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User Manual Docear

Important Note: We need your help in building a digital library. Read more...

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Windows

Linux

Mac

User Manual
under construction
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Installation
Java
Java is the programming language Docear and many other programs are written in. To run a Java program you need to install the free Java Runtime Environment (Java
JRE).
Linux and Windows users may download the latest version on www.java.com for free (on most systems it is already installed)
Mac OS 10.6 users may download Java here.
Mac OS 10.5 users may download Java here.
Mac OS 10.7 users may download Java here

First steps
more information coming soon

On first start
Workspace Location and profile name
After the first start of Docear, a dialog will open, asking you to choose a location for your workspace.

The workspace folder serves as main storage folder for all the data you use with Docear. Please find further information about the workspace here.
Multiple profiles share the same literature directory and the same projects folder. However the workspace library maps and the bibliographic data belong to the
selected profile. By defining multiple profiles, you cooperate with colleagues or friends on the same data, preserving your own view on the data. If you want to use
Docear as a single user you dont have to care about these matters. If you are not sure whether you will want to use different profiles, you can create a new profile
by simply selecting a name for it. You can find further information about the italicized terms here.
Select a folder and profile name of your choice or approve the predefined settings. You can always switch to other workspace locations by right-clicking on the empty
space of your workspace panel and selecting Switch workspace from the context menu.

Literature directory, BibTeX file and projects directory

Tell Docear where it can find your academic literature, your BibTeX file and where you want to store your mindmaps to start working right away. If you are not sure about
these paths, you can accept the default values for now. You can easily change all the settings later to adjust them to your needs. This dialog will always open if you
create a new workspace.

The Main Literature Repository contains the path to the folder where you have stored all your literature. This folder will be automatically monitored by your
Incoming map for any changes. This enables you to keep track of all the interesting ideas and bookmarks you have marked in your pdf files. You can read more
about this feature here.
Select your BibTeX file to use all your bibliographic data in Docear. This data will automatically be linked to all the PDFs you use in your maps in Docear. You
can easily edit the data with Docears integrated reference manager JabRef, as well as the standalone version of this reference manager or every other BibTeX
editor you like. To import your bibliographic data from other reference managers like Mendeley or Zotero, please read this section.
Select your Projects directory to tell Docear where you want to store the maps you create by default
Please note that all of these settings are stored inside your selected workspace folder by default. This enables you to take your whole workspace folder, store it wherever
you want, take it with you and use your data with Docear on any other computer with a working Docear installation.
You can even store Docear at the same location you store your data and use it on any other computer with a working Java 1.6 installation. Just use the All OS version of
Docear from our download page and unzip it.
You can always open this dialog to adjust your settings by right-clicking in the empty space of your workspace and selecting Change library paths from the context
menu. If you want to change the setting of only one of the paths, you can also right-click on the associated node in your workspace and select Change location from
the menu.

The Workspace
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The Docear workspace is a logical collection of your projects and resources. It holds the information of which maps you have created, which literature you use, which
reference database is used with the integrated reference manager and serves as central Input/Output interface to the user on file level.
You can simply hide or show the workspace by clicking on the small arrow at its right (see the picture below). This enables you to edit and view your maps on your whole
screen without losing the information the workspace has to offer.

Different node types

Among the nodes in your workspace some are mandatory for Docear to work correctly. These so called system nodes can be of different node types. They all share that
they cannot be renamed, deleted or copied. The Docear workspace features the following system nodes: the Workspace root node itself, Library, Literature
Repository, Projects and References.
There are three different explicitly defined node types:
A Virtual folder node works like a folder on your hard disk, except it does not have any physical location. You can add all different types of nodes except any
implicitly defined nodes to a virtual folder node. The physical location of files or folders added to this node remain the same. The Miscellaneous node in your
workspace is a virtual folder node.
A Link to folder node is a link to a physical folder on your hard disk. Its children are defined implicitly by the content of the linked folder. If you add a folder or a
file to this kind of node it will be created add the linked location on your hard disk. The Library, the Literature Repository and the Projects node represent links
to physical folders on your hard disk.
A Link to file node represents a file stored on your hard disk. You can open it by double-click, move it, copy it, rename it and remove it from the workspace.
Implicitly defined nodes represent files and folders which are stored in any folder which is represented by a Link to folder node in the workspace. They are added to their
parent automatically, hence you cannot remove them without deleting them from the represented location on your hard disk.

