Companion for using Version 14 of TheBrain for Windows and macOS.

Posted March 2024

©2024. TheBrain Technologies LP. All Rights Reserved.

TheBrain, PersonalBrain, Brain, Thought, Thoughts, and Work the Way You Think are trademarks or registered trademarks of
TheBrain Technologies LP. Other trademarks or service marks appearing herein are the property of their respective owners.
 Table of Contents

Table of Contents
Introduction ....................................................................................................................... 1
Thoughts are Information........................................................................................ 1
TheBrain’s Dynamic Graphical Interface ................................................................ 2
Cross Platform Accessibility ................................................................................... 2
About this Guide ..................................................................................................... 2
Note to macOS Users ............................................................................................. 3
Brain Terminologies ................................................................................................ 3
Installing TheBrain and Creating a Brain Account ................................................. 9
Opening Older Brains ........................................................................................... 12
Suggestions for Transitioning to Your New Brain ................................................ 14
Understanding Thought Relationships ........................................................................ 15
Families of Thoughts............................................................................................. 18
Navigating Your Brain .................................................................................................... 19
Opening a Brain .................................................................................................... 20
Opening a Brain that Doesn’t Appear as a Tab ................................................... 21
Managing Brains Using the Tabs ......................................................................... 22
Brain Tab Properties ........................................................................................23
Windows Menu.................................................................................................24
Managing Brains Using the Context Menu ........................................................... 24
Favorite Brains .................................................................................................25
Opening Content Associated with a Thought ....................................................... 26
Showing Thought Content on Hover .................................................................... 26
Previewing Thought Content ................................................................................ 26
Editing Additional Notes........................................................................................ 28
Pins ....................................................................................................................... 28
Activating Recent Thoughts: The Past Thought List ............................................ 29
Searching a Brain ................................................................................................. 31
Instant Activation..............................................................................................31
Cross-Brain Search..........................................................................................33
Searching within Attachments .........................................................................34
Using the Search Box to Search the Web .......................................................34
Additional Search Functionality ............................................................................ 36
Customizing Your Brain’s Environment ...................................................................... 38
TheBrain’s Default Settings .................................................................................. 38
Using Smart-Splitter to Arrange TheBrain Window .............................................. 38
Moving Thoughts in the Plex ................................................................................ 39
Resizing Thoughts in the Plex .............................................................................. 40

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Customizing a Brain’s Appearance ...................................................................... 42

Selecting a Theme ...........................................................................................42
Customizing a Theme’s Colors........................................................................44
Defining and Selecting Additional Colors ........................................................45
Selecting a Custom Image for the Plex ...........................................................46
Changing the Default Font in the Plex.............................................................48
Changing the Content Area’s Default Attributes .............................................49
Viewing and Selecting Prebuilt Styles .............................................................54
Copying, Pasting, Importing, and Exporting Styles .........................................55
Saving Changes ...............................................................................................56
Reverting to the Theme’s Default Settings ......................................................56
Saving Themes ................................................................................................56
Renaming a Theme .........................................................................................58
Deleting a Theme.............................................................................................58
Importing and Exporting Themes ....................................................................59
Dark Mode............................................................................................................. 60
Setting Other Preferences .................................................................................... 61
Look & Feel Preferences .................................................................................62
Behavior Preferences ......................................................................................64
Notes Editor Preferences.................................................................................67
System Preferences.........................................................................................71
Keyboard Preferences .....................................................................................72
Experimental Preferences ...............................................................................80
Creating Thoughts .......................................................................................................... 81
Creating a Single Thought .................................................................................... 81
Displaying Thought Properties and Details .......................................................... 83
Creating Multiple Thoughts at Once ..................................................................... 83
Creating Context-Sensitive Thought Names Using Commas .............................. 84
Using Parentheses to Assist with Thought Sorting .............................................. 85
Creating Thoughts with Artificial Intelligence ....................................................... 86
Creating Orphan Thoughts ................................................................................... 87
Create Thoughts from Search, Notes or Events .................................................. 88
Changing the Order of thoughts in the Plex ......................................................... 90
Copying Thoughts Within and Between Brains .................................................... 91
Merging Thoughts ................................................................................................. 94
Undoing and Redoing Actions .............................................................................. 95
Editing Thoughts and Links .......................................................................................... 96
Renaming Thoughts.............................................................................................. 96
Selecting Multiple Thoughts.................................................................................. 97
Other Selection Uses .......................................................................................99

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Forgetting and Deleting Thoughts ...................................................................... 100

Unlinking Thoughts ............................................................................................. 104
Linking Thoughts................................................................................................. 105
Link to a Thought Visible in the Plex ............................................................ 105
Link by Dragging to a Pin.............................................................................. 105
Link by Dragging to the Past Thoughts’ List ................................................. 106
Link by Selecting a Thought in the Existing Thoughts List .......................... 106
Link by Using the Selection Panel ................................................................ 107
Cancel Creation of a Link ............................................................................. 108
Changing Relationships Using Drag and Drop .................................................. 108
Customizing Thought and Link Properties................................................................ 110
Changing the Properties of a Thought ............................................................... 110
Changing the Colors of a Thought................................................................ 111
Adding a Label to a Thought......................................................................... 112
Swapping a Thought’s Name with its Label ................................................. 113
Adding an Image to a Thought ..................................................................... 114
Displaying Inherited Properties..................................................................... 120
Making Thoughts Private .............................................................................. 120
Using Thought URLs..................................................................................... 121
Thought Types and Tags .................................................................................... 123
Creating a Thought Type .............................................................................. 124
Super Types .................................................................................................. 128
Dynamic Wallpaper ....................................................................................... 128
Using Thought Tags...................................................................................... 129
Assigning and Removing Tags ..................................................................... 131
Assigning Tags to Multiple Thoughts at One Time ...................................... 131
Deleting a Tag ............................................................................................... 131
Renaming and Adding Attributes to a Tag ................................................... 133
Displaying Thoughts Based on Their Tags .................................................. 134
Tag Abbreviations ......................................................................................... 134
Additional Thought Type and Tag Features ....................................................... 135
Visible Thought Types and Tags .................................................................. 135
Hiding Visible Thought Types ....................................................................... 136
Converting Thoughts to Type or Tag ............................................................ 136
Clickable Tags............................................................................................... 137
Replacing a Tag ............................................................................................ 137
Nested Tags .................................................................................................. 137
Changing the Properties of a Link ...................................................................... 138
Link Types ..................................................................................................... 141
Deleting Link Types ...................................................................................... 142
Showing Link Direction ................................................................................. 143

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Using One-Way Links ................................................................................... 144

Advanced Navigation and Alternative Views ............................................................ 147
Changing Your View of Thoughts ....................................................................... 147
Using Outline View.............................................................................................. 150
Using Mind Map View ......................................................................................... 151
Expanding and Collapsing Generations ............................................................. 152
Presentation Mode .............................................................................................. 155
The Content Area .......................................................................................................... 156
Content Area Overview ....................................................................................... 156
Note Viewing Options ......................................................................................... 159
Creating and Formatting Notes .......................................................................... 159
The Content Area Toolbar ............................................................................ 160
Toolbar Buttons ............................................................................................. 161
Markdown Editor ........................................................................................... 162
Markdown Variations .................................................................................... 163
Viewing Multi-Column Notes......................................................................... 163
Entering Notes .............................................................................................. 164
Artificial Intelligence Writing Assistance ............................................................. 165
Generating New Notes with AI ..................................................................... 166
Modifying Existing Notes with AI .................................................................. 167
Using Drag and Drop within Notes ............................................................... 170
Tab Key Functionality in the Notes Editor .................................................... 170
Collapsing and Expanding Notes Sections .................................................. 171
Choosing a Notes Style ................................................................................ 171
Changing Text Size in Notes ........................................................................ 174
Paragraph Alignment .................................................................................... 174
Custom Font Family for Selected Text ......................................................... 174
Adding Tables ............................................................................................... 175
Table Controls ............................................................................................... 177
Table Theme Editor ...................................................................................... 178
Inserting a Table of Contents........................................................................ 179
Spell Checking .............................................................................................. 180
Inserting Horizontal Rules............................................................................. 181
Creating Check Box Lists ............................................................................. 182
Linking to Thoughts in Notes ........................................................................ 184
Creating Web Links....................................................................................... 184
Fast Linking and Creating Thoughts from Notes.......................................... 186
Capturing and Inserting Images in the Content Area ................................... 187
Mathematical Expressions ............................................................................ 188
Details on Images in Notes ........................................................................... 188
Find and Replace in Notes ........................................................................... 189

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Printing Notes................................................................................................ 189

Exporting Notes ............................................................................................ 190
Additional Note Features .............................................................................. 191
Adding and Viewing Thought Attachments ........................................................ 192
Attaching Files............................................................................................... 193
Action Menu for Files .................................................................................... 195
Attaching Web Pages ................................................................................... 196
Attaching Video and Sound Files ................................................................. 198
Action Menu for URLs ................................................................................... 199
Viewing Attachments as a Slideshow........................................................... 201
Working with Multiple Attachments............................................................... 202
Keyboard Commands for Selected Attachments ......................................... 203
Cut/Copy Attachments Within a Brain .......................................................... 203
Creating an Event as an Attachment ............................................................ 203
Adding a Template File to Your Brain .......................................................... 203
Pasting an Image as an Attachment ............................................................ 205
Using the “Save As” Command .................................................................... 205
Viewing Related Thoughts in the Content Area ................................................. 205
Thought Mentions ......................................................................................... 206
Using Related Thought Links........................................................................ 207
Hiding or Showing Related Thoughts ........................................................... 208
Collapsing and Expanding Related Thought Sections ................................. 209
Aggregating Content ........................................................................................... 210
BrainBox ........................................................................................................................ 212
Accessing BrainBox ............................................................................................ 213
The BrainBox Button ..................................................................................... 213
The BrainBox Tab ......................................................................................... 214
Sending Web Pages to BrainBox ....................................................................... 216
Sending Files to BrainBox .................................................................................. 216
Windows File Explorer Send to Integration .................................................. 216
macOS Dock Drag and Drop ........................................................................ 217
Producing Reports........................................................................................................ 218
Selecting Report Criteria..................................................................................... 218
By Types/Tags .............................................................................................. 219
Forgotten Thoughts....................................................................................... 220
Parentless Thoughts ..................................................................................... 221
Orphan Thoughts .......................................................................................... 222
Duplicate Names........................................................................................... 223
By Attachments ............................................................................................. 223
Filtering by Modification or Creation Date .................................................... 224
Sorting Report Results ........................................................................................ 225

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Refreshing or Resetting Report Results ............................................................. 225

Adding Report Results to the Selection Panel ................................................... 226
Saving and Accessing Reports........................................................................... 227
Viewing a List of Recent Changes...................................................................... 228
Find and Replace .......................................................................................................... 229
Statistics ........................................................................................................................ 230
Managing Events .......................................................................................................... 231
Creating an Event ............................................................................................... 231
Creating an Event from the Content Area .................................................... 231
Creating an Event from the Timeline ............................................................ 232
Responding to Event Reminders .................................................................. 233
Editing and Deleting Events.......................................................................... 234
Navigating in Timeline View................................................................................ 235
TheBrain Icons .............................................................................................................. 236
Online Menu Options .................................................................................................... 239
Using Mobile Versions of TheBrain ............................................................................ 240
Share, Synchronize, and Back Up Your Brains......................................................... 242
Synchronizing Your Brain ................................................................................... 243
Editing Your Online Brain ................................................................................... 245
Sharing Your Online Brain .................................................................................. 246
Creating a Brain Archive to Send Your Brain to Others ..................................... 247
Copying Thoughts into Other Applications as an Outline .................................. 248
Copying Outlines with Notes......................................................................... 249
Pasting a Text Outline as New Thoughts ..................................................... 250
Importing Information into Your Brain ....................................................................... 251
Importing Folders and Mind Maps ...................................................................... 251
Importing TheBrain 8 XMLs ................................................................................ 252
Merging Brains .................................................................................................... 252
Encrypting Individual File Attachments ..................................................................... 253
Exporting ....................................................................................................................... 255
TheBrain API.................................................................................................................. 257
Glossary ......................................................................................................................... 258

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 Introduction

Introduction
Welcome to TheBrain™, your ultimate digital memory and no limits mind mapping
software. Intelligence comes from the mind’s ability to think associatively—that is,
to leap from thought to thought, building webs of greater and greater complexity,
until new ideas are built. Associations are our inspirations. TheBrain allows you to
organize your information in the same way, without limiting you to a pre-
determined file structure. In fact, with your digital brain there are no limits. You can
create a small project-focused brain or grow your brain to hundreds of thousands
of thoughts!

Now you don't have to force any idea or project into a single folder. TheBrain
organizes information as thoughts. Unlike folder directories and search lists, a
“thought” in your brain can have many connections and contexts. Moreover,
TheBrain displays your thoughts by concept or project, linked according to how
you think. Now you can get the big picture and discover information that might
otherwise be overlooked.

Thoughts contain relevant notes, web pages, and files. Brains can be synced for
easy access from your desktop to TheBrain Cloud or your mobile devices.

Figure 1. TheBrain Interface

Thoughts are Information

TheBrain thoughts can represent just about any type of information, including
concepts, people, documents, spreadsheets, images, videos, shortcuts, and web

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 Introduction

pages. By letting you create links and associations between thoughts, TheBrain
expands to become a visual interface that reflects the way you think.

Using simple click-and-drag techniques, you’ll be able to create and navigate

through networks of thoughts in a conceptual space unique to your work habits.
When you begin using TheBrain, you will find that your computer becomes easier
to use—faster, more enjoyable, and less frustrating—helping you use your time
more efficiently.

TheBrain’s Dynamic Graphical Interface

TheBrain lets you create a simple, dynamic graphical map in which to input and
navigate all your information. Your brain starts with a single thought, to which
several other thoughts can be visually linked. These thoughts have their own
links to other thoughts and, possibly, to each other. TheBrain’s flexible structure
allows any thought to be linked to any other thought, so you are never more than
a few steps away from the information you are seeking. It’s simple to make
connections between thoughts so that they reflect the connections you make in
your mind.

Cross Platform Accessibility

Brain data is accessible from virtually any device with rich full-featured clients on
Windows and macOS plus mobile clients for iOS and Android. Additionally, you
can access your brain via a web browser by logging in at www.thebrain.com.
TheBrain’s sync service keeps all your data backed up and synchronized over
the cloud for seamless access.

This user guide is focused on the Windows and macOS software. Please visit
www.thebrain.com for information about the mobile clients.

About this Guide

The following icons are used throughout this guide to flag categories of
information:

This icon is used to identify notes.

This icon is used to flag tips and suggestions.

TheBrain is offered in two editions—Free and Pro. Icons are used throughout the
guide to flag features that are specific to the Pro edition. Features that are
available in both editions are not designated with a special icon.

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 Introduction

This icon is used to indicate that the feature is available in the Pro edition only.

Because TheBrain works on Windows and macOS, OS-specific features are

flagged with icons throughout the guide. Features that are available for both
Operating Systems are not designated with a special icon.

This icon is used to indicate that the information applies only to computers
running macOS.

This icon is used to indicate that the information applies only to computers
running Windows.

In addition:

Labels Names of buttons, menus, commands, keys, and icons appear in this font
throughout the guide in order to stand out.

Note to macOS Users

Right-clicking: Most features in TheBrain can be accessed with just a single
click of your primary mouse button. However, there are several context-
sensitive shortcuts available in context menus which appear when right-
clicking. On a Macintosh, many systems do not have a right mouse button. For
trackpad users, click or tap with two fingers. Alternatively, hold down the
Control key while you click. Note that many mice can be set up to interpret
clicks on each side of the main button differently so that Control-clicking is not
necessary. To enable this, alter the Mouse settings in the System Preferences
area of your Mac. Select “Secondary Button” for the right side of the mouse.

Ctrl key: Some features are accessed by clicking while holding down the Ctrl
key on Windows. For macOS, use the Command key.

TheBrain supports Native Apple Silicon.

Brain Terminologies

Here is a list of working definitions for the basic terms used throughout TheBrain.

Brain A collection of associated thoughts, each of which can have

content. You can create multiple brains.

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Thought The topics that you link together in your brain are called
thoughts and are the basic unit of a brain. A thought can
represent anything you want it to. It can include an icon, notes,
and one or more attachments (such as files and web sites) or it
can have no content at all and simply act as a subject heading
or organizer. Minimally, a thought has a name.

Plex The visible, graphical portion of your brain that displays your
thoughts.

Content Area The portion of TheBrain window that displays content that can
be associated with the active thought or link. Types of content
include notes, attachments (such as worksheets, presentations,
documents, videos, and images), links, URLs, and events. The
content area also displays and provides quick access to related
thoughts.

Clicking any thought or link in the plex displays its associated content in the
content area.

Figure 2. TheBrain Plex and Content Area

Active The active thought appears in the center of the plex and is
Thought the current focus. Any items attached to the thought, like
notes, files, links, and events appear in the content area.

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Figure 3. The Different Ways a Thought Can Appear

As shown below, when you click a thought, it moves to the center of the plex and
it becomes the active thought.

Figure 4. Activating a Thought

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Thought A thought is said to be a “parent thought,” “child thought,”

Relationships “sibling thought,” or “jump thought” based on its relationship
to other thoughts with which it is linked.

In your own life, you may be someone’s parent, and

someone’s child, and someone’s sibling, and someone’s
peer, advisor, or colleague. So, who are you? The answer to
that question is relative—it depends on the circumstances
and what hat you’re wearing at the moment.

Figure 5. Relationships are Relative to You

The same applies to thoughts. The relationships between

thoughts are displayed automatically, based on which thought
is active at the moment.

Whether a thought is a parent, child, or sibling depends on its

current relationship to the active thought.

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Figure 6. Thought Relationships are Relative to the Active Thought

Child Child thoughts are subtopics of the active thought. They

Thought appear in the “child zone,” below the active thought. In the
picture above, the active thought “Hobbies” has seven child
thoughts.

Parent Parent thoughts represent superordinate topics of the active

Thought thought. They appear in the parent zone, above the active
thought.

Sibling Sibling thoughts share a parent with the active thought. They
Thought appear in the sibling zone, to the right of the active thought.
In the picture above, “Family,” “Food,” “Health and Fitness,”
“Home Projects,” “My Passion,” “My Pet,” and “Personal
Finance” are siblings of “Hobbies” because they are all
children of “Personal Life.” Sibling thoughts will not be
displayed if there are more than 50 parents to show in the
current plex.

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 Introduction

Jump Jump thoughts are related to the active thought but are
Thought neither child nor parent topics. They appear in the jump zone
to the left of the active thought. Jump thoughts have an
“equal weight” relationship with the thought to which they are
related. For example, as shown above, “Hobbies” has the
various hobbies “Art and Culture,” “Gardening,” “Music,”
“Snorkeling and Diving,” “Sports,” “Technology,” and “What
I’m Reading Now” linked as child thoughts since they are
types of hobbies. “Budget” affects the amount of resources
available to spend on the various hobbies and so it is closely
related, but it is not a hobby itself. Therefore, it makes a
perfect jump thought―related, but not part of the main
thought grouping.

Gate Thoughts in the plex have three circular “gates,” each of

which is used to link a specific type of relation: The parent
gate is above a thought, the child gate is below it, and the
jump gate is to the left or right of it. A gate is hollow when
there are no links attached to it and solid when one or more
links are attached. Solid gates in a contrasting color have
links to thoughts that are not currently showing in the plex.
The color of gates is based on the current color scheme.
When you point at a gate, a highlighting circle appears
around it.

Link A link is the line that connects two thoughts. When used as a
verb, to “link” is the act of connecting thoughts to establish
close relationships. Links can also show direction to help you
visualize relationships.

Figure 7. Thought Gates

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 Introduction

Installing TheBrain and Creating a Brain Account

The first time you download and install TheBrain, you’ll be prompted to log in or
create an account if you don’t already have one. The log-in window provides the
ability to create a new account or log in to an existing account.

Figure 8. TheBrain Log-in Window

Here are the fields to complete if you’re creating a new account:

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 Introduction

Figure 9. Creating a New Account

After you click the Create Account button, TheBrain will send an email to the
address you specified.

Check for a message from [email protected]. Make sure to check your

spam folder if you don’t receive the message promptly.

When you open the message, you will see a green Activate Brain Account link.
After you click the link, you’ll see a notice confirming your success.

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 Introduction

Figure 10. Activating a New Account

Now you can return to TheBrain and log in.

Figure 11. Welcome to TheBrain

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Click “Create a Quick-Start Brain” and follow the directions on the screen to enter a
personalized name for this brain. The Quick-Start brain is actually a dynamic
resource for learning more about using your brains and you’ll find a wealth of
useful information in it. Click any of the links to see what is displayed.

You can always create a new Quick-Start brain by selecting the Create a Quick-
Start Brain command on TheBrain Help menu.

Opening Older Brains

When you’re looking at old and new brain files, note that brains created in
TheBrain 7 or 8 have filename extensions of .brain. Brains created in some earlier
versions have a .brn filename extension.

To open a .brn file that you created in a version older than TheBrain 8, first
open it using TheBrain 8 and then import the resulting brain in TheBrain 13, as
described in the steps below.

Any older Brain must be opened in TheBrain version 8.0.2.2 before it can be
imported into TheBrain 14. Version 8.0.2.2 can still be downloaded and
installed. Please contact [email protected] for a v8.0.2.2 download link.

To open a brain that you created in TheBrain 8:

1. Open TheBrain.

2. Click the File menu, then click the Import command.

All dialog boxes can also be navigated via the Tab and Arrow keys.

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 Introduction

Figure 12. Import Box for Opening an Older Brain

3. Click the Select File button, navigate to the brain of your choice, then click
the Open button when the file is selected. You will see a running progress
report.

4. When TheBrain has finished converting, you will see a “Conversion

complete” message as shown below. Click the Import button.

Figure 13. Import Conversion Progress

5. When TheBrain has finished importing, you will see the following dialog
box. Click the Open button to open the brain you just imported in a new tab
of TheBrain window.

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 Introduction

Figure 14. Open the Imported Brain in a New Tab

Suggestions for Transitioning to Your New Brain

Here are some tips for establishing a happy relationship with your brain:

You may want to attend one of TheBrain’s free online seminars on getting
started―TheBrain 101. To learn more about TheBrain 101, go to
http://www.thebrain.com/101.

Avoid “converting” to a Brain-only environment all at once. Make the transition on

a file-by-file basis so that every piece of information your brain contains will be
useful.

