Table of Content

• Program Details (Short Description, Homepage, etc.)
• Requirements
• Installation
  • Windows
  • Linux
  • Mac OS
• Operation
  • Importing Mind Maps from FreeMind 0.8.1 (or older) and FreeMind Scholar (Alpha 1)
  • Importing Mind Maps from MindManager, XMind and other Mind Mapping Tools
  • Basic Functionality
    • Disable Direct Selection
    • Create New Nodes
  • Adding References Manually
    • Link a file
    • Add a reference key
    • Link a website
    • Create a note
  • Adding Reference Keys Automatically
    • BibTeX based reference management tools (JabRef, BibDesk, Referencer, etc.)
    • Zotero
    • Mendeley
    • EndNote
    • Other Reference Managers
  • Update Reference Keys in Current Mind Map
  • Copy Reference Key to Third Party Application
  • Hide / Show Reference Keys
  • Import PDF Bookmarks
  • (De)activate Automatic PDF Bookmark Import
• Licence
• FAQ (Frequently Asked Questions)
• Contact Us

Program Details (Short Description, Homepage, etc.)

Requirements

• 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 www.java.com for free).
• About 30 MB free disk space

Installation

Windows

Linux

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 http://www.apple.com/downloads/macosx/apple/application_updates/javaformacosx106update1.html (alternatively try http://landonf.bikemonkey.org/static/soylatte/). 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.

Operation

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

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

Mendeley

Zotero

Endnote

Other Reference Managers

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)

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.

you will need the latest sourcecode:
SciPlore_MindMapping_Source_v010b.zip

you will need to install following packages:
java
java-1.6.0-openjdk
ant
ant-apache-regexp

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

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
Runtime".

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.

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).

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. (http://portableapps.com/news/2009-11-30-_java_portable_6_update_17). 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.

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