SciPlore MindMapping Manual
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SciPlore MindMapping is outdated. Please use Docear the successor of SciPlore MindMapping instead
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Table of Content


Program Details (Short Description, Homepage, etc.)

SciPlore MindMapping is a software tool for creating mind maps. Besides, features that most mind mapping software tools offer, SciPlore MindMapping has some additional unique features focusing on the needs of researchers: SciPlore MindMapping can import PDF bookmarks and (automatically) add reference keys to nodes in the mind map. The latest version is always available for free download on


  • Windows operating system (any version that supports Java - that includes Windows 95, Windows 98, Windows ME, Windows NT 4.x, Windows 2000, Windows XP, Windows Vista and Windows 7) and maybe Linux or Apple's Mac OS
  • 32Bit or 64Bit CPU
  • Java runtime environment 1.6 or later (pre-installed on many operating systems. Alternatively you can download it on for free).
  • About 30 MB free disk space



If you have downloaded the Installer just run it and follow the instructions. If you have downloaded the ZIP file, unzip it and run "SciPlore MindMapping.exe". If you are experiencing difficulties in starting the software you may also try running "SciPlore MindMapping.bat" or "/lib/freemind.jar". If you can't install the software for any reason, please contact us.


If you are experiencing difficulties in starting the software you may try running "/lib/freemind.jar". FreeMind's special help page for Linux might also be useful for you.


Mac OS

We know of some people who managed to run SciPlore MindMapping under MacOS. It is important that you have installed Java 1.6 for MacOS (alternatively try If you are experiencing difficulties in starting the software you may try running "/lib/freemind.jar". However, we are working on a special Mac OS version.




Basic Functionality

Please note that SciPlore MindMapping is based on the open source software FreeMind 0.9. Therefore, for the 'normal' mind mapping features (e.g. creating and formatting mind maps, searching in a mind map, installing plug-ins, etc.) are the same as in FreeMind. Please check out the FreeMind FAQ and FreeMind Help (available as Mind Map, PDF and other formats) for information on these standard features.

However, we want to give you some advices about the most basic features.

Disable Direct Selection

By default SciPlore MindMapping is selecting a node whenever you place the mouse pointer over it. If you do not like this feature you can disable it by selecting "By Click" in "Tools | Preferences | Behaviour | Selection Method"

Create New Nodes

You can create new nodes via "Insert | New Child Node" respectively via "Insert | New Sibling Node" or via the context menu which appears after a right click on an existing node. However, we would recommend you to use keyboard short-cuts (it's much more efficient). You can find the keyboard short cuts in the menu behind each command. For instance, a child node is created by pressing the "ins" (insert) key and a sibling node by pressing "enter".


Importing Mind Maps from FreeMind 0.8.1 (or older) and FreeMind Scholar (Alpha 1)

If you open a mind map in SciPlore Mind Mapping which was created with FreeMind 0.8.1 (or older) or FreeMind Scholar (the pre-decessor of SciPlore MindMapping), the following dialog will appear.

Unfortunately, the conversation currently doesn't work properly. You have two options:
No: In this case, notes in the old mind map will be lost. The rest of the mind map should be all right
Yes: In this case, notes are converted properly but if you have linked to files on your hard drive, special characters in (including spaces) in the file's name and path will be converted and will not be readable any more. For instance, the path "c:\my files\my pdffile.pdf" would be converted to c:\my%20files\my%20pdffile.pdf". You could solve this problem by open the mind map with a text editor and search and replacing all "%20" with " ".

In any case we recommend you to backup your old mind maps before opening them with SciPlore MindMapping!


Importing Mind Maps from MindManager, XMind and other Mind Mapping Tools

SciPlore MindMapping can import mind maps from Mindjet's MindManager X5 (.mmap). If you are using a newer version of MindManager, please open your mind map in MindManager, store it in the old X5 format and then import it to SciPlore MindMapping.

For all other mind mapping tools we have to say: Sorry, we don't have any converters. If you are lucky you find a converter with Google. If you know of a converter, please contact us and tell us its website, we will be glad to list it here.

In any case we recommend you to backup your old mind maps before opening them with SciPlore MindMapping!


Adding References Manually

As a researcher you might want to reference your sources in the mind map. SciPlore MindMapping offers different options to reference a source.

1. Add a reference key

In SciPlore MindMapping you can add a reference key (this feature is unique as far as we know). This reference key could equal the unique identifier of an entry in your reference management software (e.g. BibTeX or Zotero ID), a URL, the name of the author or whatsoever.

First, do a right click on the node you want to add a reference key at. Select "Add Reference Key".

Then enter the reference key. That's it.

2. Link a file

You can drag&drop any file on your hard drive to the mind map. SciPlore MindMapping will automatically add a link to the file in the mind map. So, if you want to add a reference, you may just link the file in which the statement you want to reference occurs in.

3. Link a Website

If you copied an URL to your clipboard just paste it in the mind map and the URL will be inserted as new node with a link to the website.

4. Create a note

If the note window is not already present, select "View | Note Windows" or press Ctrl+Shift+Less. Then you can select any node and write a note with whatever text you want (formatted if you like).