The Library node

Your library is represented by the Library node in your workspace. It contains five maps by default:
The Incoming map contains all bookmarks and annotations from the pdf files in your workspace which you have not already used in any other maps, stored in the
Library. The root node contains five different attributes:
1. mon_incoming_folder
2. min_mindmap_folder
3. mon_auto
4. mon_subdirs
5. mon_flatten_dirs
The Literature & Annotations map
The My Publications map
The Temp map
The Trash map

The Literature Repository node

Your Literature Repository node represents the main literature folder you have selected for your workspace. It should contain all your academic literature which will be
monitored by your Incoming map. You can add files to your literature repository by copy & pasting or directly dragging it from your file explorer to the node. You can also
add files to the represented folder on your hard disk and refresh the node by right-clicking on it and selecting Refresh from the context menu.
Dragging and dropping a pdf file to a node in your opened map will result in the following actions:
1. The file will be added to the node.
2. Your BibTeX file will be scanned for a file with the exactly same name. If an entry was found, the BibTeX key and other attributes will be added to your node.
3. If the added pdf file contains any bookmarks or notes, they will be inserted as child nodes to your node featuring a link to the page in your document, if you use a
compatible pdf reader. This enables you to directly jump to all the bookmarks and notes you have created in your pdf files.
By right-clicking the Literature Repository node in your workspace panel, you can open a context menu containing useful actions, e.g.: Changing the location of your
literature repository, sorting the included files, refreshing the node or adding a new subfolder.

The Projects node

The Projects represents the default folder for all your maps. By right-clicking the node, you can open a context menu offering some useful actions, e.g.: Changing the
physical folder which is represented by the node, ordering the entries alphabetically, and observe the folder for changes.
Observing the folder for changes will result in refreshing the folder content every 30 seconds. Since this feature can significantly slow down your system, depending on
how many items are in your projects folder, we have disabled it by default.

The References node

The References nodes represents the selected BibTeX file for your workspace. This file is opened in your reference manager and contains all the bibliographic data you
have collected.
By right-clicking the References node in your workspace panel, you can open a context menu enabling you to change the location of your BibTeX file.

The Miscellaneous node

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The Miscellaneous node represents a virtual folder which contains the welcome map after the first start of Docear. This map shows a brief introduction to Docear.
Right-clicking the Miscellaneous node in your workspace panel will open a context menu with all the standard actions of a virtual folder node. Since it is not a system
node, it can be removed from the workspace.

The Reference Manager

Duplicates created by Mendeley

If you export a BibTeX file from Mendeley the exported file will probably have a lot of duplicated entries. The Mendeley team knows about this issue since April 2010, but
they have not changed it yet.
Docear depends on unique references and in general it does not make any sense to have any duplicates in a BibTeX file, so please vote for Mendeley to fix it. Until they
have fixed it you can work around this bug by emptying your trash in Mendeley before exporting your reference database to a BibTeX file.
If this does not help and you still get duplication warnings in Docear, please send your BibTeX file to help@docear.org along with a comment what went wrong and we will
try to find the error and fix it for you.
more information coming soon

Mind Mapping
more information coming soon

Managing your Literature

more information coming soon

Drafting new Literature

more information coming soon

PDF Management - Importing Annotations (Bookmarks, Highlighted Text, Comments) and Jumping to Page
One unique feature of Docear is its capability to import PDF annotations (bookmarks, comments, and highlighted text) and then open the PDF on the proper page when
you click the imported bookmark in Docear. However, not all PDF readers are equally suited to work with Docear. Please read below about the capabilities of the different
PDF readers and let us know your experiences.

Activating the functions

Annotations are imported automatically when you drag&drop a PDF to Docears mind map or when PDFs are imported via the monitoring function. You can deactivate this
feature by selecting PDF -> Import Annotations from PDFsin the menu.

