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  SciPlore MindMapping
Combining Mind Maps with Reference and PDF Management
SciPlore MindMapping is outdated. Please use Docear the successor of SciPlore MindMapping instead

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Name: SciPlore MindMapping
Version: Beta 16
Available Languages: English, German, Spanish, French, Danish, Hungarian, Russian, Italian, and many more...
Manual: Online Help
Feedback: Contact us
Release Date: 2011/07/14
Licence: GNU General Public Licence (Open Source)
Based on: FreeMind 0.9. RC 7 Max
Requirements: Windows (any version since 95 - that includes Windows XP, Vista and 7) or Linux or Mac OS; Java 1.6 or higher; 30 MB on hard drive
Promoted by: This web host



Program Details


Mendeley users please read here...

Zotero users please read here...

BibTeX users: don't worry, SciPlore MindMapping is optimized for you :-)
Are you using mind mapping tools such as MindManager, FreeMind or XMind? And reference management tools such as JabRef, Endnote, or Zotero? And do you sometimes even create bookmark in PDFs? Then you should have a look at SciPlore MindMapping.

SciPlore MindMapping is the first mind mapping tool focusing on researchers’ needs by integrating mind mapping with reference and pdf management. SciPlore MindMapping offers all the features one would expect from a standard mind mapping software, plus the following special features for researchers:

Adding Reference Keys Manually
This feature allows assigning a reference key to a mind map’s node. This way, researchers can organize their ideas and reference to the origins.

Adding Reference Keys (BibTeX) Automatically
Most reference managers (e.g. JabRef, BibDesk, Referencer, ...) allow assigning a file (usually PDF) to entries in the bibliographic database. If a file that is linked in the reference database is linked by a node in the mind map, SciPlore MindMapping automatically extracts the corresponding reference key from reference database and adds it to the mind map node. Currently, this feature only works with reference databases in BibTeX format.

PDF Bookmark Import
When researchers read an article in PDF format, some create bookmarks for the most important statements in the article. The same information is likely to be needed in a mind map when structuring ideas or a new paper. SciPlore MindMapping offers the option to import bookmarks from a PDF. Each bookmark is imported as a node and each node is linked to the PDF. If the PDF is included in the user’s bibliographic database, the corresponding BibTeX key is also added.

Monitoring Folders for new PDFs
In SciPlore MindMapping you can specify a "monitoring node". This node then will list all PDF files you store in a certain folder on your hard drive: whenever you store a new PDF it is listed automatically in your mind map.

Backup your mind maps
If you want, SciPlore MindMapping makes a backup of your mind maps to our servers each time you save them in the software. That means, where ever you are, you can access all your mind maps online or in case of data loss you can restore your mind maps from our servers.

SciPlore MindMapping is based on FreeMind (0.9 RC7 Max) and 100% compatible to FreeMind. All mind maps created with SciPlore MindMapping can be opened and edited with FreeMind 0.9 and vice versa. SciPlore MindMapping is developed in Java and runs under Windows (95, 98, ME, 2000, XP, Vista, 7, etc.), Linux and Mac OS (Java 1.6 or later is required which is available for free). SciPlore MindMapping is 100% free and published under the GNU/GPL licence.

When you install SciPlore MindMapping you will be asked if you want to allow (anonymous) usage statistics. We would kindly ask you to agree because we would love to do some research on how many people are using mind mapping software, how often, etc. However, if you feel uncomfortable you do not need to activate this function and can use SciPlore MindMapping without any limitations anyway.


User feedback

Here is what users say about SciPlore MindMapping:

  • You have read my mind. You have put into practice what I could envisage yet not even come close to develop.
  • I love your product
  • You are helping to tackle the biggest obstacle to my research
  • I really like SciPlore's approach. Connecting papers through a mindmap is genious!
  • Great software, thanks!
  • I'm in the middle of my PhD and was becoming overwhelmed with the amount of information I need to manage. Nothing else was really cutting it for me and I stumbled on Sciplore.
  • Your tool is great
  • I was actively looking for some software to sort my bibliography of hundreds of scientific articles... Just when I was about to do it the long and hard way with a homemaid method I fell on SciPlore. EXACTLY what I needed, incredible, really!!! Now I can have a clear global view of the literature and can work way faster than before. More of that, SciPlore is compatible with numerous other software. It's an incredible timesaver.
  • Great software! Trying to get my adviser and all the graduate students in our lab to start using SciPlore. Keep up the efforts!
  • I very much enjoyed using Sciplore and was very impressed by its performance and options.
  • Congratulations on a great time saver and program to make PDF Bookmarks useful.
  • I'd like to thank you for the great work you're doing.
  • I want to say, that your Mindmap tool is the best tool I have seen.
  • Thank you very much for the excellent software. SciPlore has helped me organise my notes and research while undertaking my Masters degree.
  • I was greatly surprised to find SciPlore, and it seemed to be exactly what I needed for my work
  • Just wanted to say that SciPlore is a wonderful program. I use it to organize my thoughts and my research. Can't wait to see what's coming!
  • Thanks for making SciPlore!
  • I had dreamed someone would produce such a tool for organizing all the academic papers
  • SciPlore is the backbone software [...] that supports my dissertation work [...] Thank you again for your wonderful research tool [...] A fan for life! SciPlore's or mine, which ever last the longest--
  • The system of SciPlore is revolutionary for researchers
  • Thanks a lot! You're doing an extraordinary job with that software!
  • First and foremost, I would like to thank the SciPlore team for providing such an Incredible piece of software for researchers. [...] I love the bookmarking feature for importing notes from papers and I think all the implemented features for using SciPlore to write papers and theses is genius! [...] In short, I love it!
  • [SciPlore MindMapping] has completely changed the way I conduct research. It has increased my efficiency by at least 100%. :)
  • ...

What do you think?




SciPlore MindMapping Screenshot
Click to enlarge


Manual / Handbook



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We plan on publishing a series of "How To... with SciPlore MindMapping" in our blog. Here is a list of current how to tutorials.




2011/07/14 SciPlore MindMapping (Beta 16)

  • New: Bookmarks and comments in PDFs are renamed when the linking node in a mind map is renamed
  • New: PDF can now be opened on the page where the bookmark is (only Acrobat)
  • Improved: Recommendations are now also based on selection in incoming window
  • Improved: Recommendations can be deactivated
  • Improved: Smart Update is default update mechanism now, instead of thorough Update
  • Improved: Import Highlighted text is selected by default
  • Improved: Zotero and Mendeley BibTeX file support should work now more reliably, also under Linux
  • Improved: Layout of recommendations changed
  • Fixed: Under some circumstances CPU load of the software was 100% even if nothing was done
  • Fixed: Null pointer exception when last opened mind map was closed
  • Fixed: Some users could not open PDF links out of a mind map
  • Fixed: Mind Maps were destroyed in some cases when the user was using a proxy server
  • Fixed: Exception under MacOS when monitoring folder was updated
  • Fixed: Monitoring did not work for some users

2011/03/28 SciPlore MindMapping (Beta 15)

  • New: Literature recommendations with free full-text link in incoming window
  • New: Automatic Web Service check (message if an old version is used)
  • New: Logging of recommendations, usage data, and incoming window status
  • New: "Import Annotations from PDFs" is now valid globally (not only for drag and drop but, e.g. for monitoring directory)
  • New: Monitoring node works with relative path, too
  • New: Overview mind map on first start
  • Improved: Identification of comments in PDF files improved
  • Improved: Behaviour of icons in incoming window
  • Improved: BibTeX files from Mendeley with multiple files can now be read
  • Fixed: Cancelling monitoring update did not work on all computers (continued in background)
  • Fixed: Renaming imported bookmarks did not work before saving a mind map
  • Fixed: Licence was not shown when selected in menu
  • Fixed: Ref key sometimes wasn`t assigned to imported comments (bookmarks worked)

2011/01/17 SciPlore MindMapping (Beta 14)

  • New: Comments in PDFs and highlighted text can be imported
  • New: Show more BibTeX attributes in mind map (author, year, journal/conference)
  • New: Icons for most important actions in incoming folder window added
  • Improved: BibTeX processing is more tolerant
  • Improved: Incoming folder window remembers width
  • Fixed: Update reference keys did not work if one BibTeX key in BibTeX file was empty
  • Fixed: Some export formats did not work properly
  • Fixed: Status window lost focus on click on background
  • Fixed: If monitoring directory was non-existent, an exception occured
  • Fixed: Reference key was not assigned if file name had special chars