Adding Reference Keys Automatically

If you have linked an electronic file (e.g. PDF) in both your mind map and in your reference management software, SciPlore MindMapping can automatically extract the reference key. See the following picture for an example. The file "Google Scholar's Ranking Algorithm - The Impact of Articles' Age.pdf" is linked in both, SciPlore MindMapping and JabRef, a reference management software. Due to this link, SciPlore MindMapping can extract the reference key "Beel09b" from the reference database and display the key in the mind map (to do this you need to specify the reference database in the preferences first).

Whenever you drag&drop a PDF into a mind map, SciPlore MindMapping will check your reference database for an appropriate key.


BibTeX based reference management tools

Currently, SciPlore MindMapping supports reference databases in BibTeX format for automatic extraction of reference keys only. Accordingly, only reference databases of reference managers such as JabRef, BibDesk, Referencer and BibTexMng are supported.


Please read here...


Please read here...


Endnote certainly is one of the most popular reference management tools. However, SciPlore MindMapping currently does not support Endnote reference databases nor will in the future for two reasons. First, the database format of EndNote is not easy to read. Second, and more importantly, the manufacturer of Endnote, Reuters, has sued the Open Source Software Zotero. We do not want support a company with this kind of behaviour and therefore will ignore Endnote (meanwhile the case has been dismissed). We would recommend you to use JabRef or Zotero instead which are excellent alternatives to Endnote and which are both free, btw.

Other Reference Managers

From those reference managers, not using BibTeX most allow at least to export their database to BibTeX. That means you can export your database to BibTeX and use this BibTeX file with SciPlore MindMapping. However, usually the BibTeX files are not automatically updated when your reference database is modified. We would recommend you to ask the manufacturer of your favourite software to implement a feature such as that feature Mendeley offers (see above).

Update Reference Keys in Current Mind Map

When you have updated your reference database and you want SciPlore MindMapping to update your mind map with the latest reference keys use the option "SciPlore MindMapping | Update Reference Keys in Current Mind Map"


Copy Reference Key to Third Party Application

When you want to copy a reference key (e.g. BibTeX) to another application, just right click on the node and select "Copy Reference Key". Then the reference key is copied to the clipboard and you can paste it to any other application. If you are using MS Word, we would recommend you BibTeX4Word (Open Source) to manage your bibliography in MS-Word documents (installation is a bit tricky but it is worth it).


Hide / Show Reference Keys

If you feel, reference keys are displayed too intrusive, you can hide them by selecting "View | Attributes | Hide All Attributes". Similarily, you can display them again.


Import Annotations from PDFs (Bookmarks, Comments, Highlighted Text)

SciPlore MindMapping has a unique feature that is handy for researchers - SciPlore MindMapping can import PDF bookmarks, comments and highlighted text. Just drag&drop a PDF in the mind map and all annotations are imported as separate nodes. Each of the nodes is linked with the original PDF and if this PDF is linked from your reference database, the appropriate reference key is added to the node as well.

To create annotations in PDFs, you need special software since the commonly used Adobe Acrobat Reader is not able to create PDF bookmarks. We recommend either using Adobe Acrobat (which is quite costly) or the free Foxit Reader which can all, creating bookmarks, comments, and highlighting passages in PDFs. You may also try JPdfBookmarks which is free and open source but cannot highlight text (but it should run on MacOS too).

Important: Importing bookmarks works quite reliable - if you discover a problem tell us and we most likely can fix it. Importing comments sometimes leads to wired data because sometimes page numers or other data is saved as a comment by some PDF creators. We can't do anything about it. Importing highlighted text works only with very few PDFs respectively PDF readers. So far we know that you can successfully import highlighted text that was exported with Skim, or created with Adobe Acrobat and Adobe Reader X (which cannot create bookmarks). FoxitReader does not work. Please let us know your experience with other PDF readers.


(De)activate Automatic PDF Bookmark Import

To (de)activate the automatic import of PDF bookmarks (un)check "SciPlore MindMapping | Import PDF Bookmarks"


FAQ (Frequently Asked Questions)

Q: Can you add general feature 'xxx' or improve general feature 'yyy' (which will not improve the workflow of researchers and students?)
A: 99% of SciPlore MindMapping's source code is based on FreeMind. We just added some functionality that is usefull for researchers and students (folder monitoring; adding reference keys, etc.). So, if you have suggestions how to improve general functionality (regarding printing, node formatting, layout, export/import, ...) please contact the FreeMind team in their forum. Also have a look at their FAQ, general documentation and FreeMind on Linux help.
Q: Does SciPlore MindMapping runs under Linux (Fedora 12)?
A: Some user managed to run the software. We can only encourage you to try (we will publish a special version for Linux soon). One user gave us a brief description how to run SciPlore MindMapping with Fedora 12:

First I had to overcome the common JAVA *JDK usage* trouble with >sudo update/alternatives /config java

I did set the JAVA_HOME environment variable. Add: export JAVA_HOME="usr/java/jdk1.6.0_18;" @ the \etc\profile file

After that I used the |ant run| command @ the source directory

I had some trouble with compilation and had to set the LANG environment variable to en_US.ISO-8859-1 doing this

> export LANG=en_US.ISO-8859-1
> echo $LANG

compilation worked fine, a few settings of property rights later all went smooth.