What to import?
Open Tools -> Preferences -> PDF Management -> Annotations to import from PDFs to select which kind of annotations to import. Please note
that not all annotations created with all PDF readers can be imported by Docear (see next sections). Bookmarks are the type of annotations that will cause the least
trouble and that we recommend to use primarily. Comments sometimes cause problems because some PDF created store page numbers, tables and other things as a
comment.

Jump to Page of an Annotation

You can jump directly to the correct PDF pages if you use a compatible PDF reader (e.g. Adobe Reader or Foxit Reader). Linux users can use the Foxit Reader by
installing it into WINE. On Mac OS you can use Adobe Acrobat Pro, Adobe Reader and Preview. To enable Docear jumping to the correct PDF page when you open
annotations please select Tools -> Preferences -> PDF Management -> Open Annotations and select the executable of your PDF reader.
Please note, that only a few PDF readers can open a PDF on a specified page (read the next sections about compatibility of the readers).

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Compatible PDF Readers

Unfortunately, there is no perfect PDF reader you always have to compromise in some aspects. We plan on developing our own PDF reader but so far we have not yet
found the ideal PDF library and software developer. If you have experience in developing PDF applications, please let us know.

PDF X-Change Viewer

The free PDF X-Change Viewer (PDFXV) has the potential to be the best PDF Reader for Docear since Docear can import bookmarks, comments and highlighted text
from PDFs edited with PDFXV. However, you need to change one setting and this is really important: Open the Preferences (Edit -> Preferences), open the General
tab, select Always incremental save in the section saving documents for the Set Document Save Method. If you do not change the setting, PDFXV is altering the IDs
of you annotations (and mess up your entire PDF) and Docear will import your annotations multiple times.

However, be aware that this is just a work-around. It still could happen that PDFXV is changing objectIDs of your annotations and annotations are imported twice. If you
should realize such a behavior please let us know and use another PDF reader. Also, you can help us convincing the PDFXV developers to implement a permanent
solution: Please visit their forum and support our request to not change object numbers once they were created (just register in the forum and post something like me
too).
In addition, if you want Docear to be able to import highlighted text, please ensure to have the following two settings enabled.

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Adobe Reader
The free Adobe Reader X cannot create bookmarks but it creates comments (sticky notes) that can be imported with Docear. By default, highlighted text cannot be
imported with Docear but you can change this. To do so, open the preferences of Adobe Reader and tick the box Automatically open comment pop-ups for comments
other than notes.

Then, whenever you want to highlight text, mark the text, copy it to the clip board (right mouse click or CTRL+C)

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and then do again a right mouse click on the selected text, select Highlight Text and paste (CTRL+V) the text from the clipboard. This way, Docear can import the
highlighted text.

Adobe Acrobat Professional

Adobe Acrobat creates bookmarks, comments, and highlighted text that can be imported with Docear. However, to enable Docear to import highlighted text, you need to
activate the following setting in Adobes Preferences.

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You may also want to activate the setting Automatically open comment pop-ups for comments other than notes. This will open a pop-up window each time you highlight
text and you can edit the text that is imported by Docear.

Foxit Reader
The free Foxit Reader creates bookmarks and comments that can be imported by Docear. Highlighted text created with Foxit reader cannot (yet) be imported with
Docear. If you are a Foxit Reader user, please visit the Foxit Reader Forum and support our request to store highlighted text in a format Docear can read (just register and
post that you would like that feature, too).

Mendeley
Unfortunately, Mendeleys PDF Viewer is not storing PDF annotations in Adobes PDF standard format but in a local database. Therefore, you cannot access these
annotations with any other application than Mendeley. We would highly recommend to make your annotations with a standard PDF editor such as Foxit Reader and not
with Mendeley. If you already created lots of annotations, ask the Mendeley team to use Adobes standard PDF format for annotations or at least offer a bulk export for
their PDFs including annotations. But be aware that even the current export function from Mendeley (Export PDF with Annotations does not export the PDF in the
standard PDF format.

Nitro PDF Reader

At least the free version of Nitro PDF cannot create PDF bookmarks. Highlighted text cannot be imported. Comments can be created and imported.