2010/12/09 SciPlore MindMapping (Beta 13)

  • Fixed: Many bugs

2010/11/30 SciPlore MindMapping (Beta 12)

  • New: Incoming PDFs are now displayed in seperate window
  • New: 'Import All' and 'Import New' Bookmarks
  • Improved: Update of the monitoring node is now MUCH, MUCH faster
  • Improved: Better understandable error messages when the web service is not available (for mind map backup, user validation etc.)
  • Improved: Logging events are sent up to three times if connection breaks
  • Improved: Better exception handling if no internet connection exists
  • Improved: Icons are now in higher resolution
  • Fixed: On drag&drop always the absolute path was taken
  • Fixed: "Import Folder Structure" and "Monitoring Directory" had different file name conventions
  • Fixed: Reference key was not assigned if file name contained a German Umlaut (ä,ö,ü)
  • Fixed: Misidentifcitation of files when node text contained line break
  • Fixed: Cut and paste did not work between mind maps
  • Fixed: Export to XHTML, ODT etc. problems fixed

2010/09/18 SciPlore MindMapping (Beta 11)

  • New: Copy several BibTeX keys from different nodes at once
  • New: Open the folder that contains the software's log files via the menu
  • New: Keyboard shortcuts for the most important functions
  • New: Backup reminder (user is asked to activate backup after 10th software start)
  • New: Information retrieval reminder
  • New: Usage statistics implemented
  • New: More options for PDF monitoring (update automatically on opening a mind map and read (no) sub directories)
  • Improved: PDF Bookmarks are not only imported when a PDF is linked via Drag&drop but also via all other options to insert a PDF
  • Improved: Width of attributes (monitoring directroy, BibTeX keys, ...) restricted to 350px (looks better)
  • Improved: Default selection method is now "on click"
  • Improved: User name is not stored in mind maps any more
  • Improved: Preferences dialog completely renewed
  • Improved: Update info can be "paused" for one version
  • Improved: Updatecheck and usage data now via webservice
  • Improved: Smarter menu (some options are not available anymore when they would not make sense)
  • Improved: Better handling of timeouts (so far it took sometimes 30 seconds)
  • Fixed: Various errors when no internet connection was available
  • Fixed: Version in registry wasn't updated
  • Fixed: References keys for PDFs were not imported if the PDF had no bookmarks
  • Fixed: Under some circumstances references keys from Mendeley bib file were not imported (some special characters had unsual encoding)
  • Fixed: Sometimes monitoring of PDFs did not work
  • Fixed: Link to licence was broken
  • Fixed: <HTML><b>SciPlore Mindmapping</b></HTML> should not occur anymore in MacOS version
  • Fixed: Some corrupt PDF files caused SciPlore MindMapping to crash
  • Fixed: Counter for new reference keys was always one too high

2010/06/22 SciPlore MindMapping (Beta 10)

  • New: Special MacOS version released (We hope it works fine. As we have only a virtual machine to test it, some problems might still occur)
  • Improved: SciPlore MindMapping should run with Linux now
  • Fixed: Sometimes mind maps were not transfered correctly to our backup server

2010/05/07 SciPlore MindMapping (Beta 9)

  • Fixed: Under some circumstances existing mind maps were overwritten with a 0 KB mind map

2010/04/26 SciPlore MindMapping (Beta 8)

  • Fixed: Authentification for mind map backup failed even for correct user name and password

2010/04/23 SciPlore MindMapping (Beta 7)

  • Improved: Monitoring functions considers .doc, .docx, .txt, .xls, .xlsx, .odt, .rtf files in addition to .pdf
  • Improved: Increased performance of monitoring function as folders named .svn are not monitored any more
  • Fixed: In Windows, mind map file type is now SciPlore MindMapping Map (before: FreeMind Map)
  • Fixed: Monitoring function crashed when certain types of hyperlinks were in a mind map.
  • Fixed: Cancelling update of monitoring directory did not work
  • Fixed: "Copy reference key" did not work as attribute was case insensitive

2010/04/16 SciPlore MindMapping (Beta 6)