Build your brain as you go—associating thoughts as they occur naturally.

Avoid the temptation to move large folders into your brain. TheBrain can handle
this, but your brain will be cluttered with thoughts you may not need.

Remember that your first brain doesn’t need to be your only brain or your last
brain. Experiment! Create a brain just for fun, to try out the possibilities—give
yourself room to stretch and explore. Your brain is waiting!

Questions? Contact TheBrain Support Team right from within TheBrain app by
choosing Contact Us from the Help menu in TheBrain toolbar.

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 Understanding Thought Relationships

Understanding Thought Relationships

There are no rules governing the relationships between thoughts—whatever
makes sense to you is the way your brain ought to be organized. The three
primary relationship types―child, parent, and jump―can be used to express
different types of relationships. Sibling is a relationship that is derived from
child/parent relationships.

The examples in this section can help you understand the variety of relationships
and how they are used. The core concepts behind each type of relationship are
as follows:

▪ Children: Child thoughts are usually used to link more specific information or
information that represents a sub-category.

▪ Parents: Thoughts linked as Parents are usually used to link more general
information. Parents can also be thought of as higher-level categories to
classify groups of information. They serve to indirectly connect their child
thoughts as siblings.

▪ Jumps: Jump thoughts are usually used to link two pieces of information that
are exclusively related, meaning that the two items are related to each other
but neither represents a group that the other is a part of.

Let’s move on to an example to explore these relationship types. Imagine that

you are the owner of a company and you are reviewing personnel files. Each
employee has a file. You decide it makes sense to organize your employees by
department. Your brain is called My Brain. From My Brain, you create a child
thought called My Company (see Figure 15). My Brain is now My Company’s
parent thought. You create four child thoughts from My Company—
Manufacturing, Sales, Service, and Billing. These departments are sibling
thoughts of each other.

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 Understanding Thought Relationships

Figure 15. Sample Brain

Now you go to each department and create more child thoughts, one for each
employee of the department. If an employee splits time between two
departments, you can make him a child thought of both departments—he’ll
appear in both and you won’t have to duplicate his thought. In this example, Bob
is a child thought of both Manufacturing and Sales (see Figure 16). This is one of
the most powerful features of TheBrain—having one thought under more than
one heading.

Figure 16. Child Thought with Two Parents

If you own more than one company, but have one accountant for all of them, you
might want to create a thought called Accountant and link it as a jump thought to
each company, as shown below.

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 Understanding Thought Relationships

Figure 17. Jump Thoughts to the Active Thought

Imagine that Joe’s company has just purchased one of your companies. Since
Joe’s company now owns this company, Joe’s Company becomes a parent (see
below).

Figure 18. New Parent Thought

Because Joe wants to avoid a conflict of interest, the acquired company (My
Other Company) no longer uses the same accountant. So its jump gate is hollow,
while its sibling’s jump gate (My Company) maintains that link and is filled.

As you use TheBrain, you will develop a sense of the types of relationships you
wish to make between thoughts. It is always easy to change relationships by
adding and removing links (see Changing Relationships Using Drag and Drop on
page 108).

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 Understanding Thought Relationships

Families of Thoughts
It is tempting to view thought relationships as families, and indeed these different
parts of your brain are types of families, with their ancestry visually spread before
you, represented by subjects and categories. But unlike human families, a child
thought can be a parent of one of its siblings and a thought can have more than
two parents.

The complex relationships you can form in TheBrain are the source of its power.
Let’s consider sibling thoughts that also share a parent/child relationship.

Let’s say you are studying philosophy. You might have a thought called
Philosophy. Individual philosophers such as Plato and Aristotle could be child
thoughts of Philosophy. Each of these siblings, in turn, may have child thoughts.
Aristotle was a student of Plato, so you may want to make Aristotle not only a
child of Philosophy, but of Plato, so that when you’re working with Aristotle, Plato
is only a thought away.

Figure 19. Example of Parent/Child Relationships

Notice that when Philosophy and Plato are in Aristotle’s parent zone, their
relationship (Philosophy is a parent thought of Plato) is shown by the line linking
the child gate of Philosophy to the parent gate of Plato.

Clearly, TheBrain is a powerful method of organizing ideas and information. No

hierarchical file structure can provide as much cross-referenced information at a
glance. And our example is pretty basic—a fully developed brain can hold many
more relationships and much more information.

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 Navigating Your Brain

Navigating Your Brain

All thoughts can be connected—directly or indirectly—even thoughts that may
seem to have nothing to do with each other can be related through a chain of
links.

Let’s look at an example, say, the Queen of England and asparagus. You have a
thought called Queen of England. One of its child thoughts is Prince of Wales,
which has a parent thought—Famous Princes—that is also linked to the story of
the Frog Prince.

The story has another parent thought called Fairy Tales. A sibling of Frog Prince
is Jack and the Beanstalk.

Jack and the Beanstalk has child thoughts called Giant and Jack. Giant has
another parent thought called Famous Giants.

Famous Giants has a child thought called Jolly Green Giant. Jolly Green Giant
has child thoughts named after canned vegetable products, one of which is
Asparagus. Thus, the Queen of England is connected to asparagus!

Depending on the relationship you create between them, thoughts may be

closely or distantly related. Thoughts are considered to be closely related when

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they are linked directly or are siblings. In the default view of the plex, only close
thoughts of the active thought are always displayed in the plex. Thoughts that are
one additional step (generation) away from the active thought can be displayed
by expanding the view. See Advanced Navigation and Alternative Views on page
147 for information about the different view options.

Opening a Brain
When you log into TheBrain, and no brain is open, all local, synced or online
brains will be displayed as thumbnails in the Brains tab, as shown below. This is
assuming that you have already created one or more brains. Clicking on a brain
thumbnail opens that brain. Or, hold down the Ctrl key as you click to open a
brain in a new tab, leaving the Brains tab open.

Figure 20. Example of Four Available Brains on the Brains Tab

By default, brains are listed according to how recently they have been accessed.
You can also see the list of brains sorted alphabetically using the Brains tab
toolbar, shown below. All brains that are locally available are shown first,
followed by brains that are available online.

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Figure 21. The Brains Tab Toolbar

The status of whether each brain is available locally, online, or both is also
displayed. Each brain in the Brains tab will have an icon appearing in the lower-
right corner of the thumbnail. Right-click on a brain or click on the status icon to
display a menu of options for that brain, as shown below. The appearance of the
icon(s) help you identify whether the brain is Local, Synced (local and online) or
Cloud (Online only).

Figure 22. Icons Indicating Local, Synced, or Cloud

Figure 23. Status Indicator Icons

Opening a Brain that Doesn’t Appear as a Tab

If you have a brain from an older version or from a backup, it will not appear in
the Brains tab until you import it. Click the File menu, then the Import command.

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Choose the type of file you want to import, then click the Select File button,
navigate to the file of your choice, then click the Open button when the file is
selected. Click the Import button after TheBrain has finished converting the
brain.

Managing Brains Using the Tabs

The tabbed interface of the plex lets you switch instantly between brains or even
keep the same brain open in multiple Brain tabs or windows.

To re-open the Brains tab to display the Brain thumbnails, click the + icon to the
right of the last tab.

Figure 24. Click the + Icon to Open the Brains Tab

There is no limit to the number of brains you can open at once. Each time you
open a brain it will appear in a separate tab. Switch from brain to brain
instantaneously by clicking its tab. All tabs and their states are automatically
saved and restored when you quit and restart.

Tabs can be manipulated in several ways:

▪ Float tabs into their own dedicated window by dragging a tab out of TheBrain
application window. This creates a new Brain application window with just a
single tab.

▪ Merge tabs into one window by dragging and dropping. Click the tab of one
Brain window and drag the tab to another open brain, hovering over the tab
area. Then release the mouse button.

▪ Open the same brain in multiple tabs to view and edit multiple areas at a
time. This lets you view different areas of your brain at the same time, and, if
you like, use a different layout in each tab. Note that tabs are simply views
into the same brain data and changes made in one tab affect all other tabs of
that brain.

▪ Duplicate tabs. Right-click on a brain tab to duplicate it, showing the same
content in a new Brain tab.

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Brain Tab Properties

Right click on any brain tab for the option to Set Tab Color. Chose from nine
different colors. This tab will then be highlighted for as long as it remains open.
Closing the tab will reset the tab properties.

To permanently set a tab color for a specific brain, right click on a brain thumbnail
in the brains list and select Set Brain Color. The color selected will appear in the
color indicator on the brain’s thumbnail and the brain tab will be highlighted when
this brain is open. If the brain tab is open, but not currently the selected tab, the
color highlight will be visible, but minimized.

Figure 25. Selecting a Brain Color

Brain tabs can display either the brain name and the active thought name, or just
the active thought name in a more compact tab. This setting can be found in
Preferences on the Look & Feel tab.

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Figure 26. Brain Tabs displaying selected colors, brain name and active thought
name

Windows Menu
From Windows menu in the menu bar you’ll have the option to move between
brain tabs, move tabs to new windows or select a specific brain tab to be
activated.

Additionally, if you have adjusted the layout of a brain with the Smart Splitter, you
can select the option to Reset Window which will bring the plex/content area
back to their default views.

Managing Brains Using the Context Menu

You can right-click any brain in the Brains tab to display the available options.

Figure 27. The Context Menu in the Brains Tab

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Tip: Press Ctrl/Cmd + click to open a brain in a new tab from the brains list page.

Favorite Brains
If you have more than one brain and would like to keep commonly accessed
brains at the top of your brain list, you can set a brain to be a favorite.

Figure 28. Favorite Brains at the top of your Brain List

There is no limit to the number of favorite brains. To set a favorite brain, right
click on a brain in the brains list. Select Favorite Brain.

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Figure 29. Setting a Favorite Brain

Opening Content Associated with a Thought

As you navigate through your brain, the content associated with the active
thought is displayed in the content area. Notes associated with the thought are
displayed automatically. There are several ways to open an attached file or web
page:
▪ Click on the link for the attachment in the content area.

▪ Click on the attachment icon to the left of the thought’s name in the plex.

▪ Right-click on the thought, click Open Attachment on the context menu, then
click the attachment of your choice.

Showing Thought Content on Hover

By default, the content for the active thought displays in the content area. If you
prefer, you can display content for any thought your mouse pointer hovers over
by changing the setting. To do so, click the Options menu (TheBrain menu on
macOS), click Preferences, click the Behavior tab, then select the “Update
displayed content on mouse hover or keyboard highlight” check box. Close the
Preferences window when you’re finished.

Previewing Thought Content

Certain types of file attachments are automatically previewed inside of TheBrain.
These include web pages, images, text, markdown files, JSON, .html files and
PDFs. Simply click on an attachment’s tab and its preview will be shown. In the
example below, Tropical Getaways is the active thought and there are two
attachments in the content area—an image and a PDF.

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You can view multi-page PDFs, web pages, and images as a slide show within
the content area.

▪ Click the link for an attachment to open a preview of it in the content area.

▪ Click the Next or Previous arrow in the top-right corner of the attachment to
move back and forth between attachments (or back to the notes in the
content area).

▪ Click the Close button (X) to end the preview and return to the notes.

▪ Click the Open button to open the file outside of TheBrain.

Figure 30. Content Area for the Active Thought

The PDF preview features:

▪ Supported rendering for each OS

▪ Support for very large, multi-page PDFs

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▪ Thumbnails of each page, zoom, rotation, search, and printing

▪ All PDF commands can be mapped to a custom keyboard shortcut

Editing Additional Notes

Adding additional attachments to a thought, such as .md and .txt files will enable
you to also edit these attachments the same as you would a brain note.

Pins
Pins are shortcuts to thoughts to which you want quick access. They appear at
the top of the plex, just below TheBrain toolbar. No matter where you are in your
brain, the pins remain visible.

Figure 31. Pins

To create a pin:

▪ Use the Toggle Pin button in the main toolbar to create a pin for the Active
Thought or right-click the thought for which you want to create a pin, then
click Create Pin on the context menu

Figure 32. Toggle Pin Button

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To remove a pin:

▪ Use the Toggle Pin button in the main toolbar to remove the pin for the
Active Thought or right-click the pin or on a thought that has a pin, then click
Remove Pin on the context menu

Removing a pin does not remove or delete the associated thought; it deletes
only the reference to it at the top of the plex.

To use a pin to link thoughts:

▪ Drag from one of the thought gates to the pin, or

▪ Move your mouse pointer over a pinned thought and gates will appear; drag
from one of these gates to the thought you want to link

Activating Recent Thoughts: The Past Thought List

TheBrain keeps a running breadcrumb trail of your thoughts based on activation
and displays it in the Past Thought List. You can think of the Past Thought List as
the visual representation of the phrase, “train of thought”—a scrollable list of
thoughts in the order you activated them. The Past Thought List is displayed at
the bottom of the plex window.

Clicking on any thought in the Past Thought List activates that thought. Also,
when a new thought is created it appears in the Past Thought List immediately.

Figure 33. Past Thought List

The left and right arrows to the left of the Past Thought List enable scrolling to
see items that don’t fit on the display.

The most recently activated thought (the currently active thought) appears at the
right end of the list.

To use a thought in the Past Thought List to link thoughts:

▪ Drag from one of the thought gates to one of the thoughts in the Past
Thought List, or

▪ Move your mouse pointer over a thought in the Past Thought List and gates
will appear; drag from one of these gates to the thought you want to link

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In the example below, Tropical Vacations is going to become a parent of Airline

Rewards; the mouse is being dragged from the child gate of Tropical Vacations
to Airline Rewards in the Past Thought List.

Figure 34. Creating a Link using the Past Thought List

Using the Back and Forward Buttons:

▪ In addition to the Past Thought List, you can also use the Back and Forward
buttons, located near the top of the Window, to quickly retrace your steps;
these buttons work just like they do in a web browser

Figure 35. The Back and Forward Buttons

▪ Click the Back button to go back to the last active thought

▪ Once you have clicked the Back button, the Forward button can be used to
re-activate the thought you came from

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Back and Forward Mouse Buttons: The back and forward buttons available on
some mice (typically on the left side of the mouse near where you place your thumb)
may be used to navigate backward and forward in your brain. These mouse buttons
perform the same navigation as the Back and Forward buttons in the Brain toolbar,
shown above.

Searching a Brain
TheBrain includes powerful search capabilities. Indexing is performed by the
application itself and is not dependent on your OS search settings. Re-indexing
your brain is typically not necessary; however, your brain can be re-indexed by
clicking on File in the toolbar. Under the Utilities option, select Rebuild Brain
Index.

Instant Activation
TheBrain includes powerful search capabilities. The Search box is in the top-right
area of the application.

Figure 36. The Search Box

The term “instant activation” refers to TheBrain’s ability to quickly find whatever
you’re searching for and activate the related thought. You can easily scan the
search results as you type in the Search box. There's no need to click in the
Search box, your cursor is always there by default, unless you are actively typing
in the content area or another field.

A content area preview will automatically appear for each choice you highlight.

To activate one of these results, click it with your mouse or use the up-arrow,
down-arrow, page up, and page down keys on the keyboard then press the
Enter key.

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Figure 37. Instant Activate Finds Matches Based on Thought

Names, Labels, Notes, and Attachments

Accents are ignored when matching thought names. Also, when two or more
matches with the same name are found, the names of their parent or jump
thoughts are also displayed so you can differentiate them.

You can search for thoughts by typing the first letter(s) of separate words and the
letters can be in any sequence; for example, to find the “Family and Friends”
thought you could type “fa fr,” or “fr fa,” or “fa and fri.”

Figure 38. Use First Letters of Separate Words for Instant Activate

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Attachments and note search matches are identified with a yellow piece of paper
icon for notes and a paper clip icon for Attachments.

Figure 39. Search Results

When you do a search, the results are sorted with results that match thought
names first, then notes, then attachments. Within the thought name matches,
they are ranked in groups:

▪ Exact Matches—where the entire name of the thought matches the entire
query

▪ Starting Matches—where the entire query occurs at the start of the thought
name

▪ Continuous Matches—where the entire query occurs anywhere in the

thought name

▪ Matches—where every term in the query occurs somewhere in the thought

name

Within each group, thoughts that have been activated in the last 30 days will be
shown first, ordered with the most recently activated first. Thoughts that have not
been activated within 30 days are sorted alphabetically.

Cross-Brain Search
Search results will be displayed first by results in the currently open brain,
however, you’ll also see results of your search query in Thoughts and Links from
other Brains and Notes, Attachments and Events from other Brains. To keep the
search process efficient, search results will be displayed progressively - first from
your current, open brain and then from other brains.

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Figure 40. Search Results from other Brains

Clicking on any of these results will launch the specified brain/thought in a new
tab. These search results are only for brains that you have access to on the
current machine where you are searching.

Searching within Attachments

Your searches automatically include matches based on the contents of

attachments. If the text you’re searching for exists within documents including
PDFs, Word, Excel, PowerPoint and many other file formats, the documents
containing the text will be found.

Using the Search Box to Search the Web

Say you’re searching for something and come up with no hits. For example,
you’re on a neighborhood committee and you’ve volunteered to look into an issue
with squirrels. You type “squirrels” in the Search box. No results? Press the F4
key to search the web.

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Figure 41. Search-Engine Choices

▪ Click the drop-down arrow if you want to select a different search engine,
then click the Search button to begin searching the web based on what
you’ve typed.

▪ When you find a site you like, you can add it to any thought in the usual way.
The Web Search box will close automatically after you click the Search
button.

To modify, add, or reset search-engines:

▪ Click the Edit button in the Web Search box.

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Figure 42. Editing Search-Engine URLs

To customize the search-engine choices:

▪ Click and edit any URL string to customize it, or

▪ Click the Add New button to enter a name that isn’t already in the list, or

▪ Click the Reset button to return to TheBrain’s default choices

Click the OK button to save your customizations or click the Cancel button to
close the box without making changes. The original Web Search box will still be
open, still showing the text you were searching for.

Additional Search Functionality

Search has several additional capabilities that are automatically enabled.

▪ You can find and execute commands from the Search box. To begin, type a
forward slash (/) in the Search box. An alphabetical list will appear. The list
will be fine-tuned to match what you type. This option can also be accessed
from the Search Commands and Preferences option under the Help menu.

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Figure 43. Executing a Command from the Search Box

▪ External attachments are included in search results

▪ Search using acronyms (ex. find "New York Stock Exchange" by typing
"nyse")

▪ Search for thoughts starting with punctuation. You may use this as a shortcut
to provide fast access to thoughts that you always start with a certain type of
punctuation. For example, you could use this for people (@Mike, @Sally,
@Debbie, etc.) or projects (#Ridgeline, #Palmdale, #Westly, etc.)

Figure 44. Search Results for Both Internal and External Attachments

▪ Below the search box is an option for searching Childward only. Selecting this
option will limit the search results to 3 generations below the current active
thought.

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Customizing Your Brain’s Environment

You may choose to use your brain just as it’s offered “out of the box” or you may
choose to change some of the environmental settings to suit your personal
preferences.

TheBrain’s Default Settings

Without making any changes, here’s what your brain looks like:

▪ The area where your thoughts appear (the plex) will be the color and design
of one of TheBrain’s “Themes.” The initial theme is randomly selected and
you can change it at any time.
▪ The left half of TheBrain window will display your thoughts and the right half
of the window will display the “Content Area” which holds notes and any other
items you will attach to your thoughts—files, web pages, Events, etc.
▪ Your thoughts will be displayed in “Normal” view, meaning that you will see
only the direct parents, children, jumps, and siblings of the active thought.

Figure 45. TheBrain Window with Default Settings

Using Smart-Splitter to Arrange TheBrain Window

The smart-splitter controls let you manage where the plex and content area
display relative to each other in the Brain window.

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Figure 46. Smart-Splitter

▪ Click the individual left- and right-arrows (or up- and down-arrows if the
window is in “over-and-under” mode) to maximize the area the arrow is
pointing towards (either the plex or the content area).

▪ Click the double-headed arrow icon to toggle the plex to the right or left side
of the content area.

▪ Click on the two-arrow icon that forms a box to toggle between seeing the
plex and content area "side-by-side" or “over-and-under.”

▪ You can also point at the border between areas and click and drag when the
double-headed arrow appears to move the border.

Moving Thoughts in the Plex

When the default settings are in use and the plex is in “Normal” view, you can
move the thoughts in the plex up or down, vertically, by dragging (up or down) in
any blank area of the plex background.

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Figure 47. Dragging the Plex Vertically

Resizing Thoughts in the Plex

The plex is the heart and soul of TheBrain. You can change the size of thoughts
in the plex by using TheBrain toolbar or your keyboard and mouse.

To change the size of thoughts using the toolbar:

▪ Click the AA button to activate the slider, then click and slide the bar up or
down to grow or shrink the size of your thoughts.

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Figure 48. Resizing Thought Size with the Slider

To change the size of thoughts using the keyboard, mouse, or trackpad:

▪ Hold Cmd (macOS)/Ctrl (Windows) on your keyboard and scroll up or down

on your mouse wheel or trackpad while your mouse pointer is in the plex.

Figure 49. Resizing with the Mouse or Trackpad

▪ Hold Cmd (macOS)/Ctrl (Windows) on your keyboard and press - to make

thoughts smaller or + to make thoughts larger.

Figure 50. Resizing with the Keyboard

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▪ Pinch to zoom on a macOS Trackpad.

Figure 51. Resizing on a Trackpad

Customizing a Brain’s Appearance

Selecting a Theme
The Themes feature lets you choose from many built-in designs to customize the
look of your brain, including the appearance of the plex and notes in the content
area. You can change many of the default colors and the style of notes
associated with the Theme, then save the look of your brain as a new Theme.
This lets you quickly switch from one saved Theme to another.

Figure 52. Sample Themes

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To select a Theme:

1. Either click the Options menu in TheBrain toolbar (TheBrain menu on

macOS) or right-click any blank space in the plex.

2. Click the Brain Theme command.

Figure 53. Accessing the Brain Theme Dialog Box

In the Brain Theme box, you’ll see a scrollable list of available themes in the left
panel and Colors and Options tabs in the right panel. Click on any Theme to
see how it looks in the plex.

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Figure 54. The Brain Theme Dialog Box

Customizing a Theme’s Colors

Have the Brain Theme box open when you want to customize a Theme (right-
click a blank area of the plex, then click the Brain Theme command).

The default colors for virtually all items in the plex vary based on the selected
Theme. The current color for each item is shown in the circle to the right of the
item’s description. Scroll through the list in the Colors tab to get an idea of all of
the items that can be changed.

