Docear

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

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

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

Docear Beta 7 with PDF Metadata Extraction

Beta 7 is out and has one major new feature: (semi-)automatic extraction of bibliographic metadata from PDF files.  That means, when creating a new reference, you don’t have to type everything manually but bibliographic information such as title, author, year, journal, etc. is all provided to you automatically. Here is how it works:
Do a right click on a node with a PDF and select as shown in the picture
By Joeran Beel, ago

The second Freeplane/Docear Developer Conference: User Friendliness, Collaboration and Scripting

Last year in July we met the core developers of the mind mapping software Freeplane in Munich (Docear’s mind mapping component is based on Freeplane). At that meeting we decided that Freeplane and Docear would closely cooperate. Now, more than a year later it was time to meet again and discuss the next big steps in the development of Freeplane and Docear. So we met this weekend in Magdeburg, Docear’s “headquarter”. And while last year six people attended the meeting, this year we were nine participants (three from Docear, three from Freeplane and three students from HTW Berlin) plus one Freeplane developer attending via video. In the following I would like to provide a brief overview of the discussed topics and results.

The Freeplane and Docear team in Docear's office

The Freeplane and Docear team in Docear’s office in Magdeburg (Germany)

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By Joeran Beel, ago

Docear partners with HTW Berlin and welcomes five new student-developers

There is amazing news – Docear cooperates with the HTW Berlin (Berlin’s university of applied sciences for technology and economy). We will supervise the Master’s projects of five students (Alexander, Florian, Julius, Michael, and Paul). Other than at most other universities, the student’s goal is not to do some theoretical work but gaining some real-world development experience– by joining Docear’s development team. That means, we roughly double our development power and we are not talking about a few weeks internship. We are talking about the next eight months working almost half-time, so there should really be some noteworthy results. We still have to discuss what exactly “The Five” will be doing but since all of them prefer web development and design, it will be definitely something web-based. Right now we are considering a simple web-version of Docear and a synchronization add-on to sync your files between different computers and the Web. Ideally, the add-on additionally allows you to work collaboratively on the same data with other Docear users.

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By Joeran Beel, ago

Don’t be shy: Write a testimonial about Docear

Today I was giving a presentation about Docear. Among others I wanted to show how positive many researchers respond to the concept of Docear. So I assembled a little picture with quotes  about Docear (SciPlore MindMapping respectively) (see figure below).

After the presentation one of the attendees told me, he was surprised to not find any of the quotes on our testimonial page. Well, he was absolutely right. The most enthusiastic feedback we receive is by email. I have no clue why, but users seem to be a little bit shy when posting their opinion publicly.

For us, it’s really important to know what users think and their feedback – your feedback – may really help us, for instance, to convince our university to provide us with further resources (at least if your feedback is positive ;-). So, I would like to ask you: If you are a Docear user, write a short testimonial. Don’t send it by email, don’t post in here as a comment – leave it on our testimonial page, and please be a little bit enthusiastic  :-). Surely, we don’t want you to write something you do not really think. But please also don’t hold back. And of course, we are also happy to hear constructive criticism. If you have ideas on improving Docear, if there is something you don’t like, let us know in our forum and we will happily discuss the issue with you.

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By Joeran Beel, ago

Docear Beta 6 (Usability improvements)

Docear 1.0 Beta 6 is available for download. There are quite a few improvements and new features. The major change is a small icon to refresh the incoming mind map. Instead of selecting the entry in the menu, you can just click on the icon to get a new list of all your PDFs. In addition, when you create a new workspace (or start Docear for the very first time), the mind maps in the Library (Incoming, Literature & Annotations, …) will have a brief description for how to use them. We hope these two new features make Docear easier to use. Furthermore, Adobe Reader X and Professional are now correctly recognized by Docear and LaTeX users will be happy to hear that they can copy reference keys with a \cite{} prefix.

The complete changes are as follows

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By Joeran Beel, ago

Docear 1.0 Beta 5 with Zotero and much better PDF Reader support

Yesterday we released Beta 5 of Docear with two major improvements. First, Docear fully supports Zotero. That means as a Zotero user you can use Zotero as you are used to and work with the same PDF files and references in Docear. For instructions on setting up Docear for Zotero read our manual. Second, we strongly improved the support for many PDF readers. Annotations from http://www.cerience.com/products/reader
RepliGo may be imported by Docear and PDF XChange Viewer (PDFXV) now is fully supported: Docear will automatically adjust the settings of PDFXV so that all kind of annotations (highlighted text, comments, bookmarks) may be imported. In addition, on first start of Docear, or when you install a new PDF reader, Docear lets you select your preferred reader and, if the reader supports this, automatically sets the right settings for the “jump-to-page” feature (i.e. the PDF will be opened on the page of an annotation).

The screenshot shows the PDF-Reader selection dialog. It should list the following PDF readers (if installed on your system): Foxit Reader, Adobe Reader, PDF XChange Viewer, Skim, Preview. Adobe Acrobat Professional probably will be support in the next Beta. If on your system not all installed readers are displayed, please let us know.

So, which PDF reader is the most recommendable?

