subsequently, we discuss differences and validity of evaluation methods focusing on research paper recommender systems. The goal was to identify which of the evaluation methods were most authoritative, or, if some methods are unsuitable in general. By ‘authoritative’, we mean which evaluation method one should trust when results of different methods contradict each other.

Bibliographic data: Beel, J., Langer, S., Genzmehr, M., Gipp, B. and Nürnberger, A. 2013. A Comparative Analysis of Offline and Online Evaluations and Discussion of Research Paper Recommender System Evaluation. Proceedings of the Workshop on Reproducibility and Replication in Recommender Systems Evaluation (RepSys) at the ACM Recommender System Conference (RecSys) (2013), 7–14.

Our current results cast doubt on the meaningfulness of offline evaluations. We showed that offline evaluations could often not predict results of online experiments (measured by click-through rate – CTR) and we identified two possible reasons.

The first reason for the lacking predictive power of offline evaluations is the ignorance of human factors. These factors may strongly influence whether users are satisfied with recommendations, regardless of the recommendation’s relevance. We argue that it probably will never be possible to determine when and how influential human factors are in practice. Thus, it is impossible to determine when offline evaluations have predictive power and when they do not. Assuming that the only purpose of offline evaluations is to predict results in real-world settings, the plausible consequence is to abandon offline evaluations entirely.

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By Joeran Beel, ago

New pre-print: “Research Paper Recommender System Evaluation: A Quantitative Literature Survey”

As you might know, Docear has a recommender system for research papers, and we are putting a lot of effort in the improvement of the recommender system. Actually, the development of the recommender system is part of my PhD research. When I began my work on the recommender system, some years ago, I became quite frustrated because there were so many different approaches for recommending research papers, but I had no clue which one would be most promising for Docear. I read many many papers (far more than 100), and although there were many interesting ideas presented in the papers, the evaluations… well, most of them were poor. Consequently, I did just not know which approaches to use in Docear.

Meanwhile, we reviewed all these papers more carefully and analyzed how exactly authors conducted their evaluations. More precisely, we analyzed the papers for the following questions.

  1. To what extent do authors perform user studies, online evaluations, and offline evaluations?
  2. How many participants do user studies have?
  3. Against which baselines are approaches compared?
  4. Do authors provide information about algorithm’s runtime and computational complexity?
  5. Which metrics are used for algorithm evaluation, and do different metrics provide similar rankings of the algorithms?
  6. Which datasets are used for offline evaluations
  7. Are results comparable among different evaluations based on different datasets?
  8. How consistent are online and offline evaluations? Do they provide the same, or at least similar, rankings of the evaluated approaches?
  9. Do authors provide sufficient information to re-implement their algorithms or replicate their experiments?

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By Joeran Beel, ago

Docear 1.0 RC3: Improved monitoring concept, neater GUI, and many bug fixes

Today we released RC3 (Release Candidate) of Docear 1.0 (not yet on the official download page but here in the Blog only). It has one major change compared to previous Docear versions, namely we got rid of the “Incoming” mind map. In the past, most users never really got used to the idea why there was an ‘Incoming’ mind map and a ‘Literature & Annotations’ mind map. Now, there is only the ‘Literature & Annotations’ mind map but it has a special “incoming” node in which new PDFs are added. We hope that this concept is easier to understand. It also means that when you move a PDF from the incoming node to any other node in the mind map, and you create new annotations in the PDF, the new annotations are directly added to the PDF node in the mind map and there won’t be any new node in the incoming node. However, if you prefer the old concept, don’t worry. You can keep your old incoming mind map and use Docear as you were used to be.

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By Joeran Beel, ago

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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By Joeran Beel, ago

Who wants to develop Docear4LibreOffice or Docear4OpenOffice?