To change the colors in the selected Theme:

1. Click the item whose color you want to change to display your choices.

2. Click the color of your choice, click outside of the box of colors to close it,
then click Close (X) (or press Esc) to close the Brain Theme box.

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Figure 55. New Selected Color for Links

Note that while you can change the color of the shadow for thought text using
the theme’s Color tab settings, you can toggle whether or not text shadows
are displayed using the Look & Feel tab of the Preferences window (as
explained in the Look & Feel Preferences section on page 62). By default, text
shadows are displayed.

When you are happy with your color selections, click the Close button (X) in
the Brain Theme box.

Defining and Selecting Additional Colors

You can add customized colors if you don’t see the exact shade you want.

1. In the color selection box, click the color that’s closest to what you want,
then click the box next to “Custom,” then click the Define Custom Colors
button.

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Figure 56. Define a Custom Color

2. The Color window will expand to provide a slider to fine-tune the shade.
You can also select a different color and fine-tune it or type in specific RGB
or HSL numbers. Click the Add to Custom Colors button when you’re
happy with the sample color, then click the OK button.

Figure 57. Adding a Custom Color

Selecting a Custom Image for the Plex

If you want to use an image of your own instead of using one in the Themes list
of the Brain Theme box, it’s very easy to do so.

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To select your own background image:

1. Click the Options tab in the Brain Theme box, then click the Wallpaper
check box.

Figure 58. Options Tab in the Brain Theme Dialog Box

2. In the Select image file as the wallpaper window, navigate to the location
of your image file, click on it, and then click the Open button. Supported
wallpaper file formats include .jpg, .gif, and .png.

3. Click the Close button (X) in the Brain Theme box to save your new image
for the plex.

To replace, remove, or copy a wallpaper image:

▪ To replace the image, click the Select button next to the Wallpaper check
box to navigate to a different image.

▪ To remove the image, click the Wallpaper check box to toggle off the check
mark and remove the image from the plex.

▪ To copy a wallpaper image to your clipboard, click the Copy Wallpaper

button

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Figure 59. Replacing or Removing Wallpaper

To dynamically select new Wallpaper from a web site:

1. Go to a web site that offers Wallpaper files, right-click the design of your
choice, then select Copy on the context menu.

2. Return to your brain, right-click in any blank area of the plex, then select
Paste Wallpaper on the context menu.

Figure 60. Context Menu on the Plex

Changing the Default Font in the Plex

By default, the font for text that appears in the plex is Helvetica. You can change
it to any font installed on your machine:

1. Click the Options tab in the Brain Theme box, then click the drop-down
button for Font.

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Figure 61. Changing the Font for Plex Text

2. Click the font of your choice. You will see the text in the plex update
automatically.

Changing the Content Area’s Default Attributes

You can select custom colors for your notes’ text, links, page, edge, and
background. You can also change the font, size, weight (boldness), and other
attributes for the heading and body text you include in the content area—either
before or after you add it. Prebuilt Styles are also available, which you can use
as-is, or modify. You’ll see instant previews of the changes you make, before you
apply them. And, of course, you can change your changes anytime.

By default, the notes in the content area of your brains appear in a style called
“Modern,” which is a sleek and clear combination of font, color, and size.

To begin selecting different style attributes for notes:

▪ Click the Edit Notes Style button on the Options tab in the Brain Theme
box, or

▪ Click the Notes Style button in the content area toolbar

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Figure 62. Changing the Style of Notes

You can also access the Edit Notes Style dialog box from the content area
toolbar. See Choosing a Notes Style beginning on page 171.

To change the appearance of headings:

1. Click on an example heading for the level you want to change. For
example, click on “Title Example Text” to change the top-level heading.

2. Select an attribute from the context menu. Selecting Font, Weight, Color,
or Letter Spacing will take you to an additional set of choices.

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Figure 63. Style Options for Content Area Text

Figure 64. Before and After Changing a Heading Color Style

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To select a heading color that isn’t in the palette:

▪ Click Custom at the bottom of the color palette, click Define Custom Colors,
select a color you like, then click the OK button.

Figure 65. Options for Fine-Tuning Heading Text Color

To change the size of headings:

▪ Click Small, Medium, or Large in the Heading Sizes list. The sizes will
adjust automatically, based on the level of each heading.

Figure 66. Options for Changing Heading Size

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To change the color of non-heading text and other Content Area parts:

1. Click the round color sample in the left panel for the element you want to
change.

2. When the palette opens, click the new color of your choice, or click Custom
to select a different color. The example text will immediately reflect your
choice. The palette stays open so that you can see what different colors
look like when applied.

3. Click outside the palette to close it, when you’re ready.

Figure 67. Selecting a New Color for Body Text in the Content Area

To change the font or weight of non-heading text:

1. Click within any non-heading body text, then choose either Font or Weight
in the context menu.

2. To change the font, select a choice in the scrollable list that appears—you’ll
find over 1,000 options. Each has a sample of how it will appear.

3. Press Esc or click outside of the list to close the box if you don’t want to
make a selection.

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Figure 68. Changing the Font of Content Area Body Text

4. To change the weight (the width/boldness of the characters), select a

choice from the list that appears.

Figure 69. Changing the Weight of Content Area Body Text

Viewing and Selecting Prebuilt Styles

A handy way of seeing combinations of options for the content area is to visit the
Prebuilt Styles—if you see one you like, apply it to your brain and see the results

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instantly. The list of Prebuilt Styles is grouped into Light, Dark, and Fun
sections.

As you click each Prebuilt Style, you’ll see the Example Text instantly reflect the
look.

Figure 70. Selecting a Prebuilt Style

Copying, Pasting, Importing, and Exporting Styles

You can copy, paste, import, and export styles, making it easier to create new
styles. Click the Actions button to display the Copy, Paste, Import, and Export
options for Styles.

Figure 71. Selecting a Prebuilt Style

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▪ Copy Notes Style—Click when you want to apply the current notes
formatting in another brain.

▪ Paste Notes Style (available if a note style has been copied)—Click after
you’ve opened the brain to receive the style.

▪ Paste Colors Only (available if a note style has been copied)—Click after
you’ve opened the brain to receive the color choices in the copied style.

▪ Export Notes Style—Click Save after navigating to a location of your choice

for saving the style file. The filename will look like this: Style-2021-08-
13.nstyle (except with the actual date you exported the file).

▪ Import Notes Style (available if a note style has been exported)—with the
receiving brain open, choose this option, navigate to the location of the
.nstyle file, click Open when the file is selected, then click the Apply button.

Saving Changes
When you are happy with your content area choices, click the Apply button, then
close the Brain Theme box to return to your brain.

Reverting to the Theme’s Default Settings

As soon as you make any changes to a Theme, “Custom Settings” will be

selected in the Themes list.

To switch back to the original settings for any Theme, select the Theme name in
the Themes list within the Brain Theme dialog box.

Saving Themes
1. Make sure the tab with the brain that has the Theme you want to save is
active in the plex.

2. Unless the Brain Theme box is already open, either click the Brain Theme
command on the Options menu or right-click a blank area of the plex, then
click the Brain Theme command.

3. Click the Save Theme button, click Save as New (so you don’t overwrite
the original Theme), then type a name for your new theme in the field.

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Figure 72. Save a Theme

4. Click the OK button. Your new Theme will be inserted into the list of
Themes, ready for use in your other brains.

Figure 73. Newly Saved Theme in the Themes List

Your saved Theme will also include customizations you have made in the Edit
Notes Styles window.

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Renaming a Theme
1. In the Brain Theme box, click the Theme you want to rename, then click
the Rename button.

2. Type or revise the current name, then click the OK button (or press the
Enter key).

Figure 74. Renaming a Theme

3. Click the Close button (X) to close the Brain Theme box.

Deleting a Theme
1. In the Brain Theme box, click the Theme you want to delete, then click the
Delete button.

Clicking on a Theme that you want to rename will activate this Theme in your
brain. You may want to save your current Theme first (if it has been
customized) before renaming another, existing Theme.

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Figure 75. Deleting a Theme

2. Click the Delete button to confirm that you’re sure you want to delete the
Theme.

3. Click the Close button (X) to close the Brain Theme box.

Importing and Exporting Themes

Figure 76. Importing or Exporting a Theme

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To import a Theme:

▪ Click the Import button, navigate to the location of the .BrainTheme file you
want to import, select it, then click the Open button.

To export a Theme:

▪ Make sure the Theme you want to export is in the active brain tab.

▪ Click the Export button, navigate to the location where you want to save the
Theme, then click the Save button.

▪ Click OK in the confirmation box.

Dark Mode
The Dark Mode changes the windows, menus, icons and other user interface
elements to be predominantly dark grey. Dark Mode allows you to focus on your
work with subtle colors and fewer distractions.

• To switch to Dark Mode, click the Options menu, then click the
Preferences command (on macOS, the Preferences command is
located in the TheBrain menu). On the Look and Feel tab, select Dark
under the User Interface setting.

• After you give permission, TheBrain will restart and apply the change.

Figure 77. TheBrain in Dark Mode

▪ You may want to modify your Brain Theme to complement the darker
interface and tones.

▪ On macOS, the Dark Mode setting will follow your OS automatically.

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Setting Other Preferences

TheBrain’s Preferences dialog box is where you’ll find many of the settings for
adjusting how your brain works, both mechanically and visually. Preference
settings affect how TheBrain works globally―no matter which brain is open when
you make your choices.

To open the Preferences dialog box:

▪ Click the Options menu, then click the Preferences command (on macOS,
the Preferences command is located in the TheBrain menu)

Figure 78. Accessing Preferences

TheBrain Preferences are organized into these categories:

▪ Look & Feel

▪ Behavior

▪ Notes Editor

▪ System

▪ Keyboard

▪ Experimental

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Look & Feel Preferences

Figure 79. Look & Feel Preferences

User Interface

Preference Description
Compact Window Title Bar Moves the File, Edit, Thought, View, etc.
menu items up into the frame of the app.
Hide Brain Name in Tags When selected, Brain tabs will only display
the current active thought.
Theme Switch between Light and Dark Mode.

Plex

Preference Description
Default Layout: Select from Normal, Outline, Mind Map or
Normal +1,
Animation Speed Drag the slider right to reduce or left to
increase the speed with which a thought
becomes active when you click it in the plex.

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Preference Description
Wander Delay Wandering is an option to step randomly
through TheBrain, to let you see thought
associations. Drag the slider to specify the
amount of delay (in seconds) between
thought activations. The delay is shortest by
default.

Thoughts

Preference Description
Column Width Controls the minimum size that will be used
for columns of thoughts relative to the current
text size.
Spacing Drag the slider to decrease or increase
space between thoughts. The wider the
spacing, the larger and more spaced out the
thoughts will be.
Tags text You can choose not to show, only show Tag
text on hover (mouseover), or always show.
Tags icons You can choose to never show, only show
Tag icons on hover (mouseover), or always
show.
Show event indicators Event icons will appear in the bottom-right
area of thoughts that include events. This
preference is off by default.
Show note indicators Note icons will appear in the bottom-right
area of thoughts that include notes. When
this is selected, you can hover over the icons
for an instant view of the corresponding note.
This preference is off by default.
Show attachment count The number of attachments (if more than
indicators one) will be displayed on the thought icon.
Show siblings in normal This preference is on by default.
view
Context sensitive thought Context sensitive thought names are
names explained on page 84. This preference is on
by default.
Show label for active This preference is off by default.
thought
Text shadows This preference is on by default.
Use ClearType to render Applies a crisper display of thought names,
text (slower) but may require more system resources.

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Links

Preference Description
Curved Links When selected, links will be curved lines and
when not selected, links will be straight lines.
This preference is on by default.

Timeline

Preference Description
Always show thought or This preference is on by default.
link name on events
Calendar week starts on When checked, Monday will be the first day
Monday of the week. Unchecked, Sunday will be the
first day.

Behavior Preferences

Figure 80. Behavior Preferences

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Thoughts

Preference Description
On click active thought By default, the thought’s properties will
display when the active thought is clicked.
The other option is to do nothing.
Custom thought Context Click on Toggle Commands and uncheck
Menu options that you would like to have hidden.
Automatically capitalize The first letter of the name of the thought will
thoughts on creation be automatically capitalized. This preference
is on by default.
Activate last created A thought will become the active thought as
thought soon as it’s created. This preference is off by
default.
Download Icons for This preference is on by default.
Attached Email Addresses
from Gravatar

Content

Preference Description
On drag and drop of files By default, files will be copied when dragged
and dropped. The other options are that they
will be either moved or linked.
Update displayed content This preference is off by default.
on hover
Show details when This preference is off by default.
selecting attachment to
open
Show first attachment when Preference is on by default.
notes is empty
Show attachments as a list Attachments will show in the same area
instead of on separate tabs within the content
area. This preference is off by default.
Show attachment Will display the file modification date/time
modification date and time when files are viewed as a list
in list

Content Previews

Preference Description
On click attachment Select between ‘Preview when possible’ or
‘Always open in default application’.

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Preference Description
Show content previews This preference is on by default.
when searching
Automatically start This preference is on by default.
playback of media
attachments
Show page thumbnails in This preference is on by default.
PDF preview
Embedded browser for web Linked web pages will open in TheBrain’s
links built in browser.
Preview attachments Attachments being dragged and dropped into
immediately upon being TheBrain will launch in the content area
attached immediately when checked.

Other

Preference Description
Sync brains on application Closing TheBrain application will sync all
exit brains. To exit immediately when this feature
is on, simply close the sync status window.
Maximize on double-click Double-clicking either the plex or content area
of plex background or background will maximize that part of the
content tab background brain and the other part will be hidden. This
preference is off by default.
Hide brain name in tabs Removes the brain name from appearing in
the tabbed interface.
Treat touches like mouse The way the plex interprets touch events can
input be altered using the preference. More
information on this setting is available at
https://www.thebrain.com/docs/touches-info
Show accounts on brains Display all available accounts below brain
list thumbnails on the brains list tab.

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Notes Editor Preferences

Figure 81. Notes Editor Preferences

General

Preference Description
Layout Simple (all notes on one long scrolling page)
or Multi-Column (notes in thinner columns,
multiple columns will be displayed where
space is available)
Line Spacing Set notes line spacing.
Thought Icon Choose between Hide, Above, Below, and
Inline⎯the default icon placement is inline.
Emoji Size Set emoji size to Small, Medium, or Large.
Attachment Text Size Set attachment text size to Small, Medium, or
Large.
Custom Date/Time Format Use the default date/time layout or customize
your own.

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Custom date/time format for notes

Use the following format options to customize the appearance of your date/time
stamp in notes:

Characters Result

d The day of the month, from 1 through 31.

dd The day of the month, from 01 through 31.

ddd The abbreviated name of the day of the week.

dddd The full name of the day of the week.
h The hour, using a 12-hour clock from 1 to 12.

hh The hour, using a 12-hour clock from 01 to 12.

H The hour, using a 24-hour clock from 0 to 23.
HH The hour, using a 24-hour clock from 00 to 23.

K Time zone information.

mm The minute, from 00 through 59.
M The month, from 1 through 12.
MM The month, from 01 through 12.

MMM The abbreviated name of the month.

MMMM The full name of the month.
ss The second, from 00 through 59.

t The first character of the AM/PM designator.

tt The AM/PM designator.
yy The year, from 00 to 99.

yyyy The year as a four-digit number.

z Hours offset from UTC, with no leading zeros.
zz Hours offset from UTC, with a leading zero for a single-digit value.
zzz Hours and minutes offset from UTC.

: The time separator.

/ The date separator.

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Animation

Preference Description
Animate Cursor Cursor will visibly animate when clicking to
different locations in notes.
Blink Cursor Cursor in notes will blink to indicate its
location.
Highlight lines on hover Hover over any line in the notes and it will be
highlighted.

Header and Footer

Preference Description
Include Title This preference is on by default. Option to
display the Thought Label in the content area
when checked.
Mapped Links This preference is on by default.
Backlinks This preference is on by default.
Unlinked Mentions This preference is on by default.
Hide Private This preference is on by default.
Backlinks/Unlinked
Mentions

Options

Preference Description
Select adjacent text when This preference is on by default.
inserting link
Automatic smart quotes This preference is on by default.
Rename thought updates This preference is on by default.
links
Check spelling as you type This preference is on by default. Applies to
spell checking while creating thought names
as well.
Recognize emails and Properly formatted emails and phone
phone numbers numbers will be hyperlinked.
Insert link when extracting When selecting text in a note to become a
child thoughts new thought, a link to the new thought
remains on the original note.

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Display

Preference Description
Underline normal links Hyperlinked text will be underlined.
Render underscore tags as Unchecked – text within underscores will be
italics underlined. Checked – text within
underscores will be italicized.
Show markdown When checked, markdown tags will be visible
in the notes.

User Interface

Preference Description
Use compact toolbars for Some content area buttons will be grouped
notes into dropdown lists⎯all tools will be available
via the More Notes Editor Actions button.
Show link target in pop-up When checked, hovering over a hyperlink in
a note will display the linked URL.
Restore cursor and scroll This preference is on by default.
position
Mentioned Thought names Select between Show all, Show except
common words and Never show
Clicking links in notes Follows link or Moves cursor (places cursor
in the text)

Printing

Preference Description
Include title Includes title when printing the note.
Include label Include any thought label when printing
Include links and mentions This preference is off by default.
Include attachments This preference is off by default.
Prevent widows and This preference is on by default.
orphans
Prevent orphan headers This preference is on by default.

Clipboard

Preference Description
Replace pasted URL with This preference is on by default.
page title

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Preference Description
Paste without formatting as This preference is off by default.
default
Exclude color information This preference is on by default.
when pasting

System Preferences

Figure 82. System Preferences

Updates

Preference Description
Check for updates on Notification of updates on startup. Always,
startup Only free updates or Never.
Update Channel This preference affects which kind of updates
you’ll see as available when you click the
Check for Update command on TheBrain’s
Help menu. The default is Stable and the
other choices are Beta and Alpha.

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Localization

Preference Description
Interface Language The default is Automatic; however, you may
select from one of 78 different languages.
Spelling Dictionary The default is Automatic and there are many
other languages to choose from in the drop-
down list. After you select another language,
you’ll be prompted to exit TheBrain and
restart so that your change can take effect.

Storage

Preference Description
Storage The location of your brain data. The default is
to use the default working directory for Import
and Sync.

Proxy Settings

Preference Description
Use proxy server and proxy If you are unable to synchronize your brain
server requires with TheBrain Cloud due to a proxy server or
authentication restricted ports on your network, the Proxy
settings can be used to customize the
synchronization process. Check with your
network administrator for the appropriate
information for these fields. By default, the
Use proxy server preference is off.

Keyboard Preferences
Most Brain commands can be accessed by keyboard commands, which you can
customize based on your preferences. You can even export your settings to
share them with others or to transfer them from one computer to another.

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Figure 83. Keyboard Preferences

Using the Keyboard Preferences Tab

To do this … Do this …
Find a command quickly Begin typing the command in the Search
commands field in the bottom-left corner of the
Keyboard tab of the Preferences window.

As you type, the list will shorten to match what

you’ve typed. When you see the command
you’re looking for, note its shortcut or click it to
define a new shortcut.

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To do this … Do this …
Collapse the list to see Click the Collapse All button.
only major headings

You can also collapse an individual heading,

for example “Application,” to collapse or
expand just that section.
Restore the full list Click the Expand All button.

To do this … Do this …
Import shortcuts Click the Actions menu button in the bottom-
right corner of the Keyboard tab, then click
the Import Shortcuts command.

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To do this … Do this …
Export shortcuts Click the Actions menu button in the bottom-
right corner of the Keyboard tab, click the
Export Shortcuts command, select a
location for the file, then click the OK button.
The file will be named
“KeyboardShortcuts.txt.”
Restore default shortcuts Click the Actions menu button in the bottom-
right corner of the Keyboard tab, then click
the Restore Defaults command.

To define a new shortcut:

1. In the left column, expand a category of interest.

2. Click the command for which you want to create a shortcut. The row
containing the command will be highlighted and an instruction will appear
under the Preferences tabs.

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Figure 84. Creating a New Shortcut

3. With the command of your choice highlighted, press the function key or
keyboard combination of your choice. For example, you might choose to
assign the “Check for Update” command to Ctrl+Shift+U.

You can’t assign keys that are already used for common operations (such as
Ctrl-C) nor can you use letter or number keys by themselves. The Alt key can
be used as a standalone modifier

Your new shortcut will display in the list. You can delete the shortcut by pressing
the Delete key while the command is highlighted.

Figure 85. The New Shortcut in the List

If the keyboard shortcut you selected is already in use for another action, you will
have the option to “steal” the shortcut for the current selection, or cancel the
request and select a different keyboard combination.

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Figure 86. Replacing an Existing Shortcut

Default Shortcuts for Windows

Application Commands Shortcut

Exit Alt+F4
Preferences Ctrl+,

Edit Commands Shortcut

Copy Ctrl+C
Copy as Text Shift+Ctrl+C
Cut Ctrl+X
Paste Ctrl+V
Paste without Formatting Shift+Ctrl+V
Redo Ctrl+Y
Select All Ctrl+A
Undo Ctrl+Z

Navigation Commands Shortcut

Activate Tag Ctrl+G
Activate Type Ctrl+E
Backward Alt+Left
Expand/Collapse Current Thought Space
Forward Alt+Right
Navigate Down Down
Navigate Enter Enter
Navigate Escape Esc
Navigate Left Left
Navigate Right Right
Navigate to Pin 1 Ctrl+1

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Navigation Commands Shortcut

Navigate to Pin 2 Ctrl+2
Navigate to Pin 3 Ctrl+3
Navigate to Pin 4 Ctrl+4
Navigate to Pin 5 Ctrl+5
Navigate to Pin 6 Ctrl+6
Navigate to Pin 7 Ctrl+7
Navigate to Pin 8 Ctrl+8
Navigate Up Up

Notes Commands Shortcut

Bold Ctrl+B
Collapse All Ctrl+[
Collapse All Except Here Shift + Ctrl+I
Expand All Ctrl+]
Expand/Collapse Toggle Ctrl+\
Find & Replace Ctrl+F
Find Next F3
Find Previous Shift+F3
Insert Date/Time Ctrl+D
Insert/Edit Thought or Web Link Ctrl+K
Italic Ctrl+I
Open in Browser Alt+Ctrl+O
Pop up Table of Contents Ctrl+T
Print Ctrl+P
Replace Next Ctrl+F3
Replace Previous Shift+Ctrl+F3
Take Action Ctrl+L
Underline Ctrl+U

Options Commands Shortcut

Web Search F4

Thought Commands Shortcut

Create Child F6

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Thought Commands Shortcut

Create Jump F8
Create Parent F7
Forget Ctrl+Del
Open Folder Shift+Ctrl+F
Show Thought Properties Ctrl+Enter

Thought Icon Commands Shortcut

Select Stock Icon Alt+Ctrl+I

View Commands Shortcut

Collapse All Ctrl+9
Expand All Ctrl+0
Mind Map Shift+Ctrl+3
Normal Shift+Ctrl+1
Outline Shift+Ctrl+2
Zoom In Ctrl+=
Zoom Out Ctrl+-

Window Commands Shortcut

Close Tab Ctrl+W
Close Window Alt+F4
Keyboard Focus to Notes Ctrl+N
Keyboard Focus to Search Ctrl+S
New Tab Ctrl+T
New Window Shift+Ctrl+N
Next Brain Tab Ctrl+Tab
Previous Brain Tab Shift+Ctrl+Tab
Rotate Splitter Shift+Ctrl+D
Splitter Left or Up Shift+Ctrl+A
Splitter Right or Down Shift+Ctrl+S

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Default Shortcuts for macOS

Create Child Alt+Command+Down

Create Parent Alt+Command+Up
Create Jump Alt+Command+Left
Rename Alt+Enter
Focus on Plex Cmd+S
Focus on notes Cmd+N
Search Web Cmd+E

Experimental Preferences

Figure 87. Experimental Preferences

The features and settings on the Experimental tab will change from time to time
and may be removed in future versions of TheBrain.