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By Joeran Beel, ago

On the future of Docear: Funding for the next 18 months and 2nd prize at ego.Business (business plan contest)

As you might know, Docear originates from ‘SciPlore MindMapping’ which some friends and I developed as part of my PhD studies. Our work was  partly financed by my university (Otto-von-Guericke University, Magdeburg) and supported by many others such as the University of California, Berkeley. One year ago my friends Stefan and Marcel and I decided to make SciPlore MindMapping a full-time project, since then being called Docear. Luckily, we received a 100,000€ EXIST scholarship for one year  from the European Union and German Federal Ministryof Economics and Technology. Well, that year has passed quite quickly and during the last months we had to think about the future. And the future looks bright 🙂

Docear Team at the ego.-BUSINESS award ceremony

Stefan Langer, Joeran Beel, and Marcel Genzmehr from Docear at the award ceremony from ego.-BUSINESS

A couple of days ago we received a scholarship that allows Stefan, Marcel and me to work for another 18 month full-time on Docear. The scholarship is granted by the European Union and Federal State of Saxony-Anhalt in Germany. This is just awesome because when I look at the achievements from the past 12 month… I am really excited to think about what we will be able to do in the next 18 months. The scholarship is called ego.-START and we are really glad about all the support we received from the Investitionsbank Sachsen-Anhalt who helped us applying for this scholarship. And as with the previous grant, there are no strings attached. I think this is really amazing and I don’t know of any other country in the world that is that supportive to young researchers and entrepreneurs. ‘Entrepreneurs?’ you might wonder? Yes, we are considering to start a business with Docear.

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By Joeran Beel, ago

Docear 1.0 Beta 4 with literature recommendations (free full-text download)

Beta 4 of Docear is available for download. There are many minor changes and enhancements. For instance, your existing PDF reader (e.g. Foxit) is automatically pre-selected, handling BibTeX files from Mendeley improved (you can automatically resolve duplicate BibTeX keys), and we did many bug fixes. But, there is one major improvement: Docear Beta 4 offers free full-text literature recommendations.  In your workspace panel you find a link “Show Recommendations”. If you click this link, a tab will open with a list of research papers that might interest you. If you are a long-time user of Docear and also used SciPlore MindMapping, you might remember that we already had recommendations in SciPlore MindMapping. And you probably remember that they were… well, let’s face it, they were really … crappy. Docear’s recommendations are way better. From my experience I would say they are quite decent and let me tell you that the recommendations will become even better in the future. However, the quality of recommendations also depends on the field of your research. Most of our papers are the field of computer science, accordingly recommendations in this field probably are best. But maybe the best thing about the recommended papers is – they are completely free. Just click on them and they will be downloaded to your literature repository or open in your web browser. Please note, to get recommendations you must have used Docear for a while and must have added at least a few papers to your literature repository.

We are very interested in your opinion: What do you think about the recommendations? How good or bad are they? How important are recommendations for you?

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By Joeran Beel, ago

New Docear release: Beta 3 with update-check, information retrieval, licence, and several bug fixes

The third Beta of Docear was released today (download here). Besides several bug fixes, the major changes are:

An automatic update-check which informs you when a new version of Docear was released. We also have a proper licence now you have to accept when starting Docear for the first time. Of course, the main licences still remains GPL2+ but we now have additional terms of service for using our online backup etc. We also implemented an optional function to transmit your mind maps to our servers so we can use them for our research (read here for more details). We would kindly ask you to activate this function because it allows us to perform our research on mind maps and the more and better research we do, the more likely we will get additional funding from the German Government to further develop Docear. As stated in our terms of use and data processing terms, we are bound to the very strict German data privacy law and try everything to protect your data. However, if you feel uncomfortable having your mind maps analyzed by us, please just deactivate the options that are shown on first start. You can then use Docear without any data being submitted to us. Finally, you can directly register a Docear account when starting Docear the first time. This account is required if you want to backup your files to our servers. We would highly recommend this since you never know what happens to your computer and you can also access your mind maps through our web interface if you are not at home. Read also here for more information about the backup and alternatives.

Here are all the changes:

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By Joeran Beel, ago

Docear goes CeBIT

From 6th to 10th of March 2012 we will be at the CeBIT in Hannover, Germany. CeBIT is the digital industry’s biggest and most international event and always worth a visit. We will be at Halle 9, Stand A 10 to present Docear. You are welcome to visit us and get to know the Read more…

By Joeran Beel, ago

First public version of Docear released (1.0 Beta 1)

Today, on February 15th, 2012 we released the first public version of Docear. It’s a Beta version and still has some bugs and missing features but overall it will give you a thorough impression of what we consider an academic literature suite to be.

The main idea behind Docear is that you annotate everything you consider important in a PDF. That means, you highlight text, write comments, or create bookmarks in the PDF. To create bookmarks and comments, you can use almost any PDF reader (highlighting text is a bit more complicated). These PDF annotations are then imported by Docear to a mind map. In this mind map you can organize all your annotations into categories, create further nodes and add more text. With the integrated reference manager, bibliographic data can be added to each of the PDF annotations (and all other nodes in the mind map). Then, you can create a new mind map, drag e.g. a research paper, copy your annotations to the draft and if you need more information you just click on the PDF annotation and the PDF will open on the page the annotation was made. Watch this video to get a better idea of what Docear can do (watch it in full-screen mode). (more…)

By Joeran Beel, ago

Experimental Releases

We decided to make our internal test releases public. Every one or two weeks we will publish an experimental release of Docear in our forum. Those releases are not thoroughly tested but have the latest features. You can subscribe to the forum to be notified about new experimental releases (we won’t Read more…

By Joeran Beel, ago

(Bachelor) Students: Do a (Paid) Internship at Docear in Magdeburg, Germany or Berkeley, USA

We are happy to announce that we can offer paid internships to German, British, and North American (USA & Canada) Bachelor students, in cooperation with the German Academic Exchange Service (DAAD). Some of the internships are in cooperation with our partner SciPlore or for our project Mr. DLib. However, all results will be used by Docear, too. These are the internships we are offering (all in the field of software development).

Docear Internships (preferably in Magdeburg, Germany)

PDF Header/Metadata Extraction

Creating a Recommender System for Docear

Joined Internships by SciPlore/Docear/Mr. DLib (preferably in Berkeley, US) (more…)

By Joeran Beel, ago