Docear4LibreOffice and Docear4OpenOfficeA few months ago we released Docear4Word. Docear4Word is an add-on for Microsoft Word that allows you to insert and format citations and bibliographies very easily in MS Word. Many of our users love Docear4Word. However, not all of our users are using Microsoft Word but many are using OpenOffice or LibreOffice. One of them is Stephen from Uberstudent which is a Linux distribution for learners. Stephen, as many others, urged us to develop an add-on, comparable to Docear4Word, for Libre of OpenOffice. Unfortunately, we don’t have the expertise to do this.

Therefore, we would like you to help us. Do you have experience in developing add-ons for LibreOffice and/or OpenOffice? Then, please contact us. We have prepared a description of what Docear4Libre/OpenOffice should be able to do. Read it carefully, and tell us how long you would need to implement it. And don’t forget to tell us how much money you would want for it. Exactly, we are not expecting you to do it for free. We would be willing to pay something for it. Once we found an appropriate developer we will ask our users to donate for Docear4Libre/OpenOffice and give a good amount ourselves. Also Stephen will ask the users from Uberstudent to donate.

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By Joeran Beel, ago

Docear 1.0 (RC2) available with many bug fixes and better support for MacOS PDF viewers

There is a new version of Docear available for download. It’s basically the (experimental) RC1 version done right. RC2 fixes a lot of bugs that were caused by the new workspace model with multiple projects, it features a refined and polished version of the Ribbon, fixes a lot of bugs in general and supports the standard PDF viewers of MacOSX (Preview and Skim) and probably a lot of other viewers as well!

If you are still using Beta9 of Docear, a lot of things will change and improve with this new version of Docear. However converting your old maps to this new format is a one-way process (you can’t use these files with Beta9 of Docear anymore) and the process itself might take some time, depending on the size of your mind maps. Please backup your files before upgrading to Docear RC2. 

new icons

Some of Docear’s new icons in the ribbon bar

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By Joeran Beel, ago

Preview of Docear’s (Web) Collaborative Mind Mapping Tool to be presented at HTW in Berlin

Since March, Docear offers a simple web-based mind map viewer, developed with some of our volunteering students, and supported by the Freeplane team. On next Friday, July 12th, at 10:30am the students will present their final work at the HTW in Berlin. You are sincerely invited to join the presentation and be first to see Docear’s new collaboration and synchronization feature. The work is not yet ready to be released to the public but we hope to completely finish the work in the next few months. However, even the preview is really amazing! Compared to the current online viewer the new “Docear Web” offers lots of features. First of all, you can edit your mind maps online and not only on your own but together with your colleagues. The collaboration works both with your local desktop Docear and with your web-based Docear. That means, you can just start Docear Desktop as you are used to and colleagues of you may work on the same mind maps you are editing either on the Web or with Docear Desktop as well. Collaboration is in real-time, similarly to Google Docs. In addition, there is a Dropbox-like utility that synchronizes all your data between different devices (and the Web). As said, not everything is already fully functional but the preview version has at least all the basic features and gives you a very good idea what to expect for the final version.

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By Joeran Beel, ago

Docear 1.0 (RC1) released with new workspace and new UI (ribbons)

The last version of Docear was released three month ago and you might wonder what we were doing. Well, I can tell you we were really busy. Besides working on some research papers for conferences in Indianapolis and on Malta (read here and here), we finally implemented two major milestones for Docear. These two milestones actually were the last ones we had on our road-map for releasing the final 1.0 version of Docear. And here it is, Docear 1.0 (RC 1) with:

1. A new setup dialog

We have completely redesigned the dialog that appears when Docear is first started. We believe it to be much more user friendly and intuitive. We also listened to those users who criticized that our terms of service had to be accepted even when no online services were activated. Now you have the choice. You can either use Docear as a registered user and enjoy the full potential including PDF metadata retrieval, online backup, online mind map viewer, and recommendations. Or you can use Docear as a local user with no data at all being submitted to Docear and no requirement for accepting any terms of service (just use Docear as you would use any other GPL desktop software).