AI Settings

Select from a drop down menu of current/popular AI models that TheBrain will
use for AI generation features. You may also select to use your own custom
OpenAI API Key. For help with using a custom OpenAI API key, visit
https://www.thebrain.com/docs/openai-api-key-help.

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Creating Thoughts

Creating a Single Thought

There are many ways to create a thought, but most start with the same step—
choosing the thought with which the new thought will have a relationship. You will
use the chosen thought as a starting place when creating the new thought.

Generally speaking, you’ll create child thoughts more often than parents or
jumps. There are certainly exceptions, but usually, using a “top-down” approach
is helpful if you are just getting started: Create children (and jumps, as
appropriate) and let parents happen naturally.

Once you have activated the thought that will have a relationship with your new
thought, use any of these techniques to begin creating a new thought:

▪ Drag from the thought’s parent, child, or jump gate

Figure 88. Gates to Drag for Creating Thoughts

▪ Or click the Thought menu, then click the Create Child, Create Parent, or
Create Jump command

▪ Or, right-click the thought, then click the Create Child, Create Parent, or
Create Jump command

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▪ Or use a keyboard shortcut:

On Windows, press the F6 key (for a child thought), F7 (for a parent

thought), or F8 (for a jump thought)

On macOS, press the Option+Cmd+Down Arrow (for a child

thought), Option+Cmd+Up Arrow (for a parent thought), or
Option+Cmd+Left Arrow (for a jump thought)

No matter which of the above methods you use to begin creating your new
thought, the next thing you’ll see is the Thought Creation dialog box with the
cursor blinking in the field for typing in the name of your new thought.

Figure 89. Thought Creation Dialog Box

1. Type the name of your new thought in the field provided.

2. Press the Enter key or click in a blank area of the plex to save your new
thought (or press the Esc key to cancel the process and close the box).

Automatic initial-capitalization: If you type a thought name using all

lowercase letters, the first letters of words will be capitalized for you
automatically. TheBrain uses “smart rules” to determine which words should be
lowercase (such as “a,” “and,” and “of”). For example, if you’ve typed “visit the
statue of liberty” the thought name will automatically become “Visit the Statue
of Liberty.” This feature is active, by default, but you can turn it off in the
Behavior tab of the Preferences dialog box.
If spellcheck is turned on in the content area toolbar, thought names will also
be spellchecked in the Thought Creation dialog box as well as in the
Thought Properties dialog box.

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Displaying Thought Properties and Details

▪ To expand the thought creation box to include the Type and Tags buttons
(explained in the Thought Types and Tags section beginning on page 123),
click the down-arrow in the bottom-right corner

▪ To display a thought’s details (create/modify dates and ID) after the thought is
created, click the down-arrow in the bottom-right corner

▪ To hide the thought’s details, click the up-arrow in the bottom-right corner

Figure 90. Showing and Hiding Thought Properties and Details

Creating Multiple Thoughts at Once

TheBrain offers a timesaver (affectionately known as the “semi-colon trick”) for
creating more than one thought at a time.

▪ Type a semicolon (;) to separate multiple thought names in the Thought

Creation dialog box

▪ This feature can also be used while creating new Thought Types and
Thought Tags

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Figure 91. Creating Multiple Thoughts

Creating Context-Sensitive Thought Names Using Commas

It’s always good to be specific with your thought names. TheBrain has some time
savers to help you if you have repetitive information that needs to be added to
your brain. For example, say you have thoughts for each of your clients, each of
whom has a billing department. You’d like a child thought named “Billing Info” for
each of your client thoughts. However, you may not want to have identical
thought names because when you see these thoughts later you won’t be able to
tell them apart without looking at their parents.

To remedy this potential dilemma, when you type the name of the new thought,
start or end the name with a comma. The parent thought name will be added
automatically. When this thought is displayed, its name will vary depending on
the context in which it’s viewed. If the client thought is active, the client’s name
will be hidden and it will appear as just “Billing Info.” But when you activate this
thought, the full name along with the client’s name will appear.

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Figure 92. Sub-Category Thoughts

The thought will display its full name when it is active or when hovering over it
with the cursor. When its parent thought is active, you’ll see only the portion of
the name that does not repeat the parent’s name. Ensuring that each of your
thoughts has a unique name will help you find and identify them more easily.

Tip: The part of the thought’s name that is hidden is context sensitive. Say for
example that you wanted to have a single place to see the billing information for
all your clients. You might create a thought called “Billing Info” and then link to
the billing information thoughts for each of your clients, such as “New Guys,
Billing Info.” If you do this, when Billing Info is active “New Guys, Billing Info” will
appear as just “New Guys,” whereas when New Guys is active, that same
thought will appear as Billing Info. Try it―you’ll see how this can be very useful.
When thoughts are displayed in alphabetical order, the current view of the
context sensitive name will determine its position.

Using Parentheses to Assist with Thought Sorting

Adding parentheses around the first part of thought name will skip that part for
sorting purposes (unless there is a tie) when thoughts are grouped
alphabetically.

▪ To enable this feature, a thought name must have both an open parenthesis
as the first character and a close parenthesis later in the thought name.
Whitespace will be trimmed, and there must be some thought name left after
that. (Later parenthesis will be ignored.)

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▪ Note that this is mutually exclusive to Hidden Ordering Prefixes starting with a
dot. You can only have one or the other.

Example: if your thoughts are grouped alphabetically, the following group of

thoughts named:

(The) Beatles
Belle & Sebastian
(The) Bee Gees
(The) Beach Boys

would display as:

The Beach Boys

The Beatles
The Bee Gees
Belle & Sebastian

Creating Thoughts with Artificial Intelligence

Thoughts can automatically be created on any topic via TheBrain’s AI integration.
From any thought in your brain, click on the AI button in the tool bar above the
plex.

Figure 93. AI Thought Generation

The active thought will automatically be selected as the Topic Name. You will
have the option of generating a thought structure (multiple generations of
thoughts below the active thought) or generate child thoughts (one generation
below the active thought)

Additional settings will allow you to:

• Set Context Thought – Select a parent thought above the active thought
to be referenced as context for your new content. This is helpful for
general thought names. For example, a thought named “Directors” can be
given greater context by selecting a parent thought named “Silent Film”

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• Use Children for Context – If the thought already has some children,
check this box to give AI an indication of the type of content you are
hoping to see.

• Creativity – Select from 0% - 100% creative. Not seeing the results

you’re looking for? Try bumping up the creativity level and let AI start
thinking “outside the box.”

• Mode – Categories vs. List – Your results will either be categories that
your query can be placed in vs. lists of specific types of your query. For
example:

o Fruit Category: Citrus, Melons, Benefits, Impact on Agriculture…

o Fruit List: Banana, Kiwi, Lime, Strawberry…

• Language – Regardless of your default language settings, your AI query

results can be generated in one of 78 different languages.

While AI is generating your new content, you will not be able to move to a
different thought or brain tab. When complete, the new content will be displayed
in the plex and new thoughts will appear with a glowing boarder. You can review
your new content before selecting one of the three options in the banner above
the plex to either Accept changes, Redo (opens the AI pop up window with the
most recent settings) or Discard.

Creating Orphan Thoughts

When you create a thought in your brain, you usually first decide what
relationship it will have with an existing thought, but sometimes you just want to
create a thought unrelated to an existing thought.

To create a thought independently of other thoughts, type into the Search box. If
no search result is returned, hit enter and the new thought will be created as an
Orphan. This works well especially when you are looking for something and
discover you haven’t yet put it into your brain.

Tip: You can also create an orphan thought by pressing F9 on Windows or

Opt+Cmd+Right Arrow on macOS.

Figure 94. Default Windows Keyboard Shortcut for Create Orphan

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Create Thoughts from Search, Notes or Events

You can create a new thought instantly from the Search box or within Notes or
Events. Say you’d like a “Monthly Meetings” thought to be a child of “My Work,”
but you’re not sure whether you already have a thought with that name. You can
begin by searching, and if it doesn’t already exist, no need to retype the name.

To create a new thought using search:

1. Activate the thought that should be the parent, child, or jump thought of the
new thought.

2. Click in the Search box at the top-right corner of the window, then type the
name of the thought you’re looking for, or want to create if it’s not found.

3. If the thought doesn’t already exist and you want to create it:

• Press the Enter key to create it as a child of the active thought, or

• Hold down the Shift key as you press the Enter key to create it as a
parent of the active thought, or

• Hold down the Ctrl key as you press the Enter key to create it as a jump
thought of the active thought, or

• Hold down the Ctrl key as you press the Shift key, then click on Create
Orphan to create it as an orphan thought

Your new thought will be the active thought.

Figure 95. Creating a Thought from the Search Box

To create a new thought when searching finds an existing thought:

1. Press the up-arrow key. This highlights the default option—Create Child.
Note that pressing the Enter key before pressing the up-arrow key
activates the existing thought.

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Figure 96. Creating a Thought from the Search Box when the Thought is Found

2. Use any of the same key combinations for creating a new thought from the
Search box when a thought isn’t found.

To create a new thought from within a note:

1. Select the text within the note for which you want to create a child, parent,
or jump thought.

2. Right-click the selected text, then click the Insert Thought or Web Link
command. Optionally, you can revise the text in the new box that appears,
if you want a different name for the new thought.

3. Select a relationship for the new thought:

• Press the Enter key to create it as a child of the active thought, or

• Hold down the Shift key as you press the Enter key to create it as a
parent of the active thought, or

• Hold down the Ctrl key as you press the Enter key to create it as a jump
thought of the active thought

Figure 97. Creating a Thought from a Note

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To create a new thought from within an Event:

1. Open an existing Event or click and drag from the start to finish times in the
timeline to create a new Event.

2. Type a name for the new thought where you see “No thought or link” at the
top of the Event box. A new orphan thought will be created with that name.

Figure 98. Creating a Thought from an Event

Changing the Order of thoughts in the Plex

You can use TheBrain’s hidden ordering system to change the default
alphabetical ordering of thoughts in the plex to any order you prefer. To do this,
type a period and a number as the first characters of any thought name. These
characters will not be displayed in the plex. For example, try creating the
following group of child thoughts in one area:

▪ .01 Zebra

▪ .02 Walrus

▪ .03 Aardvark

The thoughts will appear in the order of Zebra, Walrus, Aardvark (without the
periods or numbers), rather than alphabetically. You can always delete or revise
the numbers in the Thought Properties dialog box.

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Figure 99. Changing Thought Order

Copying Thoughts Within and Between Brains

Thoughts, including all of their notes, properties, events, and attachments, can
be copied and pasted between brains or duplicated within a brain. When
thoughts are copied, associated thought types and link types are automatically
copied as well.

To copy a thought within the same brain:

1. Right-click the thought to be copied and then click the Copy “name of
thought” command on the context menu.

2. Activate the thought that will be the parent of the newly copied thought.

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3. Right-click within any blank area of the plex and click Paste Thought(s) on
the context menu.

4. The copied thought will automatically be linked as a child of the active

thought and it will also retain all of its original relationships.

Figure 100. Copied Thought with Two Parents

To create a duplicate of a thought:

If you just want to make a duplicate of a single thought without retaining any of its
links, you can use the Duplicate Thought command.

1. Right-click the thought to be duplicated and then click the Duplicate

Thought command on the context menu.

2. The duplicated thought will appear as a child of the original, as shown in the
figure below.

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Figure 101. Duplicating a Thought

To copy a thought to another brain:

1. Right-click the thought to be copied and then click the Copy “thought
name” command on the context menu (or activate the thought, click the
Edit menu, and then click the Copy command).
2. Open the brain into which you want to copy the thought.
3. Right-click on the background of the plex and then click the Paste Thought
command on the context menu (or click the Edit menu and then click the
Paste Thought command).
4. The thought will be pasted into the brain and linked as a child of the active
thought. It will include any attachments, thought types, notes, or other
attributes it had in the original brain.

If you have selected multiple thoughts, they can all be copied at once using the
same technique. Right-click anyplace within the Selection panel to open the
context menu. See Selecting Multiple Thoughts beginning on page 97 for
complete instructions about selecting multiple thoughts.

Paste Thought Colors:

1. Right-click on any thought with modified colors (text or background) and

select Copy “thought name”

2. Right click on another thought (in the same brain or a different brain) and
select Paste Thought Colors. This thought will then have the same text
and background colors as the thought that was originally copied. This

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feature can also be used when working with multiple thoughts in the
Selection Box.

Merging Thoughts
You can automatically merge multiple thoughts that refer to the same thing. You
can combine the links, attachments, and notes so that the resulting thought has
all of the information from those multiple thoughts.

To merge thoughts:

1. Ctrl+click on two or more thoughts that you want to merge into a single
thought. The thought names will automatically appear in the Selection
panel.

2. Right-click in the Selection panel, then click Merge (n) Thoughts.

Figure 102. Merging Three Selected Thoughts into One

When you activate the new thought, you’ll see all content that was in each of the
standalone thoughts. The name of the new thought becomes a combination of
the formerly separate thoughts, in alphabetical order.

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Figure 103. Original Content Area of Three Thoughts before Merging

Figure 104. After Merging

Undoing and Redoing Actions

Changing your mind about your actions is easy. You can undo up to 100 actions
during your current session. Actions that have been undone can also be re-
executed using the Redo command.

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Figure 105. Undo and Redo Commands

To undo an action:
1. Click the Edit menu and then click the Undo command. The list on the
secondary menu displays your most recent action first.

2. To undo your most recent action, click the first item in the secondary menu.
To undo multiple actions, select the oldest action to be undone from the list.
All actions above that action will also be undone.

To redo an action you have undone:

1. Click the Edit menu and then click the Redo command. If there are multiple
items that can be redone, a secondary menu will be displayed.

2. Click the action of your choice. As in the list of actions that can be undone,
the list is in most-recent-action-first order. All actions above the item you
click will also be undone.

The Undo and Redo lists are cleared when you sync your brain (including an
auto sync) and when your brain is closed.

Editing Thoughts and Links

Renaming Thoughts
You can easily rename any thought in its Thought Properties dialog box. When
you rename a thought, any references to it from other notes are automatically
updated with the new name.

▪ Click the thought to make it active, then click it again. You may also click the
Show Thought Properties command in the Thought menu or Alt-click a

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non-active thought. In the Thought Properties dialog box, make any edits
you want, then press the Enter key or click in the plex.

Figure 106. Renaming a Thought

Selecting Multiple Thoughts

You can select multiple thoughts in three ways:

• Hold down the Ctrl key (Cmd on macOS) as you click each thought you want
to select, or

▪ Hold down the Ctrl key (Cmd on macOS) as you drag to form a box around
the thoughts, or

▪ Hold down the Ctrl key (Cmd on macOS) as you click a gate to select all the
thoughts connected to that gate

Figure 107. Selecting Multiple Thoughts by Ctrl-Dragging (Cmd-dragging on

macOS)

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Selected thoughts are then added to TheBrain’s Selection panel for making
mass edits on large groups of thoughts at one time.

After the multiple thoughts are selected, you can apply actions—link, unlink,
forget, set thought type, and other actions you would apply to an individual
thought—to the selected thoughts en masse. When multiple thoughts are
selected, they are listed in a Selection panel on the left side of the plex and they
are highlighted in the plex itself.

Figure 108. Selection Panel and Selected Thoughts

To de-select individual thoughts:

▪ Hold down the Ctrl key (Cmd on macOS) as you click a thought (either in the
plex or in the Selection panel) to de-select just that thought.

To close the Selection panel and de-select all thoughts:

▪ Click the Close button (X) in the top-right corner of the Selection panel. The
button will turn red as you point to it and after the panel is closed the thoughts
will no longer be selected in the plex.

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Figure 109. Closing the Selection Panel

To perform actions on selected thoughts:

▪ Right-click in an empty area of the Selection panel and select the action of
your choice on the context menu. The entries in this menu are also displayed
in the Edit menu.

Figure 110. Selection Panel Context Menu

Other Selection Uses

Once you have created a selection, you can also use it for other things besides
what you see in the menu. For example, you can limit searches to selected
thoughts. In the example below, only “Debbie Miller” is found because it is the
only thought name beginning with “D” that is currently selected.

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Figure 111. Limiting Searches to Selected Thoughts

Forgetting and Deleting Thoughts

When you no longer need a thought, it can be forgotten or deleted. A forgotten
thought may be remembered and restored later, or deleted. A deleted thought is
gone forever. This is similar to the Recycle Bin/Trash feature on your desktop
which stores your deleted files until you choose to remove them permanently.

To forget a thought:

▪ Right-click the thought to be forgotten, then click Forget Thought Name in

the context menu, or

▪ Click the active thought to be forgotten, click the menu button in the Thought
Properties dialog box, then, click the Forget Thought Name command.

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Figure 112. Forgetting a Thought in its Thought Properties Dialog Box

Once a thought has been forgotten it will disappear from the display. If you want
to access it again later temporarily, you can do so by turning on the display of
forgotten thoughts. You can also permanently delete forgotten thoughts or you
can remember them.

To access forgotten thoughts:

1. Click the Options menu, then click the Show Forgotten Thoughts
command. Any forgotten thoughts will appear grayed out in the plex.

Figure 113. Forgotten Thoughts in the Plex

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2. Notice the “Showing Forgotten Thoughts” message above the pins. This
reminds you why some thoughts are grayed. You can use forgotten
thoughts just like normal thoughts as long as they are displayed. Click the
View Report button to work directly with the forgotten thoughts.

Figure 114. Forgotten Thoughts in the Report Tab

3. You can click on a thought in the Reports tab to activate it.

To delete all forgotten thoughts using the Reports tab:

▪ Click the Reports tab menu button, then select Forgotten from the Thoughts
drop down menu. You can then click on the context menu button and select
Delete Forgotten Thoughts. Alternatively, you can use the Ctrl key (Cmd
on macOS) to select multiple individual forgotten thoughts and then delete
only those.

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Figure 115. Using the Report Tab to Delete All Forgotten Thoughts

▪ You can click the Refresh button on the Reports tab to update the list.

Closing the Forgotten Thoughts dialog box hides the forgotten thoughts. You
can also reinstate forgotten thoughts by clicking the Remember All command
in the Reports tab menu. You can also reinstate an individual forgotten
thought by right-clicking in the plex, then clicking the Remember thought name
command on the context menu.

It is generally recommended to forget thoughts when you don’t need them so that
you can easily retrieve them if you change your mind. If you are sure you will
never need a thought again and you do not want to be able to remember it in the
future, you can delete it immediately without forgetting it first.

To delete a thought instantly:

1. Hold down the Shift key (for Windows)/Alt key (for Mac) as you right-click
the thought to be deleted. The context menu will be displayed, showing the
Delete thought name command in place of the Forget thought name
command.

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Figure 116. Shift-Right-Click Context Menu for a Thought

2. Click the Delete thought name command. The thought will be permanently
deleted. See Selecting Multiple Thoughts on page 97 for forgetting or
deleting multiple thoughts at once.

When a file attachment is deleted, the file is placed into an internal trash folder
in case the delete needs to be undone. When undo is cleared, the trash is
emptied. The files are then moved to the OS trash/recycle bin so you have
further opportunity to recover the file if needed.

Tip: If you delete something by accident you can still recover it if you use the
Undo command immediately.

Unlinking Thoughts
To unlink thoughts:

▪ Right-click the link, then click the Unlink command on the context menu

Tip: If you are moving a thought from one place to another by linking and
unlinking it, it is generally easier to do the unlinking after you have done the
linking. This avoids making the thought into an “orphan,” a thought with no
relatives.

If you have difficulty telling which link you are pointing at with the mouse, just
look at the highlighted thoughts. When the mouse pointer is over a link, it is
highlighted along with the two thoughts it connects. This makes it easy to tell
which thoughts will be unlinked if you click on the link.

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In addition to being able to unlink thoughts one link at a time, you can also select
multiple thoughts to unlink several of them at once. To do so:

▪ Select the thoughts you want to unlink by holding down the Ctrl key (Cmd on
macOS) and clicking on each one, or Ctrl drag (Cmd drag on macOS) a box
around thoughts in the same area

▪ Activate the thought from which you wish to unlink the selected thoughts

▪ Right-click in the Selection panel and select the Unlink Selection command

Linking Thoughts
As noted previously, links are power. Not only do links allow for associations that
group thoughts conceptually, they allow information to be stored in and
accessible from numerous places.

A single thought may have relationships with multiple thoughts. For example,
you may want a thought named “Aunt Mary” to be a child of your “Mentors”
thought and also a child of your “Family” thought. If your Aunt Mary is also
helping you plan your next vacation, her thought may also be a child or jump
thought to your “Vacation” thought. The possibilities are endless.

There are several ways to link to existing thoughts, as described in the following
sections.

Link to a Thought Visible in the Plex

When the thoughts you want to link are both visible in the plex, you can simply
drag from the desired gate of one thought in the plex to another thought in the
plex. Note that the thought you drag from or to does not have to be the active
thought.