Preview (Mac OS)

Please let us know your experiences with Preview. Which types of annotations can Docear import?

jPdfBookmarks
jPdfBookmarks is open source and runs on Windows, Linux and Mac. It creates bookmarks that can be imported by Docear. However, jPdfBookmarks cannot highlight
text or create sticky notes.

XPDF and XJournal (Linux)

As a Linux user you can use most of the Windows PDF viewers together with Wine (e.g. Foxit, Adobe and PDF XChange). However, if you want a native open source
solution, try XPDF with XJournal for annotations. We have not tested this, but some users reported that it works well. Please let us know your experience.

Other PDF Readers

Please let us know your experience with other PDF readers. At least importing bookmarks should be no problem with any of them.

Working with other Reference Managers

Standard BibTeX Managers
You can use all standard editors and reference managers for BibTeX files in parallel with Docear

Mendeley
Using Mendeley and Docear in conjunction is simple. You only have to ensure to use the same reference data and the same PDF files in both, Mendeley and Docear.

Using the same reference data

Mendeley has a feature to create and update a BibTeX file that can be used with Docear. To activate this function in Mendeley, select Tools -> Options ->
BibTeX and ensure all settings are as in the screenshot. The Path is not fundamentally important but ideally it should be within the workspace of Docear. Please use
folders instead of groups to organize your pdfs in Mendeley. Groups will lead to duplicates in your BibTeX file.

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To activate the function in Docear just do a right click on your reference file in the workspace window and select Change Location , then select your Mendeley
BibTeX file (it is called library.biband it is located in the Pathspecified above)
Important: Do any changes on your reference data directly in Mendeley. Do not change reference data in Docear because all changes made in Docear will be overwritten
by Mendeley. If you like, visit the Mendeley support forum and vote on the idea that Mendeley synchronizes BibTeX data in both directions.

Using the same PDF files

We highly recommend deactivating the functions Sort files into subfolders and rename document files because otherwise problems might occur in Docear when files
are automatically renamed by Mendeley.

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If you have activated the function Organize my files in Mendeley (and we recommend using this function), it is important to specify the same directory you have
specified in Mendeley as your literature repository in Docear. To do so, do a right click on literature repository in the workspace window and select Change
location . Select the same directory you have specified in Mendeley.
If you do not have activated the function Organize my files in Mendeley, you need to use the folder you are watching in Mendeley as literature repository in Docear.
You find this folder in Mendeley in the Optionsin the tab Watched Folders.

Please note: If you are using Mendeley and Docear in conjunction, you should use Mendeley for reference management but not for making annotations in PDF files.
Annotations made in Mendeley cannot be read by Docear (and other standard compliant PDF readers). Click here for more information.

Known issues
Some Mendeley users reported that Docear tells them their Mendeley BibTeX file would contain duplicate BibTeX keys. This is a very annoying error but we cant do
anything about it. Please ask the Mendeley team to implement a proper BibTeX export that is not producing duplicate keys. Vote for this idea and this idea.
Also, Mendeley does not include entries set to Details need review. Please vote here to have Mendeley include all entries in their BibTeX export.

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Zotero
If you want to use Zotero together with Docear, follow the next steps
1. Export Zoteros references as shown on the screenshot to a BibTeX file. Save the BibTeX file in a location that will be part of your Docear workspace, e.g.
c:\university\zotero.bib. Important: you need to this every time you add an item to Zotero. Unfortunately, Zotero has no auto-export function. You might ask the
Zotero developers to implement a feature that automatically updates a BibTeX file, once a new entry was added in Zotero.

2. Select your Zotero BibTeX file in Docear (right mouse click on References).

3. After selecting the BibTeX file, you need to tell Docear where Zotero saves your PDF files.
1. First, open the Change location dialog in Docear (right mouse click on Literature Repository)

2. Select the folder in which your PDFs are. In Windows 7, the path looks like this

4. To have a better overview in Docear we would recommend making the following setting (Monitoring Settings Flatten directories), but this is optional.

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Endnote
If you find a way how to switch from Endnote to BibTeX/Docear or using both in conjunction, please let us know.

Other Editors
please let us know your experiences.