Docear's new setup dialog

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By Joeran Beel, ago

Three new research papers (for TPDL’13) about user demographics and recommender evaluations, sponsored recommendations, and recommender persistance

After three demo-papers were accepted for JCDL 2013, we just received notice that another three posters were accepted for presentation at TPDL 2013 on Malta in September 2013. They cover some novel aspects of recommender systems relating to re-showing recommendations multiple times, considering user demographics when evaluating recommender systems, and investigating the effect of labelling recommendations. However, you can read the papers yourself, as we publish them as pre-print:

Paper 1: The Impact of Users’ Demographics (Age and Gender) and other Characteristics on Evaluating Recommender Systems (Download PDF | Doc)

In this paper we show the importance of considering demographics and other user characteristics when evaluating (research paper) recommender systems. We analyzed 37,572 recommendations delivered to 1,028 users and found that elderly users clicked more often on recommendations than younger ones. For instance, users with an age between 20 and 24 achieved click-through rates (CTR) of 2.73% on average while CTR for users between 50 and 54 was 9.26%. Gender only had a marginal impact (CTR males 6.88%; females 6.67%) but other user characteristics such as whether a user was registered (CTR: 6.95%) or not (4.97%) had a strong impact. Due to the results we argue that future research articles on recommender systems should report demographic data to make results better comparable.

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By Joeran Beel, ago

Docear at JCDL 2013 in Indianapolis (USA), three demo papers, proof-reading wanted

Three of our submissions to the ACM/IEEE Joint Conference on Digital Libraries (JCDL) were accepted. They relate to recommender systems, reference management, and pdf metadata extraction:

Docear4Word: Reference Management for Microsoft Word based on BibTeX and the Citation Style Language (CSL)

In this demo-paper we introduce Docear4Word. Docear4Word enables researchers to insert and format their references and bibliographies in Microsoft Word, based on BibTeX and the Citation Style Language (CSL). Docear4Word features over 1,700 citation styles (Harvard, IEEE, ACM, etc.), is published as open source tool on http://docear.org, and runs with Microsoft Word 2002 and later on Windows XP and later. Docear4Word is similar to the MS-Word add-ons that reference managers like Endnote, Zotero, or Citavi offer with the difference that it is being developed to work with the de-facto standard BibTeX and hence to work with almost any reference manager.

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By Joeran Beel, ago

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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By Joeran Beel, ago

We offer a paid internship for Bachelor students from Greece, Italy, Portugal, and Spain

We are glad to announce that we, again, will offer a paid internship in cooperation with the German Academic Exchange service (DAAD). If you are an undergraduate student, interested in software engineering or statistics, and coming from the Greece, Italy, Portugal, or Spain, get yourself started and do an 8-12 weeks internship in summer or autumn 2013, fully paid. And if you are not applicable to apply for the internship – please tell your friends to apply! 🙂

Your project

Your research question to answer will be “How to provide (better) research paper recommendations to our users?”. As such, it will be your task to support the Docear team in researching how the interests of Docear’s users can be identified from the users’ mind maps and how these interests can be matched with interesting items to recommend. You will do literature research, create new ideas, analyze user data, and implement new recommendation approaches in JAVA. Of course, you don’t have to do all of this alone – you will be closely cooperating with the Docear team. Your work will be integrated into Docear and used by thousands of researchers around the world. If your work is outstanding, we will write a research paper with you.

Requirements

You should have a profound knowledge of the programming language JAVA. Knowledge in statistics, machine learning, other programming languages (especially C/++ or Python) and/or MySQL, neo4j, Hibernate, Jersey, REST Web Services, Tomcat, and Apache is a plus, but not a requirement. Of course, we would appreciate if you spoke German but it would be no problem if you only spoke English. We would prefer, if you apply for a long internship (12 weeks) but you can also apply for a shorter internship. If you are interested in combining your internship with writing a Bachelor thesis, please let us know in advance (this would be highly welcome). You can start at any date you want in summer or autumn 2013.