In the Normal view, the display of thoughts is limited to close relations. You may
find it useful to expand the view when linking thoughts, because you can see
more thoughts at once.

Link by Dragging to a Pin

You can Link to a thought that is not visible in the plex if it has a pin. Simply drag
from the appropriate gate to the pin. When you want to link a thought to many
other thoughts, create a pin of the thought so you can quickly link to it. A pin’s
gates appear when you point at the pin with the mouse.

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Figure 117. Link by Dragging to a Pin

The relationship you establish by linking a thought to a pin is between the

thoughts; if you delete the pin, the Link between the thoughts is still intact.

Link by Dragging to the Past Thoughts’ List

You can link a thought in the plex to a thought in the Past Thought List. Like pins,
gates for a thought in the Past Thought List appear when you point at the past
thought with the mouse.

Figure 118. Link by Dragging to a Thought in the Past Thoughts’ List

Link by Selecting a Thought in the Existing Thoughts List

You can also link by using the Thought Creation dialog box:

1. Make the thought you want to link from the active thought, then start
creating a thought by dragging or using the Thought menu. The Thought
Creation dialog box appears.

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2. Type the first few letters of the name of the thought you want to link to.
Double-click on the thought you want to link when you see it in the Existing
Thought List that appears below (or click it once, then click in the thought
name field and press the Enter key).

Figure 119. Create a Link by Starting to Create a Child Thought

Link by Using the Selection Panel

Thoughts in the Selection panel can be linked to the active thought using the
Selection menu:

1. Select the thought or thoughts you want to link using Ctrl-click (Cmd on
macOS) or by holding down the Ctrl key (Cmd on macOS) as you drag a
box around the thoughts if they’re next to each other.

2. Activate the thought in the plex to which you want to link.

3. Right-click the Selection panel, then click the link command of your choice
in the context menu.

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Figure 120. Linking Using the Selection Panel

Cancel Creation of a Link

Press the Esc key while dragging a link to abort the process. (The mouse button
should still be held down while you press Esc.)

Changing Relationships Using Drag and Drop

Say that you decide that your “Product Promotions” thought shouldn’t really be a
child of your “Customer Service” thought. Instead, it should be the child of
“Business Development.” You can quickly change relationships between
thoughts in a single step: Hold down the Shift key while linking a thought to a
new parent. All of the current parents will be unlinked automatically. Note that
even if a thought has more than one parent, all of the former parents will be
unlinked.

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Figure 121. Shift-Dragging to Change Relationships

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Customizing Thought and Link Properties

You can change the colors of thoughts and links globally using the Brain
Theme dialog box (see the Customizing a Brain’s Appearance section on page
42). This section explains how to view and manage the properties of individual
and selected thoughts and links. Changed settings override the global defaults.

Changing the Properties of a Thought

To open the Thought Properties dialog box, use any of these methods:

▪ Click the active thought, or

▪ Click the thought once to select it, then a second time to open the box, or

▪ Alt-click the thought (whether or not the thought is active), or

▪ Right-click the thought, then click Show Thought Properties on the context
menu, or

▪ Click the thought to select it, click the Thought menu in the menu bar, then
click the Show Thought Properties command

Figure 122. Thought Properties Dialog Box

Press the Enter key or click anywhere outside of the dialog box to close it and
save any changes.

You can use the Thought Properties dialog box to:

▪ Rename a thought

▪ Add or edit a thought Label

▪ Add or change a thought Type

▪ Add or change a thought Tag

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▪ Mark the thought as Private or Public

▪ Customize the thought text or background color (just this thought; global
changes are done in the Themes window)

▪ Add or change the thought's icon

▪ Review the thought's creation/modification history and ID. The ID is not

normally needed but may be useful when troubleshooting.

▪ And, using the Thought Properties Actions Menu button (three horizontal
lines):

o Forget the thought

o Create a Pin

o Set as the Home thought

Changing the Colors of a Thought

While thought colors are set globally in the Brain Theme box, you can override
these settings for individual thoughts. To begin, activate the thought, then click
on it or Alt-click on any inactive thought.

Note that the individual changes you may make to thoughts, such as their color
and background, override the settings in the Brain Theme box.

To change the text color of a thought:

▪ In the Thought Properties box, click the upper color square, click the color of
your choice, then click outside of the box of colors.

Figure 123. Text Color in the Thought Properties Dialog Box

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To change the background color of a thought:

▪ Click the lower color square, click the color of your choice, then click outside
of the box of colors.

Figure 124. Background Color in the Thought Properties Dialog Box

To swap a thought’s text color with its background color:

▪ Click the double-headed arrow next to the two color sample squares in the
top-right area of the Thought Properties dialog box.

Figure 125. Swapping Text and Background Colors

You can use the same techniques to fine-tune new colors for thought text and
background as you can use to define colors globally in the Brain Theme box.
Please see the Defining and Selecting Additional Colors section on page 45 for
details.

Adding a Label to a Thought

Labels are hints that appear below thoughts when you point the mouse at the
thought.

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Figure 126. A Thought Label

To add a label during thought creation:

1. While typing a new thought name, add a pipe symbol (|) and anything after
will become the thought’s label.

Figure 127. Adding a Pipe Symbol During Thought Naming

To add a label to an existing thought:

1. Activate the thought, then click on it or Alt-click on any inactive thought.

2. Type the text for the label in the Label field, then press the Enter key.
When you point at the thought, the label text will appear in a box below the
thought.

Figure 128. Label Field in Thought Properties Dialog Box

Swapping a Thought’s Name with its Label

You can swap a thought’s name with its label by clicking the Switch button
(double sided arrow) in the Thought Properties dialog box. This can be very
useful when the default label and name are assigned based on a URL and the
automatic naming isn’t optimal for your purposes.

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Figure 129. Swapping Label and Thought Names

Adding an Image to a Thought

In any thought, you can attach an icon from TheBrain’s built-in selection, an
image from a file of your own, an image from notes or attachments in the active
thought, or a screen capture. These pictures provide a visual boost to your brain.
When you point to the icon next to the thought, the picture zooms to a larger size
automatically.

Figure 130. A Thought Icon

To insert an icon from TheBrain’s built-in icon library:

1. Click the thought icon box in the upper left of the Thought Properties box,
then click the Select Stock Icon command.

Figure 131. Select an Icon from the Built-in Library

2. With the Browse radio button selected, click any of the categories in the left
panel. (See the TheBrain Icons section on page 236 for more about icon
choices.) Click an icon of your choice to add it to the thought. The Thought
Properties dialog box will close automatically when an icon is selected.

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Figure 132. Icon Choices

To insert an image from a file as a thought icon:

1. Click the thought icon box, then click the Choose File command.

Figure 133. Choose a File to Use as an Icon

2. Navigate to the file of your choice, then click the Open button. Supported
file formats for images include .jpg, .png, and .gif.

To create a thought icon from an image in the Content Area:

▪ Click the image to select it, right-click it, then click the Copy to Icon
command in the context menu.

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Figure 134. Copy to Icon Command in the Image’s Context Menu

To create a thought icon from one of its attachments:

▪ Right-click the attachment, then click the Copy to Icon command in the
context menu.

Figure 135. Copy to Icon Command in the Attachment’s Context Menu

The new icon will appear to the left of the thought name at the top of the content
area and on the active thought in the plex.

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Figure 136. Thought with its New Icon

To insert a screen capture of an image as a thought icon:

1. Make sure the screen item you want to capture is visible, then activate the
thought and click on it or Alt-click on any inactive thought.

2. Click the thought icon box, then click the Capture Image command.

Figure 137. Capture Something on the Screen to Use as an Icon

3. Your brain will be hidden temporarily and red cross hairs will appear on the
screen. Drag a rectangle around the area to be captured by dragging the
mouse in a diagonal line from one corner of the rectangle to the opposite
corner, then releasing the mouse button.

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Figure 138. Using the Crosshair to Capture an Image

4. When you release the mouse, the image will be in the Icon area of the
Thought Properties dialog box.

Tip: To capture from the Brain window itself, press the Tab key to toggle its
visibility. You will see the crosshairs and you can drag to select the area of your
choice.

While the captured item will become a picture, the source can be anything―a
company logo, a photo, or part of an Excel worksheet or PDF file.

To paste an image you copy from somewhere else:

1. Copy the image using standard techniques. For example, you may right-
click an image on a web page, then click the Copy Image command.

2. After the image is copied, from the Thought Properties dialog box, click
the thought icon box or right-click on a thought in the plex and select the
Paste Icon command.

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Figure 139. Capture Something You’ve Copied to Use as an Icon

To copy an image from the thought to someplace else:

Images you capture can be copied and pasted as attachments, pasted into
notes or the plex, or used as icons.

1. Click the thought icon box, then click the Copy Icon command.

Figure 140. Copy the Icon to Use Elsewhere

2. The icon you copied can be pasted elsewhere, such as in a thought’s

content area or elsewhere on your computer.

Favicons being displayed as the thought icon can be copied as well.

To change a thought’s icon, repeat the steps above. The icon will be replaced.

To delete a thought’s icon:

▪ Click the thought icon box, then click the Delete Icon command.

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Figure 141. Removing a Thought Icon

Displaying Inherited Properties

All inherited properties, such as from a thought type’s icon, label or colors, are
displayed in the properties dialog.

Thought types or tags are also clearly indicated.

Figure 142. Properties Dialog Improvements

Making Thoughts Private

Thoughts may be marked “Private.” Private thoughts will appear with a small lock
icon shown below and to the right of the thought. The lock appears whether the
Private thought is active or not. If you make your brain publicly viewable on the
web, private thoughts remain hidden from view by read only visitors. To mark a
thought as “Private,” click the lock icon in the Thought Properties dialog box.

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Figure 143. A Private Thought

Using Thought URLs

Each thought in TheBrain is available via a unique URL. A thought URL can be
used to create links to thoughts from external third-party applications or from
other brains. Thought URLs can also be used within TheBrain as another way to
connect thoughts via links within notes or as attachments to thoughts.

Thought URLs can be added as hyperlinks in many third-party applications so

that when the link is activated, TheBrain will go to the referenced thought.

To copy a thought URL:

▪ Right-click the thought (or click the Edit menu), then click the Copy Local
Thought URL command.

Figure 144. Copying a Thought URL

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To paste a copied thought URL so it will be another thought’s attachment:

1. Activate the thought to which it should be copied (which may be in the

original brain or any active brain), then right-click the thought (or click the
Edit menu).

2. Click Add Attachment and select the Paste Web Link command. The
URL will be added to the thought as an attachment.

Figure 145. Pasting a Thought URL

To paste a thought URL after it has been copied so that it becomes a

hyperlink in a note:

1. In the note, select the text that will be the link using one of the two methods
below:

▪ If the text happens to be the name of a thought you want to link to, it will
have a dotted underline—click within the underlined text

▪ If the text isn’t the name of a thought, just drag through it to select it

2. Click the Insert Thought or Web Link command in the content area
toolbar (or right-click and select it from the context menu).

3. Select the thought in the drop-down list, then click outside of the list to close
it and create the link.

When you click the link, the thought will open and you can click its attachment(s)
to view them in the content area.

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Figure 146. Inserting a Hyperlink in a Note

Thought Types and Tags

If you have several thoughts with which you want to share common attributes,
such as color and an icon, you may want to create a thought type so that these
attributes can be easily applied to many thoughts. This is one use of thought
types.

For example, you may want to create a “person” type for all thoughts that
represent people in your brain. This type might have a label— “Person”—and a
specific color and icon so that all people in your brain stand out and can be easily
recognized.

Type thoughts can be edited by activating them and using the Thought
Properties dialog box, just as you would for any other thought. You can assign
attributes, such as icons, notes, and attachments, to type thoughts.

Figure 147. Three “Person” Type Thoughts

Once a type has been applied to a set of thoughts, it can also be used to create
reports of all thoughts of that type.

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When a type has been assigned to a thought, that thought is said to be an

“instance” of the type. For example, if you have a thought named “Jane” of the
“Person” type, the Jane thought is said to be an instance of the Person type.

Creating a Thought Type

Thought Types can be created from the Activate Type button in the main
toolbar.

1. Type the new Thought Type name or type multiple new Thought Types
separated with a semicolon

2. Select New Type

Figure 148. Creating a New Thought Type

To create a thought type from within the plex:

1. Activate the thought you want to be the first instance of the new type, then
click the thought to open its Thought Properties dialog box.

2. Click the Type button, then click the New Type command. Alternatively,
you can right-click the thought, click the Set Type command, then click the
New Type command.

3. Enter the name of the type you want to create, then press the Enter key.
Click outside of the Thought Properties dialog box to close it.

4. If you used the context menu to create the new type, the type will appear as
a thought in the plex. Type thoughts are special and have an oval border
when active and inactive to distinguish them from other thoughts.

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Figure 149. An Active Type Thought (“Person”)

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To do this ... Do this ...

Locate and Enter the Type’s name in the Search box as you would to
Activate a Type search for any other kind of thought, then click the
thought matching result in the drop-down list.

OR
Activate any thought associated with that type, and click
on the Parent thought Type if it is visible.

OR
Click the Activate Type button in the menu bar, then click
the type of your choice or begin typing the name of the
type to locate it quickly if the list is long.

Delete the active Click the active Type thought to open its Thought
Type thought Properties dialog box, click the menu button, then click
the Delete thought name command.

Note that unlike normal thoughts, types cannot be

forgotten and remembered. Deleting a type removes it
from your brain permanently.

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To do this ... Do this ...

Set a thought’s Use any of these methods:
Type
▪ Open the thought’s Thought Properties dialog box,
click the Type button, then click the type of your
choice, or

▪ Right-click the active thought, click the Set Type

command, then click the type of your choice, or

▪ Click the Thought menu when the thought is active,

click the Set Type command, then click the type of
your choice

▪ Link the thought as a child of the type

Set a thought’s Click the Set Type button in the Thought Creation dialog
Type during box, then click the type of your choice.
thought creation
Remove a Type Use any of these methods:
from a thought
▪ Open the thought’s Thought Properties dialog box,
click the Type button, then click the Untyped button,
or

▪ Click on the checked Type to unselect it, or

▪ Right-click the active thought, click the Set Type

command, then click the Untyped button, or

▪ Click the Thought menu when the thought is active,

click the Set Type command, then click the Untyped
button

▪ Unlink the Thought as a child of the type

Create new Drag down from the Type thought’s child gate and
thoughts linked continue creating the thought as usual.
to the active
Type thought
Create a Super Drag up from the parent gate of a Type thought, then
Type continue creating as usual or link to another existing Type
thought.
Reuse a Type in Copy and paste type thoughts from one brain to another
another brain the same way you copy and paste other thoughts.

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Tip: To arrange your display by thought types, right-click on the plex background,
click Arrange Thoughts by, then click Type.

Attributes that are assigned to a thought type are inherited by all instances of
the Type but will be overridden if there are attributes assigned directly to the
thought itself. For example, if you have a thought named “Jane” of the type
“Person,” you can assign an icon of a smiley face to the Person type and it will
appear next the Jane thought and all other instances of the Person type. But, if
you then assign a picture of Jane as the icon for that thought, the picture will
appear on that thought (only) instead of the smiley face. Likewise, a label
assigned to a specific thought would override the label of any thought type
assigned to that thought.

Super Types
TheBrain supports multiple levels of types for advanced modeling. Just like a
thought can have a type, each type may in turn have a super type. To set a super
type, open a thought type that should have the super type, then click the Type
button. The new type will be a parent (or super) type of the active type. The
attributes assigned to a super type are inherited by its sub types and instances.

Super types can be used when there is a category of thoughts which is a subset
of a larger category. For example, the thought type “Person” could be the super
type of the type “Executive.”

To see how to find groups of thoughts that share one or more of the same
Type, please see the Producing Reports section beginning on page 218.

Dynamic Wallpaper
Another advantage of using thought types in your brain is being able to utilize
dynamic wallpaper. This enables you to change the wallpaper of the plex, based
on the type of the current active thought.

To set up a dynamic wallpaper:

1. Navigate to a thought type.

2. Right click and select Set Dynamic Wallpaper

3. Navigate through your machine to locate the desired wallpaper image and
click Open.

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Figure 150. Setting Up Dynamic Wallpaper on a Thought Type

Figure 151. Navigating to a Thought with a Dynamic Wallpaper assigned to its Type

Navigating to any thought that is associated with a Thought Type containing

Dynamic Wallpaper will fade the current background and transition to the
Thought Type Wallpaper.

Using Thought Tags

If there are multiple attributes you would like to add to your thoughts, you can
create thought Tags. Tags are useful for flagging thoughts that you want to be
able to reference as a group, without them having to share a common parent. For
example, you may want to create a “To do” Tag so you can get a list of all of
these thoughts very quickly.

Tag thoughts can be edited by activating them and using the Thought
Properties dialog box, just as you would for any other thought. You can assign
attributes, such as icons, colored text and colored backgrounds to Tag
thoughts.

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Thoughts can have one or many Tags at the same time. Tag thoughts are global
for a brain and displaying Tag text and icons can be toggled on and off in the
Look & Feel tab of the Preferences window.

Figure 152. A Thought with a Tag

To create a thought Tag:

1. Activate the thought to which you want to attach a Tag, then click the
thought to open its Thought Properties dialog box.

2. Click the Tags button, then start typing a name for your new Tag.
Alternatively, you can right-click the thought, click the Set Tags command,
then click the New Tag command and start typing a name for your new
Tag. You can also create multiple Tags at the same time by typing a semi-
colon between each Tag name, just as you can do to create multiple
regular thoughts at the same time.

3. Press the Enter key. Click outside of the Tags list to close it, then click
outside of the Thought Properties dialog box to close it. The new Tag will
be attached to the active thought.

Figure 153. Creating a New Tag

Alternatively, you can right-click the thought or click the Thought menu, click
the Set Tags command, then click the New Tag command and start typing a
name for your new Tag. Press the Enter key when you’ve finished.

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You can also assign one or more Tags to a thought (regular or Type thoughts)
while you’re creating the thought by clicking the Tags button in the Thought
Properties or Thought Creation dialog box.

Assigning and Removing Tags

You can assign and remove Tags using the same general technique as for
creating them. The only difference is that instead of typing a new name, you
select (to attach) or deselect (to remove) the Tag name(s) in the list.

As shown below, currently assigned Tags are preceded with a check mark. Click
an assigned Tag to remove it and click any Tag in the list to assign it to the active
thought. This makes it easy to assign and remove multiple Tags at a time.

Figure 154. Assigning and Removing Tags

Assigning Tags to Multiple Thoughts at One Time

If you want to assign Tags to multiple thoughts at once, first select them, then
right-click in the Selection panel. Click the Set Selection Tags command, then
click the New Tag command or on any of the Tag names in the list.

Deleting a Tag
1. Click the Tags button on the toolbar, then click the Tag of your choice to
activate it.

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Figure 155. Opening the Tags List

2. Either right-click the thought or click the Thought menu, then click the
Delete “Thought name” command. You can also open its Thought
Properties dialog box, click the menu button, then click the Delete
“Thought Name” command.

To delete multiple Tags at one time:

1. Click the Tags button on the toolbar to display all Tag names in your brain.

2. Ctrl-click each Tag you want to delete. The Tag is added to the Selection
tab to the left of the list.

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Figure 156. Deleting Multiple Tags List

3. When all the Tags you want to delete are selected, right-click in the
Selection tab, then click the Delete (#) Thoughts command. (Remember
that Tags are also thoughts themselves.)

Unlike normal thoughts, Tags cannot be forgotten and remembered. Deleting a

Tag removes it from your entire brain permanently.

Renaming and Adding Attributes to a Tag

You can change the properties of Tags, just as you change the properties of
regular thoughts—colors, icons, and attachments.

1. Click the Tags button on the toolbar, click the Tag of your choice, then click
the Tag thought to open its Thought Properties dialog box. You can also
click any tag that is visible in the plex to navigate to that tag thought.

2. You can make the same customizations as you can to any thought while
you’re in the Tag’s Thought Properties dialog box. When you’re finished
making revisions, press the Enter key.

Renaming a Tag changes the Tag throughout your entire brain.

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Displaying Thoughts Based on Their Tags

You can show all thoughts with the same Tag by using Search:

▪ Begin typing the Tag name in the Search box, then click the Tag name when
it appears. Tags may be indicated with any icon that has been assigned to
them. When you click the Tag name in the Search hit list, all thoughts
assigned to that Tag will be displayed in the plex.

Tag Abbreviations
Along with adding icons to Tags and customizing their names with color, you can
also attach an “abbreviation” for the full Tag name. Abbreviated forms of the
name can serve as hints for what the Tags represent while giving the plex a
cleaner appearance.

In the Look & Feel tab of the Preferences window, you can change the Tags
text setting to “Show always” if you want the abbreviations to show. Hovering
over a thought with Abbreviated Tags or Tag icons will then display the full Tag
name.

Figure 157. Tag Icons and Abbreviations

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Figure 158. Pointing at a Thought Hides the Abbreviation and Shows the Full Name

To enter a Tag abbreviation:

▪ In the Tag’s Thought Properties dialog box, type the abbreviation in the field
below the Tag’s name, then press the Enter key.

Figure 159. Creating a Tag Abbreviation

Additional Thought Type and Tag Features

Visible Thought Types and Tags

Types and tags can be visible in the plex. Want to see a type or tag as a child
thought? Just link any existing type or tag thought as a child, or as a jump.
Optionally, types are visible as parent thoughts as well.

Figure 160. Visible Parent Type and Child Tag

Linkable types and tags eliminate the need to create two thoughts when you
want to show all instances of a type or tag within the plex.

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▪ Types are visually distinguished by rounded sides.

▪ Tags are visually distinguished by chamfered (diagonal) corners.

Hiding Visible Thought Types

Thought types being visible in the plex is optional.

▪ To prevent a thought type from being visible in the plex, right click on a
thought type and uncheck the option for Visible when Parent of Active
Thought

Figure 161. Toggling the Visibility of a Thought Type

• This setting can also be modified globally by clicking on File, selecting

Utilities and clicking on Make All Types Visible/Hidden as Parents

Converting Thoughts to Type or Tag

You easily change a normal thought into a type or tag at any time:

▪ Right-click on a thought and select Convert to Type or Tag

Figure 162. Convert to Type or Tag

▪ Tags and types can easily be changed into a normal thought

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Clickable Tags
Tag icons that show on thoughts are clickable. Click any tag that is visible in the
plex to navigate to that tag thought.

Replacing a Tag
You can easily move a thought through a project cycle or simply re-classify its
tag attributes. To quickly replace a thought’s tag:

▪ Right-click on a tag to open its context menu.