Q: Does SciPlore MindMapping runs under Linux (Fedora 13)?
A: Some user managed to run the software. We can only encourage you to try (we will publish a special version for Linux soon). One user gave us a brief description how to run SciPlore MindMapping with Fedora 13:

you will need the latest sourcecode:

you will need to install following packages:

then type in a terminal:

export LANG=en_US.ISO-8859-1

after doing this SciPlore starts with the following command from the sourcedirectory in a terminal:

ant run

Q: Does SciPlore MindMapping runs under Linux (Ubuntu 9.10)?
A: Some user managed to run the software. We can only encourage you to try (we will publish a special version for Linux soon). One user gave us a brief description how to run SciPlore MindMapping with Ubuntu 9.10:
It also runs fine on Ubuntu Linux 9.10- within the File Browser, I
right-clicked on lib/freemind.jar and selected "Open with OpenJDK Java 6

Q: How can I create bookmarks in a PDF under Linux?
A: One user told us the following:

Foxit Reader 3.2.1 and better works well on Linux, using Wine (and winetricks to set up the ODBC layer that for some reason, Foxit Reader demands). On Linux under Wine, Foxit Reader is able to create proper PDF bookmarks within PDF files, including (some at least) of those PDF files it displays as "Secured" ie with some sort of password. native_mdac is not required (at least for Ubuntu 10.4; I didn't try it with any older version). The "Foxit Reader.exe" will need to be taken from an installation of Foxit Reader on Windows, or a PortableApps version installed on Windows. Make sure to take "Foxit Reader.exe" not "FoxitReaderPortable.exe"

Read also here.

Q: How can I create PDF bookmarks with MacOS

Adobe Acrobat is the first choice in terms of features. However, it is pretty expensive. It seems that JPdfBookmarks is the only free tool running on MacOS but: it cannot highlight text but only create bookmarks (you could kindly ask the developer to implement text highlighting).

We know that many people use Skim for making annotations etc. in PDFs, however SciPlore MindMapping is not (yet) supporting Skims special file format. It is on our todo list to support Skim but with (very) low priority. So, either you have to wait several months (at least) or, if you are a programmer, you do it yourself - eventually SciPlore MindMapping is open source (feel free to send us your new code).

Q: In the video is shown how SciPlore MindMapping extracts the title from PDFs and renames the PDFs according to the title. How can I activate this function?
A: This was only a demonstration in the video. We are working on title extraction and hope to have this function implemented soon.
Q: Is there a portable version of SciPlore MindMapping?
A: No, not yet. BUT one of our users reported how to run SciPlore MindMapping from a flash drive:
I just wanted to let you know that I've successfully installed and run SciPlore MindMapping of a flash drive. I unzipped the Zip file to a directory there and then Launched Freemind.jar using the Java Portable Launcher installed under the Portable Apps Suite. ( I tried this because my workplace computer is locked down and I could not update Java to the JRE required to run SciPlore. Running it from the flash drive using the latest portable java worked great.
Q: Is there an iPhone/iPad or Android version of SciPlore MindMapping
A: No sorry and there won't be one anytime soon. BUT: SciPlore MindMapping is compatible to FreeMind's file format and there are some applications that import and export to FreeMind on the iPhone or Android. Check out the following apps and tell us which one you like most: Thinking Space (Android), Mind Map Memo (Android), FreeMindLite (iPhone), iThoughts (iPhone), and iBlueSky (iPhone). If you don't like these applications search with Google for a better one (just search for FreeMind compatible mind mapping applications - they will most likely work with SciPlore MindMapping too).
Q: Is SciPlore MindMapping compatible with FreeMind?
A: Yes. All mind maps you create with SciPlore MindMapping can be opened and edited in FreeMind 0.9 and vice versa.
Q: When I click a PDF bookmark in the mind map, the PDF opens on the first page and not where the bookmark points to. Why?
A: When you import PDF bookmarks with SciPlore MindMapping, only a link to the PDF file is created not to the bookmarked page. We are working on this feature but it is difficult because not all PDF readers support such a function. (yes, we showed this feature in the video but this was only a demonstration). But you can help us: Visit the forum of FoxitReader, register an account and tell the FoxitReader team that you want this function.
Q: Is there an easy way to synchronise my mind maps and PDFs between my home and work computer?
A: There is no build-in solution but we recommend 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 advances solution and want to work with different people on the same data, we recommend SVN respectively TortoiseSVN.
Q: I activated the function to backup my mind maps to SciPlore's server. How can I access the mind maps?
A: You can access the backup of your mind maps after loggin in at soon (it will take some more time before we have completed the website to access them). However, if you have experienced data loss, please provide us with your login data and we will send you the mind maps by email.

Contact Us

If this manual could not answer your question, please do not hesitate to contact us. We want to make SciPlore MindMapping the best mind mapping software for researchers. So, any comment is helping us - tell us what you like about SciPlore MindMapping, what you don't like, report bugs, send us your feature requests and ask if you didn't understand how something is working.