Release Notes

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

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

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

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

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

Docear’s PDF Inspector: Extracting titles from PDF files

A while ago we released Docear with automatic metadata extraction. Several users asked us if this functionality was also available as stand-alone tool. Therefore, we decided to create a little tool which we name “Docear’s PDF Inspector”. Docear’s PDF Inspector extracts titles from PDF files not from the PDF’s metadata but from its full-text. More precisely, Docear’s PDF Inspector extracts the full-text of the first page of a PDF and looks for the largest text in the upper third of that page. This text is returned as title. Of course, this does not always deliver the correct title (e.g. sometimes the journal name is formatted in a larger font size than an article’s title) but in about 70% you will get the correct one.  The main features of Docear’s PDF Inspector are

  • Extracts titles from PDF files with good accuracy (~70%) and excellent run-time (few milliseconds per PDF in batch mode)
  • Usable as library (other tools can easily integrate Docear’s PDF Extractor to extract titles from PDFs.
  • Usable as stand-alone command-line application (returns a PDFs’ title on the command line)
  • Usable in batch mode (stores the extracted titles into a CSV file)
  • Reads all PDF versions (other tools such as SciPlore Xtract or ParsCit are using PDFBox for processing the PDFs. However, PDFBox sometimes has problems extracting text from PDFs not being 100% compliant to the PDF standard – Docear’s PDF Inspector is more tolerant)
  • Written entirely in JAVA 1.6. Hence, Docear’s PDF Inspector runs on any major operating system, including Windows, Linux, and Mac OS, without any other tools required (besides the JAVA run time environment, of course)
  • Completely independent of further tools – you only need Docear’s PDF Inspector, that’s it (e.g. SciPlore Xtract requires pdftohtml to be installed)
  • Released under the GNU General Public License (GPL) 2 or later, which means it is completely free to use and its source code can be downloaded and modified by anyone.

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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

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

Docear4Word 1.0 RC1 available for registered users

Docear4Word is ready to release but before we make it available for public download, we would like to publish another test version for our users. We have fixed several bugs, and added the feature to select a BibTeX file. By default, Docear4Word used the BibTeX file that is specified in Docear but you can specify any other BibTeX file you want. We also enhanced the field mapping but we cannot guarantee that everything is perfect. If you are missing some information in your bibliography (that are available in the BibTeX file), please let us know. But be aware that the reason might be the citation style – not all citation styles do show all fields. So, before you report some missing information, please test several citation styles and if they all don’t show a certain piece of information – well, than probably it’s a bug of Docear4Word.

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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

Docear4Word – First Beta published for registered users

Wow, today really is a special day. First, we released Beta 4 of Docear with literature recommendation, and now… we have the pleasure to present Docear4Word (Beta). The Beta of Docear4Word is a fully functional Microsoft Word Add-on to create formatted references and bibliographies in over 1,700 citation styles (APA, IEEE, ACM, Havard, Chicago, …).  Similar to  Zotero, Mendeley, and other reference managers we use the citation style language (CSL) and citeproc-js. However, in contrast to MS-Word Add-Ons of other reference managers, Docear4Word is not a proprietary tool functioning only with its own database. Docear4Word works with any BibTeX file from any BibTeX reference manager (at least it should ;-)). Of course, there is BibTeX4Word, a tool offering similar functionality as Docear4Word (and also working with any BibTeX file). However, BibTeX4Word is very difficult to install, not really easy to use, and there are not that many citation styles as far as we know.

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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

Docear4Word is on its way (CSL based Microsoft Word Add-On for BibTeX)

It’s half a year ago that we announced the development of a Microsoft Word Add-on to insert BibTeX based references in the same way as Zotero, Mendeley, Endnote and other references managers do. A major requirement for the add-on was to use the citation style language (CSL) which allows using over 2,000 citation styles. Well, it has been (and still is) a long and hard way to go (maybe we will elaborate on this later). However, I just want to let you know that the work on Docear4Word is going on and we are just before a first test release – I hope that in two or three weeks the first demo is ready to be released (for the beginning we probably make it available to registered users only, so register now :-)).

For now, here is a little teaser to give you an idea what is coming: the first screenshot of Docear4Word. Please let us know your ideas for the Add-On: What should it be able to do? What do you like about the MS Word add-ons from other reference managers? Probably we won’t be able to consider your wishes for the first version but maybe for Docear4Word 2.0.

Docear4Word - First Screenshot

Docear4Word – First Screenshot

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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

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