▪ Select the option Replace Tag with and select another tag.

Figure 163. Replacing a Tag

Nested Tags
Tags can be organized under each other so they are easier to organize, navigate
and apply.

▪ Link two existing tags with a parent/child relationship to sub-categorize

▪ You may also open a tag’s properties to assign it as a sub category of

another tag

▪ Nesting can include multiple tags and multiple layers

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Figure 164. Nested Tags

Changing the Properties of a Link

Links between thoughts are normally unnamed. You can name a link by giving it
a “label.” Just like thoughts, links can have Types, notes, and Attachments. You
can control the way they appear in order to clarify relationships or just to create a
more pleasing view of your brain, based on your personal preferences. You can
also manipulate links in order to add or change relationships between your
thoughts.

Just as each thought has its own Thought Properties dialog box, each link has
its own Link Properties dialog box.

To open the Link Properties dialog box, use any of these methods:

▪ Double-click the link, or

▪ Click the link once to select it, then a second time to open the box, or

▪ Alt-click the link (whether or not the link is connected to the active thought),
or

▪ Right-click the link, then click Properties on the context menu, or

▪ Click the link to select it, click the Link menu in the menu bar, then click the
Properties command

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Figure 165. Link Properties Dialog Box

To add a label to a link:

1. Open the Link Properties dialog box for the link, then type a label name in
the Label field.

Figure 166. Adding a Label to a Link

2. Press the Enter key, or click outside of the Link Properties dialog box to
close it. The label will appear on the link and will be enlarged when the
mouse points at the link.

To change the color of a link:

1. Open the Link Properties dialog box for the link, then click the color box.

2. Click the color of your choice in the color palette, click outside of the palette
to close it, then press the Enter key, or click outside of the Link Properties
dialog box to close it.

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Figure 167. Changing the Color of a Link

This changes the color for the individual link. You can set link colors globally in
the Brain Theme box (please see the Customizing a Theme’s Colors section
on page 44 for details).

To change the width of a link:

▪ Open the Link Properties dialog box for the link, click the Default button,
click the width of your choice, then click outside of the Link Properties dialog
box to close it.

Figure 168. Changing the Width of a Link

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Tip: You might want to widen links to illustrate the strength of particular
relationships between thoughts.

Link Types
Link types are used to assign commonly-used relationships between thoughts
that share a label, color, and width so they can be easily recognized. Link
properties and types will be retained even if the two linked thoughts change their
relationship but remain linked (for example, if a child thought becomes a jump
thought of the original thought).

In addition to setting their color, you can add labels to link types and you can
change the width of the link to call special attention to relationships.

1. Open the Link Properties dialog box for the link, then click the Type
button.

This button will display “Untyped” if there is currently no Type assigned to the
link and it will display the type name if there is already a Type assigned.

2. If there’s an existing Type in the list that you want to use, click on it to
select it. Otherwise, click on New Type, then type the name for the new link
in the field that will be displayed.

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Figure 169. Creating a New Link Type

2. Press the Enter key to close the Link Properties dialog box.

Figure 170. Appearance of a Link Type in the Plex

If a Link has both a Type and a label, the label will show in the plex. While the
Type won’t be displayed in the plex in this case, it can still be used to find all
thoughts connected to links of that Type.

Tip: Point the mouse at a Link Type or label to magnify it in the plex.

Deleting Link Types

1. Open the Link Properties dialog box for the link that has the Type you
want to delete, then click the Edit button to open the Type Properties box.

2. Click the menu button then click the Delete command.

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Figure 171. Deleting a Link Type

To see how to find thoughts that share one or more of the same link Type,
please see the Producing Reports section beginning on page 218.

Showing Link Direction

By default, links do not show a directional arrow. You can add directional arrows
that will appear on the link that points to or from the source thought.

Figure 172. Directed Links

▪ A directed link shows an arrow in the middle of the link. If the link has a label
or a Type, the arrow will be next to the text. The arrow is magnified when the
mouse hovers on it. Directional arrows can provide visual cues that are
particularly useful when there’s a link label. For example, for the link label
“Inspired” (shown below), the link’s directional arrow shows that “Hank
Williams” was a source of inspiration for Elvis. This is also very useful when
you want to represent flows between items like financial relationships.

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Figure 173. Hank Williams Inspired Elvis

To set link direction:

1. Open the Link Properties dialog box for the link to which you want to add
direction. Then:

▪ Click the icon to the left of the One-way check box to switch between
non-directed, directed, and directed in the reverse.

Figure 174. Setting the Direction of a Link

Using One-Way Links

▪ One-way links appear when the source of the link is active and the source
thought is already visible.

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▪ One-way links are indicated by an arrow with a rectangle at its base.

Figure 175. One-Way Link

One-way links are useful where thought A is relevant when thought B is active,
but thought B is not relevant when thought A is active.

For example, you may want to see what company a person worked for when the
person is the active thought. However, for a large company with thousands of
employees, you may not want to see all of the employees when that company is
the active thought. Creating a “works for” link type and making it one-way is a
good way to do this.

To make a Link one-way:

1. Open the Link Properties dialog box for the link to which you want to add
direction. Then:

▪ Select the One-way check box to make the selected link one-way. Note
that one-way links cannot be non-directed.

Figure 176. Selecting Link Direction

To set Link direction for link Types:

You can also set link direction for link types. The direction of a link type is
inherited by instances of the type and can be overridden by the instance.

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Figure 177. Selecting a Link Type Direction

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Advanced Navigation and Alternative Views

Changing Your View of Thoughts

There are three views for displaying your thoughts:

▪ Normal view: For focusing on the active thought and displaying information
pertaining to its parent thoughts above, child thoughts below, and jump
thoughts to the left.

Figure 178. A Brain in Normal View

▪ Outline view: For a more expanded, primarily hierarchical view of your

thoughts.

Figure 179. A Brain in Outline View

▪ Mind Map view: For a horizontally expanding symmetrical layout.

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Figure 180. A Brain in Mind Map View and Expanded

In addition to selecting a view, you can expand and collapse the display of
thoughts in all views to show more or fewer generations.

TheBrain automatically remembers the last view you used and selects it by
default. For example, if you select Outline view and then close TheBrain, the next
time you open it, Outline view will be active.

Three ways to change to a different view:

▪ Click the Layout button in TheBrain toolbar, then click the view of your
choice, or

▪ Right-click in the plex, click the Layout command, then click the view of your
choice, or

▪ Click the View menu in the menu bar, then click the view of your choice

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Figure 181. Three Ways to Select a View

Tip: The check mark in the menu identifies the current view.

A rule of thumb for when you might use each view is to use Normal view when
you’re creating thoughts and navigating the plex, use Outline view when you
want to see a more traditional structure, and to use Mind Map view for viewing
and analyzing the “big picture.”

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Using Outline View

Figure 182. Plex in Outline View

Providing a clean, organized way of looking at your thoughts, Outline view

enables a fast, easily understood overview of the active area of your thought
network. The level of detail can go as deep as you want while maintaining an
ordered view.

When the plex is in Outline view, you can show or hide generations of children
for individual thoughts. To see if a thought has child thoughts that aren’t currently
showing, point the mouse at the thought.

▪ On mouseover, a plus sign (+) icon will appear above the top edge of the
thought’s outline if there are child generations to display. Click the + icon to
expand and show that thought’s children.

▪ On mouseover, a minus sign (-) icon will appear below the bottom edge of the
thoughts’ outline if child thoughts can be collapsed or hidden. Click the - icon
to hide that thought’s children.

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Figure 183. Showing/Hiding Additional Generations of Individual Thoughts

Using Mind Map View

Figure 184. Mind Map View

The Mind Map view allows switching the focused thought without changing the
layout for when you want to view and alter various pieces of content while
keeping the view mostly static. Traditional mind map layouts can be created
instantly from any thought.

To navigate to another thought in your plex while in Mind Map view, right-click
the desired thought and select Activate Thought.

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Figure 185. Changing the Active Thought without Changing the Layout

As with Outline view, when the plex is in Mind Map view, you can show or hide
generations of children for individual thoughts by pointing the mouse at a
thought, then clicking the plus sign (+) or minus sign (-) icon to show or hide
the thought’s children.

Expanding and Collapsing Generations

Besides expanding and collapsing individual thoughts in Outline view or Mind

Map view, as explained in the previous section, you can also expand and
collapse generations of all thoughts in all views.

Figure 186. Expanding or Collapsing from the View Menu

In Outline and Mind Map view, you can also use the buttons on the toolbar to
expand or collapse all visible thoughts by one generation.

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Figure 187. Expanding or Collapsing by One Generation

In Normal view, the Expand and Collapse by one generation on the toolbar
work the same way as the Expand All and Collapse All commands on the
View menu.

Figure 188. Jane’s Brain in Normal View with All Collapsed

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Figure 189. Jane’s Brain in Normal View after Expanding All

Tip: The vertical scroll bar on the right side of the plex indicates that there are
more sibling thoughts in that area which are not currently visible.

Figure 190. 5 Generations of Thoughts

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Presentation Mode
Presentation Mode makes your brain full-screen, hiding the title bar, menu bar,
toolbar and Brain tabs. On both Windows and macOS the taskbar and dock are
also hidden. Presentation mode is an excellent viewing option when using your
brain for effective and focused discussions.

▪ Enter Presentation Mode by selecting it from the View menu

▪ Keyboard shortcuts can be used for functionality that is hidden from the
current view, such as switching amongst open Brain tabs without exiting
Presentation Mode

▪ Just start typing to search and the controls appear and disappear as needed

Figure 191. Before and after switching to Presentation Mode

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The Content Area

You can think of the parts of TheBrain’s content area as personal assistants who
are ready to help when asked. You can give any of them the day, week, or year
off if you choose not to use their services, but they’re all standing by, ready to
assist you—-at the click of your mouse.

The content area keeps all of your thought-specific notes and attachments.
Attachments can be files, web pages, pictures, and more.

Figure 192. TheBrain’s Content Area

Content Area Overview

Here are some handy things to know about the content area:

▪ By default, the content area shows content attached to the active thought. If
the active thought has no content, the content area shows only the thought’s
name and related content (or placeholders for related content to come).
However, if you want to see the content for thoughts you point at with the
mouse, select the “Update displayed content on hover” option in the
Behavior tab of the Preferences window. (Please see the Behavior
Preferences section on page 64 for more information about setting global
user interface preferences.)

▪ A red border highlights the content area when the content belongs to a
moused-over thought.

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Figure 193. Content of an Inactive Thought after Behavior Preference is Changed

Preferences are global; whatever options are selected when one brain is active
will also be selected in your other brains. Of course, you can change your
preferences at any time.

▪ With one click, you can move the content area to any side of the plex—
above, below, left, or right. See the Using Smart-Splitter to Arrange TheBrain
Window section on page 38 for details. While you’re working on content you
might find it convenient to maximize the content area.

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Figure 194. Maximizing the Content Area

▪ The size of the content area depends on the size of TheBrain window, but
when the plex and the content area are side-by-side, you’re in control of how
much of the available space each area occupies. Just point the mouse at the
line between the two areas and when the double-headed arrow appears, drag
left or right to change the proportions.

Figure 195. Making the Content Area More Wide or Narrow

Tip: To work with the content area in a separate window, click the New Window
command on the File menu. Then, maximize the plex in one window and the
content area in the other. Changes you make in one window will be reflected in
the other because you’re working with the same brain, however, the windows
won’t be in synch. In other words, making a thought active in one window won’t
make it active in the other.

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Note Viewing Options

TheBrain formats its notes using markdown. Users have the option of either
viewing the markdown syntaxes (formatting tags) while editing, or staying in a
WYSIWYG editor and using the buttons in the content area toolbar for all
formatting. The option to toggle on/off this setting can be found in Preferences
under the Notes Editor tab. Look for the Show Markdown checkbox.
Additionally, you can switch this setting with a button in the content area toolbar
with the Show Markdown button.

Figure 196. The Show Markdown Button

Even when Markdown is hidden, some keyboard shortcuts will still be operational
such as shortcuts for bulleted lists, ordered lists, checklists, titles, subtitles,
headings and block quotes.

Creating and Formatting Notes

Take a note, capture your ideas, or create your next literary masterpiece!

Figure 197. A Note-Worthy Note

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The Content Area Toolbar

The content area toolbar is quite robust—don’t feel like you have to use every
feature for every note. You’ll see many of the tools you’re familiar with from word
processing and email applications. And when you want your note to look “just so”
you’ll have an excellent array of options at your fingertips.

Depending on how wide you’ve made your content area, you may see the fully
expanded toolbar or the compact version. Either way, you’ll have access to all
tools via buttons providing access to the additional commands. By default, unless
the content area is stretched wide, the compact version of the toolbar will be
displayed.

Tip: To show the expanded toolbar even if the content area isn’t very wide,
deselect the “Use compact toolbars for Notes” check box in the Notes Editor tab
of the Preferences window. (Please see the Behavior Preferences section on
page 64 for more information about setting global user interface preferences.)

Figure 198. Compact and Expanded Versions of the Content Area Toolbar
Unlike earlier versions of TheBrain software, the content area toolbar is always
on display when the content area is open, but does not have your cursor focus.

Figure 199. The Compact Content Area toolbar

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Here are the buttons that show when the expanded content area toolbar is
displayed. The annotations point out special buttons you may not see in other
text editors.

Figure 200. Buttons on the Expanded Content Area toolbar

All Notes features are always available no matter which content area toolbar—
compact or expanded—is displayed.

Toolbar Buttons
Content Area toolbar buttons (in order of appearance):

▪ Text Size – Use the text size slider to resize the notes

▪ Paragraph Style —choose from:

o Normal
o Title (H1)
o Subtitle (H2)
o Heading 1 (H3)
o Heading 2 (H4)
o Heading 3 (H5)
o Heading 4 (H6)
o Code
o Unordered List
o Ordered List
o Checkbox List

▪ Bold, Italic, Underline and Code

▪ Strikethrough, Superscript, Subscript, Foreground Color, Background Color,

Font and Remove Formatting

▪ Unordered, Ordered and Checkbox Lists

▪ AI Writing Assistance – This button will always be visible, even when the
Compact Toolbar is enabled.

▪ Outdent and Indent

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▪ Left, Center and Right Justify Text

▪ Link

▪ Insert: Date/Time, Table, Special Character, Capture and Insert Image,

Mathematical Expression, Horizontal Rule, Page Break and Table of
Contents

▪ Attach: Link to File/Folder/URL, Add Markdown File, Paste, Add from

Brainbox, Add File from Template, Create Event, Open Thought Folder,
Capture Image to Attachment, Copy Path to Thought’s Folder, Template Help

▪ Find and Replace, Show Word Count, Spellcheck as You Type and
Show/Hide Markdown

▪ Note Style, Print, and Export

▪ Compact Toolbar and Markdown Reference

Markdown Editor
Notes in TheBrain are created using a next-generation markdown editor. This
improved version of markdown enables more capabilities than standard editors
for a superior editing experience. As mentioned, the visibility of markdown tags
can be turned on/off with the Show Markdown button in the content area toolbar.

▪ Unlike other markdown editors, TheBrain enables direct rendering of

formatting, images, and more without requiring a "preview" window.

▪ With the Show Markdown setting turned on, you’ll have text-based, inline
code formatting: Ability to type text that converts into formatting, such as:

o “[ ] “ (or “- “) to create a checkbox – “+ “ for a pre-checked checkbox

o ** for bold
o “* “ at the start of a line to create a bullet list
o Block quotes using “>“

Spaces are now ignored while typing between two markdown tags. For example,
typing a full sentence in between “**” and “**” will keep the text bold. Earlier
versions of the markdown editor would remove formatting each time a space was
added.

Toolbar-based formatting: Not familiar with markdown? A toolbar that works just
like you're used to that will also help you learn the text equivalents.

Use the question mark icon link in the content area toolbar to TheBrain
Markdown Reference Guide for more clarity on how you can utilize markdown by
typing directly into the notes.

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Figure 201. Link to TheBrain’s Markdown Reference Guide

Markdown Variations
TheBrain has updated the markdown tags for designating underlined text to be
more in line with traditional markdown specifications. This new setting in
Preferences on the Notes Editor tab defaults to off (unchecked). Existing note
content from earlier versions of TheBrain will remain in the same formatting. For
example, the following markdown tags will designate underlined text:

This word is still _underlined_.

Checking the option for Render underscore tags as italics will change the word
to be italicized.

This word is now _italicized_.

The markdown formatting commands for underscoring now utilizes an

underscore and bracket:

This word is _{underlined}_ in TheBrain 13.

Figure 202. Render Underscore Tags as Italics

Viewing Multi-Column Notes

By default, your notes will display as a single page. Long notes will utilize a scroll
bar to navigate in a linear direction. This is called the Simple View. If desired,
multi-column notes can be displayed. In Preferences, under the Notes Editor
tab, the Layout setting can be toggled between Simple and Multi-column.

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Figure 203. Switching to Multi-Column Layout

Figure 204. A Multi-Column Note

If you are still seeing just a single column in Multi-column Layout, try giving the
content area more screen real estate. Use the smart splitter to make the plex
smaller. Multi-column notes are best suited for high resolution monitors.

Entering Notes
To enter a note, activate the thought to which the note pertains, then click in the
open area of the content area and begin typing. The content area toolbar will
remain displayed whenever the content area is visible.

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Notes are saved automatically when another thought is activated and will be
saved when closing a brain and prior to an unlikely crash in the application.

You can use all of the standard techniques you use in other text editors when
you type, revise, and format TheBrain notes:

▪ Automatic word wrap controls line endings. Press the Enter key to begin a
new paragraph.

▪ Either apply formatting as you go or select existing text before you apply
formatting such as bold, italics, underlining, and color.

▪ Standard text selection techniques:

o Drag the mouse through text to select it, or

o Click at the beginning of the text, then hold down the Shift key as you
click at the end of the text to select all text in between, or
o Double-click to select an entire word, triple-click to select an entire line

▪ To apply formatting to an entire paragraph, such as lists—bulleted,

numbered, or check marked—just click anyplace within the paragraph.
There’s no need to first select the entire paragraph.

▪ Standard keyboard shortcuts—such as Ctrl-C for Copy, Ctrl-V for Paste,

and Ctrl-A for Select All—work as you would expect in notes. (On macOS,
the standard Command key shortcuts also work.) You can copy and paste
within notes and between TheBrain and other applications.

▪ To toggle a check box on or off, follow a link, or open an attachment in the

content area, press the Ctrl+L keyboard shortcut.

Double space to create a period in notes on macOS.

One special feature for TheBrain notes is that if no text is selected and you
select a formatting command such as bold, highlighting, or change in typeface
or font size, the formatting will apply to the entire word in which the cursor is
currently blinking.

Tip: You can press Ctrl-Z (or click the Edit menu, then click the Undo
command) to immediately undo your most recent action in notes.

Artificial Intelligence Writing Assistance

Notes can be automatically generated for any thought in your brain with the help
of AI. This can be done from scratch or in addition to an existing note.

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Additionally, AI can be used to improve, modify, edit and summarize an existing

note in a variety of different ways.

Generating New Notes with AI

To create a new note from scratch, navigate to your desired thought and click on
the AI button in the content area toolbar. Select Generate Note.

Figure 205. Generate a Note with AI

The active thought name will be automatically selected as the Topic Name, but
this field can be modified for clarification if needed. You will also have the option
to modify the following settings:

• Set Context Thought – Select a parent thought above the active thought
to be referenced as context for your new content. This is helpful for
general thought names. For example, a thought named “Directors” can be
given greater context by selecting a parent thought named “Silent Film”

• Use Children for Context – If the thought already has some children,
check this box to give AI an indication of the type of content you are
hoping to see.

• Creativity – Select from 0% - 100% creative. Not seeing the results

you’re looking for? Try bumping up the creativity level and let AI start
thinking “outside the box.”

• Word Count – Specify between 50 – 1000 words for your new note with
the Word Count Slider.

Tip: Although the maximum word count is 1000, you can always add more text
manually later, or use AI to expand on existing content.

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• Language – Regardless of your default language settings, your AI query

results can be generated in one of 78 different languages.

Figure 206. Modifying the AI options

Your new note will be populated word by word. Output will match the language of
the input text. While the note is generating, it is not possible to navigate to
another thought or brain tab.

Once completed you can scroll through the new note to review what AI has
generated. When your review is complete, select one of three options in the
banner above the note to either Accept changes, Redo (opens the AI pop up
window with the most recent settings) or Discard.

Modifying Existing Notes with AI

There are many ways that existing notes can be modified and/or improved with
the help of AI. After each modification, you can review the edit prior to clicking on
Accept, Redo or Discard. Additionally, you’ll see a drop-down menu that will
allow you to view the original note, new note, or merged note to help you decide
if you would like to keep the changes. Merged notes will display new text in
green highlights and removed text in red highlights with strikethrough.

TheBrain allows you to transform your entire existing note or a selection within a
note with the following options:

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Summarize Note

Regardless of the note length, a summery of its content will be added to the
bottom of the note. Longer notes may have longer summeries.

Rewrite Note

Rewrite any note in a unique style or format. There’s no limit to the parameters
you can provide to TheBrain AI. Try one of the following styles to see the
different types of results:

• Poetry

• Patent Application

• Motivational

• Formal or Casual

• Modern Slang

• Legal

• News-Report Style

• William Shakespeare

Correct Spelling & Grammar in Note

Corrects all spelling and grammar mistakes and/or suggests new options.

Tip: After a Correct Spelling & Grammer in Note modification, it may be a good
time to review changes in the merged view before accepting AI’s alterations.

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Figure 207. Viewing Merged Changes

Organize Note

AI will review the content of your note and restructure it accordingly. Typically,
this will result in a shorter and more concise note.

Expand Note

Taking quick notes, or just jotting down a bulleted list or outline? Let AI turn this
fractional data into a complete and well structured note.

Auto-Complete Note

Writer’s block?... AI will pick up where you left off and complete your existing
note for you. This feature will even finish your content and line of thinking if you
stopped mid-sentence.

Extract Action Items From Note

AI will review the contentment of the note and generate a checklist at the bottom
of the note for action items that were referenced and need to be completed.

Translate Note

Convert an entire note, or just the selected text to any one of 78 different
languages.

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Using Drag and Drop within Notes

You can move images, links, and text in a note via drag and drop. You can also
drag note content to external applications.

• To move text, first select the text, then drag the selection

• To move an image or link, start dragging it, then drop it when the cursor is
where you want the image or link to be

Press the Escape key to stop dragging.