  • New: Title is extracted from BibTeX file and displayed in mind map
  • New: BibTeX files created by Mendeley can now be processed
  • Fixed: On software update, old preferences are taken
  • Fixed: Several internal bugs
  • Fixed: Saving mind maps produced error when not internet connection was available

2010/04/02 SciPlore MindMapping (Beta 5)

  • New: Backup mind maps to
  • New: Information retrieval on your mind maps
  • Improved: Monitoring works with relative paths
  • Improved: Titles for status messages
  • Fixed: Monitoring function imported all bookmarks in all nodes not only in the monitoring node
  • Fixed: Nested bookmarks were not imported
  • Fixed: Only one PDF was imported when several files were drag&dropped to the software
  • Fixed: Defect PDFs were not imported
  • Fixed: Java check showed misleading error messages

2010/03/15 SciPlore MindMapping (Beta 4)

  • New: Java Check (if Java is not installed, the user is notified)
  • New: Entries from right mouse click dialog are now in main menue as well
  • New: Logging is activated by default
  • New: Update to FreeMind's code base 0.9 RC 7
  • New: Java 1.6 required instead of Java 1.5
  • Improved: Monitoring folder do not list files that are linked elsewhere in the mind map
  • Improved: Optimal Width is now applied automatically to reference attributes
  • Fixed: False notifcations should not appear any more
  • Fixed: Header of mind maps is now correct

2010/03/08 SciPlore MindMapping (Beta 3)

  • New: Monitoring function for folders to import PDF files
  • New: Video showing SciPlore MindMappings capabilities now available on YouTube
  • Improved: Replaced PDF Box library with JPod library from BerliOS
  • Fixed: Bookmarks from PFDs created with Adobe Acrobat 9.x were not imported
  • Fixed: Bookmarks from PDFs with two or more dots in the filename were not imported
  • Fixed: PDFs without bookmarks are now correctly imported
  • Fixed: PDF bookmarks were not imported when a PDF was added via file dialog

2010/01/19 SciPlore MindMapping (Beta 2)

  • New: Preference Dialog is now repared for performing information retrieval on mind maps, backups, etc.
  • New: Update PDF bookmarks in mind map (via context menu)
  • New: Reference key can now be copied as cite\{Reference Key} to clipboard
  • Improved: Code base updated from FreeMind Max RC4 to FreeMind Max RC6
  • Improved: When editing the reference key manually, the focus now is set automatically on the reference key and not the attribute name splmm_refkey
  • Improved: Source code cleaned and redundancies removed
  • Improved: All strings are now in the appropriate properties file
  • Fixed: When changing a BibTeX key in the BibTeX database, the key is now updated correctly in the mind maps
  • Fixed: Attribute bug (splmm_refkey was sometimes called SPLMM REFKEY)

2009/11/15 SciPlore MindMapping (Beta 1)

  • First public version of SciPlore MindMapping


If you like SciPlore MindMapping, you have various options to support its development.

  1. Spread the word: tell your friends and colleagues of SciPlore MindMapping
  2. Go to the project webpage on SourceForge and rate SciPlore MindMapping. Just click the blue "thumb up" symbol on the right side and enter a short review if you like (no registration requiered).
  3. If you have a homepage place a link to and/or on it
  4. If you have Java skills, join our team and contribute actively to future versions of SciPlore MindMapping

If you want to cite SciPlore MindMapping in your blog or academic article, please reference to this website or use following bibliographic data:

Jöran Beel, Bela Gipp, and Christoph Müller. 'SciPlore MindMapping' – A Tool for Creating Mind Maps Combined with PDF and Reference Management. D-Lib Magazine, 15(11), November 2009. Brief Online Article. doi: 10.1045/november2009-inbrief.



If you are interested in a co-operation (for researching mind maps, integrating SciPlore MindMapping with your own reference or PDF management tool, etc.) please contact us.


SciPlore MindMapping is based on others peoples' great work. We have to give credit especially to FreeMind which SciPlore MindMapping is based upon and JPod which we use to import PDF bookmarks.



SciPlore MindMapping is published under the GNU Licence. That means, SciPlore MindMapping is Open Source and you can basically do everything you want with it. You can distribute it, give it to friends, and even modify it and you do not have to pay for it. However, for the exact licence check out the original GNU/GPL licence page.

Contact Us

If the 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.


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

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