Extracting PDF Metadata

more information coming soon

The Docear web service

Docear web service options
Backup & Versioning
If you activate this function, all your mind maps are stored on our server each time you save a mind map in Docear (of course, the original file remains on your computer).
If you are not online at the time of saving, a copy is created and uploaded to our server the next time you are online. Your backups can be accessed through our web
interface and you can not only access the latest version of your mind map but also all other revisions. That means, if you realize you did a mistake or you deleted a mind
map by mistake, you can restore your mind map easily. In future we plan to backup your reference data and PDFs as well, but for now only mind maps are stored on our
server. If you use our backup feature, we will do some basic statistical analysis on your data. That means we will analyse how many users have how many mind maps
(min, max, avg), how large mind maps are (file size), how often they are edited, etc. But we will not look into you mind maps.
If you are interested in a excellent backup solution, not only for your Docear data, you might also want to have a look at Backblaze. Blackblaze permanently creates
continuous online-backups of all your files on your computer for 3.96$/month. Some members of Docear are using Backblaze are and absolutely happy with it.
Alternatively, you could have a look at Mozy who is offering a similar service but up to 2 GB storage are completely free. Our experience with Mozy is not as positive as
with Backblaze but the free version is certainly worth a try if you cannot spare 3.96$ a month.

Synchronizing between computers

We are planning on offering a tool for synchronizing your data between different computers but this will take at least a few month more of work. Meanwhile, we
recommend using DropBox for synchronising files. DropBox gives you 2GB free space for synchronizing any files you want and is really easy to use. And if 2GB are not
enough you can get more if you pay for it. If you need a more advanced solution and want to work with different people on the same data, we recommend SVN
respectively TortoiseSVN (however, this is not easy to setup).

Data privacy
If you dont want, we do not collect any data. You can just download Docear, install it, use it without any registration and we will not collect any data about or from you*.
However, we would be very happy if you share some of your data with us and allow us to analyse it. One reason why we originally developed Docear was because we
wanted to research how researchers work, how mind maps look like and how to provide literature recommendations to researchers (see also our publications and fields of
research). Therefore, in Docears preferences you can enable the option to share your data with us and allow us to analyse it**. Your data includes your mind maps,
PDF files, BibTeX file and usage data of Docear. We assure you that we will not give your personal information (such as name, email. etc.) or entire mind maps to third
parties. For details please have a look at our TOS or contact us.
* When you visit our website, your IP might be stored temporarily by us and by Google Analytics which we use to analyse the usage of our website.

Docear Web
Someday there will be a web version of Docear but it certainly will take a while. Meanwhile, be aware that Docear is using a compatible file format with Freeplane and
FreeMind. That means all web based mind mapping applications that can read FreeMind and Freeplane mind maps, should also be able to read Docear mind maps. Let
us know which online mind mapping tools work best with Docear.

Docear Mobile
Someday there will be a mobile version for Android and iOS but this will take a while. Meanwhile, be aware that Docear is using a compatible file format with Freeplane
and FreeMind. That means all mobile mind mapping applications that can read FreeMind and Freeplane mind maps, should also be able to read Docear mind maps.
Some potential candidates include Thinking Space (Android), Mind Map Memo (Android), FreeMindLite (iPhone), iThoughts (iPhone), and iBlueSky (iPhone). Let us
know which mobile mind mapping tools work best with Docear.

Import & Export

LibreOffice
LibreOffice can export their documents to FreeMind. Since Docear can read the FreeMind file format, you could export your LibreOffice documents and open them in
Docear via the FreeMind export.

Trouble Shooting
Log files
Docear is logging all errors. To open the folder containing the log files, start the software and select Tools -> Open User Directory. The folder logs contains all log files.
If Docear does not start, you find the log folder in C:\Users\<your_username>\AppData\Roaming\Docear (Windows) and ~/.docear (Linux).
Please always send our log files when you are reporting an error.

Clear/Delete Settings
If Docear does not work any more as it should, you can try deleting all settings. On next start, Docear will behave as if freshly installed. To do so, select Tools -> Open
User Directory and delete the content of the folder that has opened. If Docear does not start, open a file manager (e.g. Windows Explorer) and delete C:\Users\
<your_username>\AppData\Roaming\Docear (Windows) or ~/.docear (Linux).

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