Tab Key Functionality in the Notes Editor

When you’re typing in the Notes editor, the Tab key performs different functions
based on:

▪ Where the cursor is

▪ Whether text is selected

As in most text processing software, holding the Shift key while pressing the
Tab key reverses the direction of the action. For example, wherever pressing
Tab shifts text to the right, pressing Shift+Tab shifts text to the left.

If no text is selected and the cursor is within or at the start of a paragraph:

▪ The first line of the paragraph (whether it is one line or many) is indented
approximately five spaces each time the Tab key is pressed.

When the cursor is in a list item (bullets/check boxes/numbered lines):

▪ The entire list entry is indented approximately five spaces each time the Tab
key is pressed.

When the cursor is in a title, subtitle, heading, or subheading:

▪ The level of the heading is decreased each time the Tab key is pressed. The
heading level is increased each time Shift+Tab is pressed. For example, to
change a Heading 4 to a Heading 3, you would click in the text and press
Shift+Tab. (Heading 3 is a “higher level” than Heading 4.)

When the cursor is in a table:

▪ Pressing the Tab key moves the cursor to the next cell.

Tab characters can’t be inserted into the middle of a line of text. If you want to
align text into columns, it’s most efficient to format using a table.

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Collapsing and Expanding Notes Sections

You can collapse sections of your notes based on headings, tables, and list
items. This helps you navigate through large documents more easily. Collapsing
lets you focus on a particular area while writing or reviewing content. When
you’re ready, you can expand any or all sections.

Two ways to expand or collapse Notes sections:

• Hover over the area to the left of the notes, then click the down-arrow to the
left of the section to collapse the entire list. This symbol will become a right-
arrow which you can click to expand the section.

Or

• Right-click in the area where there are notes, then click an option of your
choice. Optionally, before you right-click, click in a specific section if you want
to collapse or expand just that section.

Choices on the context menu include: Collapse All Except Here, Expand All,
Collapse All, Expand Here, and Collapse Here.

Figure 208. Options for Expanding or Collapsing Note Sections

Choosing a Notes Style

You can choose the style of the notes in the brain that’s open by clicking the
Notes Style button in the content area toolbar. The style you choose applies
globally to all notes in a single brain, so you can choose a style that matches the

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look of each of your brains. You can use a different style for each different brain
in TheBrain window.

Notes style and formatting will be preserved if you copy and paste a note’s
content from one thought into another. To easily copy an entire note, right click
anywhere inside the note to use the Select All option.
From the note’s context menu, you can also select Copy as Text or Copy as
HTML for pasting into other applications.

▪ To select a style, click in the Notes tab, click the More button, then click the
Notes Style command (or just click the Notes style button if the toolbar is
expanded), then click a style of your choice from the Edit Notes Style box.

Figure 209. Setting the Notes Style

Note Styles also follow a “responsive web design guidelines” approach which is a
fancy way of saying that any note you create will look great whether it is viewed
on a 30” monitor or a 4” mobile device.

You can also apply a Notes Style to a Theme, so that it will be in place when
you use that theme with another brain. The techniques for fine-tuning the
various Style attributes are the same, whether you start in the content area or
the Brain Theme dialog box. For details about viewing and changing the
appearance of notes in the content area, please see Changing the Content
Area’s Default Attributes beginning on page 49.

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Figure 210. Appearance of Some Notes Styles

Each Note Style has a set of paragraph styles that help you format your notes
consistently. If you don’t choose a paragraph style, the text is automatically
attached to a paragraph style named “Normal.”

Figure 211. Paragraph Styles

Paragraph styles apply to entire paragraphs. To select one, just click anyplace
with the paragraph, then click the paragraph style of your choice. If you change
to a different Notes Style, the text will change accordingly, based on the
paragraph styles you’ve selected.

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Changing Text Size in Notes

In addition to changing the size of text by choosing different notes and paragraph
styles, you can quickly adjust text to a size that is most comfortable for you. It’s
as easy as clicking the AA Text Size button, then dragging the slider up or down!

Figure 212. Slider for Making Note Text Larger or Smaller

Paragraph Alignment
Quickly adjust paragraph alignment to left, center or right. Place your cursor
anywhere in a paragraph and click on the desired justification.

Figure 213. Paragraph Alignment

Custom Font Family for Selected Text

Place your cursor anywhere in a paragraph, then click the Font button to select
from of over 900 font families. Fonts are consistent across platforms, so your
notes will look the same on Windows, macOS and mobile devices.

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Figure 214. Fonts

Move through large sections of the font list using the Next and Previous buttons.

Adding Tables
Create tables inside of the content area by clicking on Insert and selecting Insert
Table. Tables can also be created by copying and pasting from Excel, Word or
tables in other notes. When Show Markdown is active, to start a new table, type
a word or sentence surrounded by pipe symbols, such as: “|this is a new table|.”
Tables can include formatting and images, and cells can be right, center or left
justified, using the content area toolbar buttons or with markdown formatting.

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Figure 215. A Table Inserted in the Content Area

When adding a table, you may select the number of columns and rows. More
can be added at a later date if necessary.

Figure 216. Inserting a New 7x6 Table

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To make a table with no header, leave the cells in the header row empty (only
pipe characters and optional justification tags). The header will not be visible
when editing and will completely disappear when printed or in view mode.

Multiple cells can be selected at once for group formatting by clicking and
dragging, or use the arrows above or next to a column or row. Right click on an
arrow to select from the following options:

• Justify Left

• Justify Center

• Justify Right

• Duplicate

• Delete

• Move Up/Left

• Move Down/Right

When multiple cells are selected:

• Press the delete key to clear the cells. If an entire row or column is
selected, it will be removed.

• Cut, copy and paste can be used to move cells within a table or from one
table to another.

• You can even select a group of cells, copy it, then paste elsewhere in the
document to create a new table.

• If normal content (not made of multiple cells) is copied and then multiple
cells are selected prior to pasting, the content will be duplicated into every
selected cell.

Table Controls
Edit any cell by clicking inside that cell and using the available buttons in the
content area toolbar. Only formatting options that are available will be accessible,
others will be greyed out.

Click and drag on any bar in your table to adjust the column width. Select arrows
on the left for rows and on the top for columns to then drag and drop to move its
location in the table.

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Click anywhere in an existing table and then click on the table icon on the upper
left-hand corner of the table to activate a Table Controls Bar below the content
area toolbar.

Figure 217. Table Control Bar

From here, you can move selected rows and columns left, right, up, down or
duplicate the selected cells. Buttons will only appear for options that are possible
depending on which cells are selected. From the Table Controls Bar, the Table
Theme Editor can also be opened.

Additional commands are available by right clicking in a table, such as Move,

Justify, Select All in Table, Split Table and Toggle Table Toolbar.

Table Theme Editor

Selecting Table Theme Editor from the Table Controls bar will open a pop-up
window that allows you to further customize the color settings of the entire table
and/or the first row. New cells and content added to the existing table will then
follow the same color settings. A sample table will display the colors that are being
selected. The following options are customizable:

• Text

• Background

• Alternate Row Background (every other row, starting with row 1)

• Table Lines

• First Row Text, Background and Lines

• First Column Text, Background and Lines

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Figure 218. Table Theme Window

Over 20 different Prebuilt Styles are also available from the Table Theme
Editor.

Inserting a Table of Contents

You can easily add a Table of Contents into any existing note. The Table of
Contents will provide quick links to all Titles, Subtitles, Headings, and
Subheadings. You can also see a quick pop-up Table of Contents.

To insert a Table of Contents:

▪ Click in the note where you want the Table of Contents to begin, then click
the Insert button and select Insert Table of Contents option in the content
area toolbar. When Show Markdown is activated, type [/toc/].

The Table of Contents that is created will only include the content that appears
below it.

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Figure 219. Table of Contents

To delete a Table of Contents:

▪ Click just above the Table of Contents, then press the Delete key, or click just
after the Table of Contents, then press the Backspace key.

To view a pop-up Table of Contents:

▪ For a quick pop-up window that contains the note’s Table of Contents, right-
click in the note or press Ctrl+T.

Figure 220. Pop Up Table of Contents

Spell Checking

A spell checker is automatically at work for your notes. Possible misspellings are
automatically highlighted and you can right-click to view suggestions. Click the

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suggestion of your choice to replace the misspelled word. You can customize the
dictionary by adding words to it.

Figure 221. Spell Checker in a Note

If you prefer not to see misspellings flagged as you type:

▪ Click in the Notes tab, click the More button, then click the Check Spelling
as You Type command (or just click the Check Spelling as You Type
button if the toolbar is expanded).

Figure 222. Disabling Spell Checking

This is a toggle command. When you want to turn the feature on again, follow
the same procedure.

Real-time spellchecking also applies to creating and editing thought names.

Inserting Horizontal Rules

You can insert horizontal rules (lines) for organizing notes into sections visually.

▪ Click in the note where you want the horizontal rule to appear, click the Insert
button, then click the Insert Horizontal Rule command.

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▪ Horizontal Rules can also be added manually by typing 3 hyphens, even

when Markdown is hidden.

Figure 223. Inserting a Horizontal Rule

Typing 10 hyphens will create a Page Break in the note; however, this option is
only enabled when Show Markdown is activated.

To remove a horizontal rule:

▪ Click within the rule to select it, then press the Delete key. If there is a rule
between two paragraphs, the rule will also be deleted if you select and delete
the paragraphs before and after it.

Creating Check Box Lists

You can create a quick check box list and mark the items as complete or
incomplete. You can either create the list as you type or turn any existing text into
a check box list after you select it.

1. Click in the note where you want to type the first item to appear, click in any
paragraph, or select multiple paragraphs.

2. Click the Toggle Checkbox List button in the content area toolbar.

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3. When a task is complete, click the check box to display a check mark or
click it again to remove the check mark if you decide the task isn’t complete
after all.

Figure 224. Formatting Text as a Check Box List

To see ALL of your To-Do items in one place:

▪ Click the Right Panel button in the upper-right area next to the Search box or
click the To Do List command on the View menu.

Figure 225. Two Ways to Open the To Do List for All Thoughts

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The To Do List panel is displayed:

Figure 226. A To Do List for All Thoughts

When you click a check box in one location, such as the To Do List panel, it is
automatically checked off in the other location (the thought) and vice versa.

Linking to Thoughts in Notes

TheBrain has a built-in feature that automatically marks note text that matches
any thought in your brain with a blue dotted underline. You can then choose to
quickly create a link to that thought. This is explained in the Thought Mentions
section beginning on page 206.

Creating Web Links

Web links can easily be inserted, edited, and identified within your notes for the
active thought. Use any of these three ways:

▪ Type in the URL, or

▪ Paste in the URL from the clipboard after you copy it (any selected note text
is automatically linked to the URL), or

▪ Drag the URL in from a browser

The web link will be identified and processed automatically.

Hyperlinked text in notes can be displayed and activated in several different

ways. In TheBrain Preferences open the Notes Editor tab. Under User Interface,
the option to Show Link Target in Pop-Up can be selected. This will show the full
URL of a hyperlink in Notes when clicking on the linked text. Additionally, the

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option for Clicking Links in Notes can be set to Follows Link (automatically
launches URL in default browser) or Moves cursor (places cursor in the text
without activating the URL).

Figure 227. A Target Link Pop-Up on Hyperlinked Text

Videos from YouTube are embedded into notes in a playable form

automatically. Just drag and drop from your browser into your notes.

Figure 228. Dragging a Web Link into a Note

▪ The URL will be replaced with the title of the page it links to—and you can
easily edit the title by clicking within it and using standard typing and deleting
techniques. If you delete the brackets around the link text, the connection to

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the URL will be broken—just use the Undo command on the Edit menu or
press Ctrl-Z if you delete a bracket by accident.

Figure 229. Revising Link Text in a Note

Copying an image pasted in a note will put the image on the clipboard.

Fast Linking and Creating Thoughts from Notes

Pressing Ctrl/Cmd+K is a shortcut to:

• Insert a link to an existing thought

• Create a new thought

• Link to a URL

• Edit or remove a link

After you press Ctrl/Cmd+K:

1. An edit box opens so you can begin typing a URL or the name of the
thought you want to perform any of these activities on. Or, if you select text
or a URL first, that text will appear in the edit box.

2. Double-click the entry that appears to insert a link to that item in the note.
For example, double-clicking “Volunteer Opportunities” in the example
below creates a link to that thought in the notes for “Goals.”

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Figure 230. The Ctrl/Cmd+K Shortcut

3. If an existing link is selected, you’re ready to begin editing it. To remove the
link, just delete its name in the edit box.

4. If you type a URL, it will be inserted.

The link command includes all the features of Quick Thought Creation so you
can insert all types of relationships easily.

Alternatively, you can type [[ to link or create thoughts.

Capturing and Inserting Images in the Content Area

You can take a screen capture of virtually anything you can see on the screen
and then insert the image into the content area.

▪ Click the Insert button in the content area toolbar and select Capture and
Insert Image.

▪ Your brain will be hidden temporarily and red crosshairs will appear on the
screen in place of your cursor.

▪ Click and drag a rectangle around the area to be captured as an image in

your note.

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Figure 231. Capture Image from the Content Area Toolbar

Mathematical Expressions
Insert LaTex mathematical expressions directly into your notes by using the
Insert button in the toolbar or placing the proper text surrounded by $$. A real
time display of your mathematical expressions will be displayed while editing.

Example of a mathematical expression:

Input:

$$mr\left(\frac{2\pi}{T}\right)2 = G\frac{mM}{r2} \rightarrow T2 =

\left(\frac{4\pi2}{GM} \right)r3 \rightarrow T2 \propto r3$$

Result:

A common reference guide for LaTex mathematical symbols can be found at

https://www.caam.rice.edu/~heinken/latex/symbols.pdf or
https://en.wikibooks.org/wiki/LaTeX/Mathematics

When Markdown is hidden in notes the typed shortcut of $$ can still be used to
insert mathematical expressions.

Details on Images in Notes

Select an image in a note to see its size as a percentage. The size display will
update as the image is being resized.

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Figure 232. Image Size Displayed as a Percentage When Selected

Find and Replace in Notes

Click the Find & Replace button in the content area toolbar to open the Find and
Replace fields. Type the text you’re searching for in the Find field and the
replacement text in the Replace field. All matches to the Find field will be
highlighted in the note. Use the arrow keys move back and forth between each
occurrence to preview when you’ll be replacing. Use the Replace button to
replace specific instances one at a time, or the All button to replace all instances
of your search criteria.

Your cursor will remain on the current selected highlight when you close the
Find/Replace fields.

The Find field can be used independently, without content in the Replace field
if you are just looking for specific text to be highlighted within a long note.

Printing Notes

To print the active note, press Ctrl-P or click the More button, then click the Print
command (or just click the Print button if the toolbar is expanded). The Print
dialog box will open and you can fine-tune your print request.

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Figure 233. Printing a Note

Exporting Notes
Click the Export button in the content area Toolbar. You will have the following
options:

• Create Document – You will have the option to create a PDF, HTML,
Markdown or Text file. Custom settings that are selected will be
remembered for future exports. Customizable settings include:

o Options

▪ Thought Titles

▪ Thought Labels

▪ Links and Mentions

▪ Use web thought URLs

▪ Force white page

o Format

▪ PDF

▪ HTML

▪ Markdown

▪ Text

o PDF Options

▪ Page size

▪ Orientation

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▪ Text Size

▪ Page number footer

o Markdown Options

▪ Convert to “CommonMark”

• Open in Browser – Note will open as HTML in your default web browser.

Additional Note Features

Word and Character Count

The number of words for each note displays in the bottom-right corner of the
content area toolbar. Hovering over the word count for each individual note will
display the character count of that note. You can toggle the display on or off by
selecting the Show Word Count button on the expanded content area menu or
the compact toolbar’s drop-down menu.

Search Web from Notes

Select any text in your note and press F4 on your keyboard (or your customized
Web Search keyboard shortcut) to open the Web Search dialog box, pre-
populated with the selected text.

Delete By Word

The content area supports keystrokes to delete by word, rather than one
character at a time:

▪ Ctrl+Backspace = Delete to start of current word (equal to Ctrl+Shift+Left,

Backspace on macOS)

▪ Ctrl+Delete = Delete to start of next word (equal to Ctrl+Shift+Right, Delete

on macOS)

`Search Brain for`

Select a word or phrase in any note and right click. Select the option of Search
Brain for “Selected Text” to see if that word or phrase appears elsewhere
within the same brain.

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Edit Link Context Menu Commands

Once a link has been added to notes, you can right-click on it to edit it. If the link
is a URL, you can edit its text. If the link is to a thought, you can search for and
select a different thought.

Resizable Images and Videos

Images and videos that have been pasted into a note can easily be resized. Click
on the image or video to highlight it. Each image will have eight resizing points.
Click and drag on any resizing point to resize the image.

Copying Images from Notes

When a picture in the content area is copied (by right-clicking it and selecting the
Copy command), pasting into Paint or Word will paste the image itself.

Pasting into notepad or some other text-only application will paste the markdown
text that references the picture.

Additionally, you can right-click an image in the content area and select Copy as
Image.

Adding and Viewing Thought Attachments

In addition to notes, each thought in your brain can have content associated with
it such as web pages and a multitude of file attachments. You can drag and drop
attachments, create them from scratch, and use any of the other options
provided by the Attach button in the content area toolbar. To access your
attachments, just click their links in the content area.

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Figure 234. The Attach Button in the Content Area

Attaching Files

You can use standard “drag and drop” techniques to add file attachments into
your brain from other programs to a thought or to create new thoughts.

To drag and drop one or more items into the Content Area of a thought:

1. Make sure the thought to which you want to add the attachment is currently
the active thought and that the content area is visible.

2. Position the window containing the item you want to attach so that it and
the content area are both visible, then drag the selected item to the blank
area under the thought name in the content area. A dashed outline around
the thought name shows you that you’re about to attach the file to that
thought. You can select multiple items and drag them all at the same time.

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Figure 235. Dragging and Dropping a File into the Content Area

Specifying your Drag and Drop Preference

By default, all files that you drag and drop into your brain will create a copy of the
original file. You can easily change the default to suit your environment. Please
see the Behavior Preferences section on page 64 for information about viewing
and changing the “On drag and drop of files” setting.

Tip: You can also override the current drag and drop setting in the Preferences
window by holding down the following keys as you drag and drop:

In Windows
In macOS
▪ Link to file = Alt
▪ Link to file = Ctrl
▪ Move file = Shift
▪ Move file = Cmd
▪ Copy file = Ctrl
▪ Copy file = Alt

Attaching Links to Files and Folders without Dragging

You can also add a file attachment to the active thought without dragging and
dropping.

To insert a link in the active thought to a file or a folder:

1. Click the Attach button in the content area toolbar.

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2. Click Link to File or Link to Folder, navigate to the item, then click the
Open button.

Figure 236. Using Link to File to Add a File Attachment

4. The content area will display the details of the new attachment.

Figure 237. Content Area after a Link to a File is Attached

From here you can click the X button to return to the notes, click the up-arrow
button to open the attachment, use the left- and right-arrow buttons to move back
and forth between other attachments in the same thought or to move back to the
notes, or click the Actions button to access more choices for handling the
attachment.

Action Menu for Files

▪ Open: Open the selected attachment in its default application.

▪ Rename: Change the name of the selected attachment.

▪ Properties: Display all attributes of the selected file in a separate dialog box;
based on the default application, there may be properties you can change.

▪ Delete: Delete the selected attachment (you will be not be prompted to

confirm the deletion but you can use the Edit menu to Undo the deletion).

▪ Copy: Copy the selected attachment to the clipboard; you can then paste the
attachment elsewhere in your brain.

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▪ Cut: Place the selected attachment into the clipboard; the attachment will be
removed from its current location when it is pasted elsewhere in your brain.

▪ Move File into/out of Brain: Switch this attachment between internal and
external storage; if you are moving the file out of your brain, you will be
prompted to specify the destination folder.

▪ Copy File into/out of Brain: Switch this attachment between internal and
external storage; if you are moving the file out of your brain, you will be
prompted to specify the destination folder.

▪ Copy File Path: Copies the location so that you can paste it elsewhere,
including the Search box; for example, you may want to see if the file is
elsewhere in your brain.

▪ Show in Explorer: Shows where the file resides outside of your brain.

▪ Encrypt: Ensures that it is impossible to recover the file contents without a

password.

Attaching Web Pages

Adding URL attachments to your brain is a simple process. TheBrain’s built-in

browser will display each web page in the content area.

TheBrain’s built-in browser has recently been updated and supports more types
of web content than ever before. Many web pages can event be interactive
(Google Docs, Sheets, etc.) from within the content area.

The easiest method for linking a web page into your brain is to simply drag and
drop it into your brain. Click on the URL icon in the address bar of any browser
and drag into one of several different locations to add the web page as an
attachment:

▪ Drag and drop to the plex to create new thoughts. The thought name will be
the URL of the web page or what is contained in the <title> tag of the URL,
which you can easily rename as you would any other thought. A link to the
page will appear under the thought name in the content area and clicking that
link will open the page in TheBrain’s built-in browser. Online non-HTML
content, such as online .PDF files will be renamed with the file name.

▪ Drag and drop onto existing thoughts in the content area. This will simply add
the web page as an additional attachment link. The thought name will not be
updated.

▪ Drag and drop into the body of an existing note for a hyperlink.

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Figure 238. TheBrain’s Built-In Web Browser

Adding a Web Page by Typing or Pasting its URL

You can also add a web page attachment to the active thought by clicking the
Attach button in the content area.

▪ Click Link to URL, paste or type the URL address into the empty field, then
press the Enter key.

Figure 239. Adding a Web Page Attachment using the Attach Button

If the URL you are attaching to your thought already exists as an attachment on
another thought, you’ll have the option to cancel, add, navigate to the Attachment
or replace the attachment.

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The name of the duplicate URL will be displayed in the warning message.

Figure 240. URL Exists

TheBrain’s built in browser allows you to open archived web pages for
attached URLs. In the context menu for any URL attachment, select Open
Using Wayback Machine.

Attaching Video and Sound Files

TheBrain 13 includes a built-in media player that can enables playback of several
common video and audio files.

To activate the video player, select a video file attachment. The video will be
previewed and the player controls will be shown near the bottom of the window.
To activate the audio player, use an audio file attachment.

The primary controls are: play/pause, advance by 10 seconds, and rewind by 10

seconds. There is also a timeline that can be dragged to go directly to a specific
time in the video and a button to open the file in an external player. The numbers
at the left of the timeline show the amount of time that has elapsed while the
numbers at the right of the timeline show the amount of time remaining.