Important: If you don’t want to program but have profound knowledge in statistics you are also very welcome to apply. In this case you will support us evaluating how good our current recommender system is, and you will help us generating ideas for improvements. Please indicate in your application clearly that you are not interested in software development but in statistics.

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By Joeran Beel, ago

Docear Beta 9 with several bug fixes and feature enhancements

The 9th Beta of Docear is available for free download. It contains no new features but several bug fixes and feature improvements. One improvement includes the removal of line breaks in imported annotations. So far, when you highlighted text over several lines in a PDF, Docear imported the lines breaks of the highlighted text which sometimes caused a not so nice layout. In the new Docear you can do a right click on a node that links an annotation and select “PDF->Remove lines breaks from annotation”. Bug fixes include a  fix for the bug that the Adobe Acrobat Professional PDF Viewer wasn’t recognized under MacOS. On Linux the splash screen does not hide any more the setup screen on the very first start of Docear. For a detailed list of all changes see the following change log. And keep in mind – we are always looking forward for your feedback and don’t forget to have a look at the new preview of Docear’s Online Viewer.

Feature Enhancements:

  • #678 Adobe Acrobat Professional is included in PDF Viewer recognition on MacOS
  • #782 Function to remove line breaks in annotations
  • #784 More default file types to be imported

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By Joeran Beel, ago

Preview of the Docear Online Viewer

A few month ago we announced to develop an add-on allowing researchers to collaborate on the same data. Well, we haven’t finished this completely yet but the first step is done. In the past few month we developed an online viewer that allows you to view your backuped mind maps in your web browser. Right now the viewer is only capable of displaying very small mind maps but it’s our highest priority to improve the performance so you can also view larger mind maps. In addition, the online viewer displays only the basic elements such as nodes and edges. Other features such as attributes are not yet displayed but, again, we are working on it :-). Of course, this is just the beginning. As a next step Docear Online will allow you to edit your mind maps online. The following step will enable you to work simultaneously with different researchers on the same data either in your browser or with your desktop version of Docear.

docear online preview

To have a look at the preview version of Docear Online, go to https://my.docear.org and log in with your Docear user name and password. You will be able to view all those mind maps that have been created with the desktop version of Docear and that have been backuped with it. Simply select your mind map in the upper-right corner in the menu. To activate the backup function start Docear Desktop and open Tools->Preferences->Online Services->Manage Docear Service Settings.

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By Joeran Beel, ago

Docear4Word 1.01 with bug-fixes and some enhancements

Today we released Docear4Word 1.01. The add-on for Microsoft Word allows you to manage your Docear references (and any other references stored as BibTeX) directly within Microsoft Word. Version 1.01 includes the following changes. Download it here!

  • Added warning message if a BibTex file is considered corrupt, rather than just ignoring it. (#740, #692)
  • BibTex load now also supports CP1252 codepage.
  • Unexpected exceptions now logged to the log file. (#740)
  • Added workaround for missing BibTex keys. We create a new one of the form “_Unknown_XX” where XX increase with each missing key within the file.
  • DEV: Added MLA.csl sample file.
  • Fixed bug where the ID was being used instead of the Name.
  • Made toolbar dropdown wider.
  • Added warning message and instruction when no BibTex database is configured. (#740)
  • Parser now copes with no tags present.
  • Removed paragraph formatting from within Field code as it influence formatting in the main document.
  • JSON is now stored within the Field with space separators and LineFeeds since it could influence formatting in the main document. (#729)
  • Updated Citeproc.js to v1.0.426 which fixed these issues:
    • Incorrect trimming of punctuation. (#743)
    • “Tri-graph” styles not working. (#694)
    • Failure to load some styles containing comments.
  • BibTex Lexer now supports unix line endings. (#692)
  • Issue tag is now supported (#743)
  • Fixed bug with Issue and Number casing.

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By Joeran Beel, ago