As the window is resized, the video player and its controls scale to fit within the
available space with the controls appearing in a translucent overlay on top of the
video when insufficient vertical space is available.

A fading animation is utilized to hide and display the controls as necessary when
video is playing. For audio files, the controls are displayed in the center of the
available space and do not fade out at any time.

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Figure 241. TheBrain’s Built-In Media Player

Supported File Types

Media Type Windows and macOS Windows Only macOS Only

mov, mp4, h264, h263,
Video mpeg, mpg, avi, mkv, mkv 3gp
wmv
Audio mp3, wav, aac, ts, flac pcm, wma aiff, ac3

Tip: Attachments can be moved between thoughts by using drag and drop
directly from the content area to another thought that is visible in the plex.

Action Menu for URLs

An attachment that is a web page has a slightly different menu—and it’s also
slightly different based on whether it’s showing in the note or with the attachment
“in place,” meaning in TheBrain’s built-in browser. Access the menu by either
right-clicking attachment in the note or by the Actions menu button in the content
area where the web page is displayed.

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Figure 242. URL Attach Menu in Notes and in Place

▪ Preview in Place: Open the page within the content area in TheBrain’s built-
in browser.

▪ Open: Open the selected web page in its default application.

▪ Open Using Wayback Machine: Open an archived web page for the URL.

▪ Rename: Change the name of the selected attachment (not the URL itself).

▪ Edit Location: Change the URL address for the selected attachment.

▪ Attachments as a List: By default, attachment links appear one after

another, wrapping to a new link when there are more than fit in one line. This
option shows each link in a separate paragraph.

The rest of the commands work as they do for file attachments.

When a thought’s attachments are modified, the modification date of the

thought is also automatically updated, improving the accuracy of your searches
and filters.

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Viewing Attachments as a Slideshow

Use the Next and Previous navigational arrows in the top-right corner of the
content area toolbar to browse through attachments.

Figure 243. Next and Previous Arrows

To view attachments as a slide show:

▪ Click the first attachment, then click the Next button to display the next
attachment.

▪ For multi-page attachments, click a thumbnail to jump to a specific page.

▪ To return to the notes, just click the Close button (X) at the start of the Notes
toolbar (or keep clicking the Previous button until the notes appear).

To view pictures in notes as a slide show:

▪ Double-click the image you want to see first to maximize it, then click the
Next button to display the next picture.

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Figure 244. A Picture from Notes in Slideshow Mode

Working with Multiple Attachments

You can add multiple attachments to thoughts and you can have many types of
attachments for a single thought. For example, if you have a thought for a
person, you might attach their blog as a web page, and their resume in a file—all
in the same thought.

Multiple attachments can be brought into TheBrain at a single time using drag
and drop or copy/paste.

When there is more than one attachment, the number of attachments is

displayed on the thought icon. For example, the thought shown below has two
attachments:

Figure 245. Number of Attachments Indicator

For keyboard navigation, when opening a list of attachments for a single thought,
the first attachment will automatically be selected.

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Keyboard Commands for Selected Attachments

You can use your keyboard to move the cursor from notes, up into the
attachments area to select individual attachments that are associated with a
thought. Once an attachment is selected, the following keyboard shortcuts can
be used:

• Space = Open/Preview

• Enter = Rename

• Backspace/Delete = Delete (confirmation prompt will display)

• Ctrl/Cmd+C = Copy

Cut/Copy Attachments Within a Brain

Existing attachments within a brain can be cut or copied onto your clipboard. You
can then paste to a new thought in the same brain, a different brain, or to a
different directory/location on your system. Right click on an attachment, or use
the arrow keys to navigate the cursor up to a selected attachment while editing a
note

Creating an Event as an Attachment

You can use the Create Event command on the Attach menu in the content
area toolbar to add events to your thoughts. Please see the Managing Events
section on page 229 for details.

Adding a Template File to Your Brain

There may be types of files that you create frequently that share a common look
and feel. For example, you may prepare correspondence using a common
letterhead. You can designate template files that will be at your fingertips
whenever you create attachments.

To create a template file:

1. Click the Attach button in the content area, then click the Add File from
Template command.

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Figure 246. Adding a File from a Template

2. In the Create File from Template tab, any previously created templates
will appear under the “User Templates” heading and the built-in templates
will appear under “System Templates.” Click the file type of your choice.

Figure 247. Selecting a Template

3. The associated application will open and you can begin creating your file.
Save as usual. After you close the file, TheBrain window will appear. Note
that you can switch back and forth between windows—including
TheBrain—as usual, as you’re working. By default, the new file will have the
same name as the active thought and it will be saved as an internal file.

Remember to click on Template Help under the Attach button if you want to add
new and/or custom file types to your existing template list.

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Tip: If you edit one of the files in your templates folder, save it under a new name
in order to preserve your original template.

Pasting an Image as an Attachment

If you have copied an image, you can click the Attach button in the content area,
then click Paste Image. The image will become both an attachment for the active
thought and its icon. Common file types such as .jpg, .gif, .png and .svg will all
preview in TheBrain content area.

Additionally, multiple image files can be copy/pasted or drag/dropped into

TheBrain as attachments at a single time.

Figure 248. Pasting In an Image

Using the “Save As” Command

You can use any application’s “Save as” command to create a new file inside
your brain. For example, if you have opened a Word file that is an internal
attachment to a thought, you would click the File menu, click the Save as
command, then enter the name of the new file to create. The new file will
automatically appear in a tab of the thought’s content area.

Viewing Related Thoughts in the Content Area

Have you ever wondered whether content in one thought’s note is referencing
another thought in the same brain or even if the thought you are on is being

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referenced in another note—but you figured it might be too complicated to go

searching? Without your having to do anything, the content area displays all
related thoughts.

Related thoughts do not have to be visible in the plex in order to display in

the content area.

Thought Mentions
When a thought name appears within notes, your brain recognizes it
automatically as a “mention.” Both plural and singular forms of the text are
recognized, so exact matches are not required.

Figure 249. A Thought Mention Underlined in a Note

Right-click on a Mention in a note to either link to or activate this thought.

Figure 250. Context Menu When Right-Clicking on a Mention

Below the note are options for displaying more related content within the same
brain by opening Mapped Links, Backlinks, or Unlinked Mentions in a footer that
can appear below the note:

Mapped Links: Thoughts that are connected in the plex as parents,

children, jumps, or siblings (but do not necessarily
have text in common)

Backlinks: Thoughts whose notes link to the active thought

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Unlinked Mentions: Thoughts whose notes contain the name of the

active thought⎯even if not explicitly linked

Click on any thought name in this display to navigate to that thought. Right click
on any thought name to open a context menu with the following options for
modifying the relationship between the active thought and the selected thought:

• Link as Parent

• Link as Jump

• Link as Child

• No Mapped Link (unlink)

While mapped links refer to thought names, backlinks and mentions display both
the names of the related thoughts and the context of the notes in which they
appear.

Figure 251. Content Area with Related Thoughts in the Footer

Using Related Thought Links

You can activate any related thought by clicking its link in the content area footer.
This enables you to add content to one note from another via links or mentions.

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Figure 252. Two Kinds of Links for Related Thoughts

• Click a solid blue link to activate that thought.

• In the footer, click a dashed underline link to display the Link this Mention
command. Once it’s linked to the existing mentioned thought, it will move
from the Unlinked Mention section to the Backlinks section in the
content area.

Figure 253. After an Unlinked Mention is Linked

Note that while links appear in blue by default, you can easily change their
color. To do so, select Brain Theme in the Options menu, then click the color
of your choice on the Colors tab for the Links entry. Click Save Theme to
save your change.

Hiding or Showing Related Thoughts

To hide mapped links, backlinks, or unlinked mentions in the content area:

• Right-click in the Notes area, then click Show Mapped Links, Show
Backlinks, and/or Show Unlinked Mentions in the context menu.

To restore the thought names and/or links and mentions:

• Right-click within the Notes area and click Show Mapped Links, Show
Backlinks, and/or Show Unlinked Mentions in the context menu.

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Note that hiding or showing related thoughts is global and applies to your entire
brain.

Figure 254. Context Menu Below Notes

You can also use the Notes Editor tab in Preferences to hide or display links
and mentions in the content area.

Figure 255. Links and Mentions Section in Notes Editor Preferences

Collapsing and Expanding Related Thought Sections

When you hover over the area to the left of the related thoughts, you’ll see down-
and right-arrows.

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• Click the down-arrow to the left of the current thought name to collapse the
entire list. This symbol will become a right-arrow which you can click to
expand the entire list.

• Click any other down- or right-arrow to expand or collapse that section or item.

Figure 256. Collapsing or Expanding Sections

You can also collapse and expand sections within note text in a similar way when
Heading styles are used.

Aggregating Content
The data in your brain can be aggregated automatically with just a few simple
mechanics. When data is aggregated, you can see content from notes about the
same subject throughout the thoughts in your brain all at the same time. This
ability is powerful and magical!

In the example below, the four backlinks comprise every note that begins with a
“George” heading throughout the brain, organized by the name of the thought
that contains one or more “George” headings.

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Figure 257. Aggregated Data for “George”

To prepare data to be aggregated:

1. Create a thought whose name represents the information you want to see
aggregated. In the Figure 257 example, that thought name is “George.”

2. In any thought that has information about “George” (following this example),
precede the information with a standalone paragraph. This paragraph
should simply have the text that matches the name of the thought for which
you want aggregated data—“George” in our example. The text should be
attached to a Heading stye.

Figure 258. “George” is Formatted as a Heading 3

3. Link the Heading by right-clicking it, then selecting Link (thought name).

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Figure 259. Linking the Heading to the Thought of the Same Name

4. In this scenario, the backlink content on the George thought will display all
text until it comes to the next #3 (Heading) formatted text.

Any time you activate the “George” thought, you’ll see the information
aggregated, as in Figure 257.

When selecting text in a note, you will have the option to Add Linked
Thoughts to Selection if backlinks are also selected.

BrainBox
BrainBox lets you send information to your brain quickly and easily. Just click the
icon in the top-right corner of TheBrain for Windows or macOS for instant access.
Use BrainBox for adding information on the go, from your desktop, from the web,
anything that you want to quickly capture into your brain, to be categorized later.

To add content from the web to BrainBox, first install the BrainBox extension in
your preferred browser. Go to https://www.thebrain.com/docs/brainbox and
follow the instructions there.

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Accessing BrainBox

The BrainBox Button

At any time, when you have a brain open, use the BrainBox button in the upper-
right corner of the window to add previously captured content into your brain.

1. Click on a brain to open it.

2. Navigate to the desired thought where you want to add your content.

3. Click on the BrainBox icon to display its content.

4. Hover over or click any item to display the choices for the item.

Figure 260. The BrainBox Button

5. From here, the file or web page can be:

▪ Added as an internal attachment on a new child thought below the

current active thought. The new thought name will be the file or web
page name

▪ Added as an internal attachment to the active thought

▪ Opened in its default application

▪ Renamed, deleted and other actions applied from the context menu
button

▪ The context menu will also allow you to either Move from BrainBox to
the active thought or Copy from BrainBox

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The BrainBox Tab

An alternative way to view and manage the content of your BrainBox is available
by opening BrainBox in its own tab.

To open BrainBox in its own tab:

▪ Click the Open BrainBox button, click the drop-down Show Commands
menu, then select Open BrainBox in New Tab.

Figure 261. The BrainBox Tab

Use the BrainBox tab to review, edit or delete existing content in your BrainBox.
If you move your BrainBox tab to a new window, you can then drag and drop
items into another Brain. You may also select multiple items in BrainBox at a
single time to drag into a Brain or right click and delete.

OR on
mouseover

Figure 262. Editing Content of The BrainBox

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1. Point to or click an item listed in the BrainBox to select it.

2. Use the context menu or the choices that appear on mouseover to:

▪ Open item in its native application for preview

▪ Edit the file or link name

▪ Edit the URL

▪ Open in Explorer or Finder

▪ Delete the item from your BrainBox

Multiple items can be selected in BrainBox allowing you to move, copy or delete
multiple items at one time

Figure 263. Working with Multiple Attachments in BrainBox

Additionally, from the BrainBox Show Commands menu, you can access the
BrainBox Folder or access BrainBox documentation available at
https://www.thebrain.com/docs/brainbox.

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Sending Web Pages to BrainBox

Add information from any web browser with a single click. When you find a page
you want to capture to be organized later in TheBrain, just click the BrainBox
extension button or bookmarklet (depending on your browser).

You must be logged into your brain account at https://app.thebrain.com in the

browser you are using in order for the web page to be successfully added into
your BrainBox. If you are not logged in, clicking on the BrainBox extension from
your browser will prompt you to do so in the status screen. Once you have
logged in, return to the desired web page and click the BrainBox button again.

You can use the browser extension or bookmarklet from any computer, even if
TheBrain application is not installed on that device.

Figure 264. Clicking on the BrainBox Extension

Sending Files to BrainBox

Send copies of individual files into your BrainBox to be organized and associated
with thoughts at a later time. No additional setup for this feature is required.

Windows File Explorer Send to Integration

From Windows File Explorer, right-click on any file and select BrainBox from the
Send to submenu. TheBrain will be started if it is not already running and the file
will be added to BrainBox. To set up the Windows File Explorer integration, install
and run TheBrain 13.

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Figure 265. Sending a File to BrainBox

macOS Dock Drag and Drop

Launch TheBrain application if it is not running already. From any Finder window,
drag and drop any file to TheBrain icon in the macOS Dock. The file will be
added to BrainBox. You can also drag the icon from the title bar of many macOS
apps.

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Producing Reports

Reports are an excellent way to manage large groups of thoughts in your Brain.
To open a brain's Report area, click the View menu then click the Report
command. You may also click on the Right Panel button next to the search box.
The report pane is resizable.

Figure 266. Viewing the Report Area

Selecting Report Criteria

The Thoughts drop-down list includes the following options and each selection
provides additional criteria choices for fine-tuning your reports.

Figure 267. Thought Options for Reports

You can run reports based on the criteria discussed below.

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By Types/Tags
The By Types/Tags option in the Thoughts drop-down helps you filter thoughts
in your Report by checking for specific thought Types and Tags for thoughts
and/or for links. All thoughts or links that don’t meet the criteria will be excluded
from the report. By default, thoughts of any Type will be included.

▪ Click the field to the right of Types (which will display “Any” if no Types have
been selected yet), then select the check box for each thought Type to be
included. Click outside of the list to close it.

Figure 268. Selecting Thoughts by Types

Use the Tags field to filter thoughts based on your assigned Tags.

Figure 269. Filtering a Report by Tags

Clicking on a Tag in the list will add a “+” next to it, indicating that you want to list
thoughts that have that Tag. Clicking the same Tag again will add a “-“ next to it.
This indicates that you do not want thoughts with that Tag listed. Clicking the
same Tag once more will remove it from your list of filtered Tags.

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Figure 270. Filtering With and Without Tags

Use Types and Tags together in a report for some incredibly powerful thought
filtering. When your report is displayed, you can click on any result to
immediately navigate to the thought.

Forgotten Thoughts
The Forgotten thoughts selection allows you to quickly view and access any
thoughts you have forgotten in a brain.

Figure 271. Forgotten Thoughts Report

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With Forgotten selected in the Thoughts drop-down, you can use the menu
button to add all forgotten thoughts in your report to your Selection, remove
all forgotten thoughts in your report from your Selection, permanently delete all
forgotten thoughts in your report, or remember all forgotten thoughts in your
report.

Figure 272. Choices for Forgotten Thoughts

As soon as you click any forgotten thought in the list, a “Showing Forgotten
thoughts” message will display above the plex. Click any forgotten thought in the
report to display that thought in the plex.

Figure 273. Showing Forgotten Thoughts

Parentless Thoughts
Select Parentless in the Thoughts drop-down to quickly view and access any
thoughts that do not have a parent.

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Figure 274. Parentless Thought Report

Viewing a Parentless Thought Report is great for tying up any loose connections
or finding groups of disconnected "satellite thought clusters" in your brain for
easy reconnection and clean-up.

Orphan thoughts will also appear in a Parentless Thought Report. Jump

thoughts (when they have no Parent) will frequently appear in this report as
well.

Orphan Thoughts
Select Orphan in the Thoughts drop-down to quickly view and access any
thoughts that do not have any other connections.

Figure 275. Orphan Thought Report

Viewing an Orphan Thought Report is an excellent way to find lost thoughts or

thoughts that may have inadvertently been disconnected at some point. Is there
a thought you know you had in your brain? Try running an Orphan Thought
Report to see if it was previously unlinked by accident.

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Duplicate Names
Select Duplicate Names in the Thoughts drop-down to quickly view and access
multiple thoughts with the same name.

Figure 276. Duplicate Names Report

Viewing the Duplicate Thoughts Report can help you organize and manage your
brain to make sure you are getting the most out of your information with quick
access to the most important thoughts.

By Attachments
Select By Attachments in the Thoughts drop-down to quickly view and access
all thoughts that have an attachment. By default, only internal attachments will be
included and you can use the Type drop-down list to fine-tune as needed.

Figure 277. By Attachments Report

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Filtering by Modification or Creation Date

All report options except Duplicate Names can be further narrowed down using
the Time drop-down selections. This is incredibly useful for finding information
modified within a specific date range and allows for even more in-depth reporting.

Figure 278. Filtering Thoughts in a Report by Modified Date

▪ Select Modified, Created, or Event to specify what the date range should
pertain to. For example, select Modified if you want to see thoughts you
made changes to within a specific period of time.

▪ Click in the first date field to display a calendar, then select a date; click in the
“to” date to select an end date.

▪ Additionally, you can click on the context menu button to select from a preset
list of date ranges:

o Last Day
o Last 2 Days
o Last 7 Days
o Last 14 Days
o Last 30 Days

▪ Select Any if you want to remove the time criteria.

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 Producing Reports

Sorting Report Results

Use the Sort drop-down to switch the list order of your report results between
Name, Date Modified, and Attachment Size.

▪ Reports sorted by Name will appear in ascending order, A-Z

▪ Reports sorted by Date Modified will appear newest first

▪ Reports sorted by Attachment Size will appear with the largest total
attachment sizes highest in the list

Figure 279. Sorting Thoughts in a Report

Refreshing or Resetting Report Results

▪ Click the Refresh button to update the list of thoughts that match your report
criteria.

Figure 280. The Refresh Button

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▪ Click the Reset button to clear all report criteria except the Thoughts field
and the Sort field selections.

Figure 281. The Reset Button

Adding Report Results to the Selection Panel

▪ Click the menu button, then click Add All to Selection. All report results will
be added to the Selection panel where you can apply actions to the thoughts
all at one time. Right-click in the Selection area to see your choices.

Figure 282. Adding Report Results to the Selection Panel

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Saving and Accessing Reports

Reports can be saved and used again at any time.

To save a report:

1. Click the Save as command on the menu.

2. Type a name for your report, then click the OK button.

Figure 283. Saving a Report

To open a saved report:

1. Click the Saved Reports command on the menu.

2. Click the name of the report you want to open.

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Figure 284. Saving a Report

Viewing a List of Recent Changes

You can view a quick report of all changes you’ve made recently to thoughts.
Your thought modifications are now logged and instantly viewable in a
chronological display of the previous 1,000 created and modified thoughts.

Modifications can include:

▪ Renaming

▪ Editing, adding or deleting attachments

▪ Any edit to the thought notes

▪ Renaming

▪ Linking or unlinking to another thought

To view your recently modified thoughts, simply click on the clock icon to the right
of the Search box. Modified thoughts will be displayed starting with the current
date. When you hover over a thought, a comprehensive, time-stamped report of
the exact modification(s) appear in a pop-up next to the name.

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Figure 285. Recently Modified Thoughts and Links

Find and Replace

Find and replace all occurrences of text within thought names and labels, link
labels, external attachment paths and URLs.

▪ Includes support for regular expressions.

▪ Can be applied to the entire brain or to a group of selected thoughts.

▪ Changes are undoable however it is still highly recommended that you create
a brain Archive (.brz) prior to performing a large Find and Replace operation
on an important brain.

To begin replacing:

1. Open the File menu, select Utilities, then select Find and Replace.

2. Enter the text to be replaced and the text to replace it with.

3. Specify where the text occurs. The available locations are:

▪ Thought Names

▪ Thought Labels

▪ Link Labels

▪ External Attachment Paths

▪ Attached URLs

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4. Use the check boxes to specify whether letter case is to be ignored and if
you want to use regex (regular expressions, which allow sophisticated
pattern matching capabilities).

5. Preview your results prior to executing the change and click Replace when
you’re ready.

Figure 286. Find and Replace

Additionally, the content area toolbar has its own Find and Replace functionality.

Statistics
Curious about the content of your brain? Click the File menu and select
Statistics to view in-depth details such as:

▪ Date Generated

▪ Last Sync Date

▪ Number of Thoughts

▪ Number of Links

▪ Average Number of Links per Thought

▪ Internal File Size and Total Icon Size

▪ Number of Notes, Attachments, Web Links, Icons and more …

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Managing Events

Your brain has its own built-in Calendar. You can access it from the content area
or the Timeline View to add and modify events and integrate them with your
thoughts. You can view your Calendar a day, week, month, or year at a time.

TheBrain also has several different ways to assist you with managing your time,
so you’ll know when events are taking place, when content was edited and when
projects are due.

Creating an Event
You can create a new event from the content area or from the Timeline. Both
methods give you full access to all event settings. Events support spellcheck and
markdown formatting in their descriptions.

Creating an Event from the Content Area

1. Select the thought with which the new event will be associated.

2. Click the Attachment button in the content area toolbar, then click Create
Event.

Events created from the content area are automatically associated with the
active thought, but you can easily detach them.

Figure 287. Creating a New Event in the Content Area

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Use the event editor pop-up to enter details about the event. By default, the
name of the event is the name of the active thought.

As shown below, you can specify start and stop times and dates and add a label,
description, and location in the event editor pop-up. You can make the event
recurring and set up a reminder. You can also color code an event—so that all
events of a specific type (personal, marketing, finance, etc.) will appear in your
Timeline view in an identifiable color. Event will inherit from colors from
associated thoughts.

Figure 288. The Event Editor

Creating an Event from the Timeline

1. Unless it is already open, display the Timeline by clicking the Timeline
command in the View menu or the Timeline button to the left of the Search
box.

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Figure 289. Launching TheBrain Timeline

2. Drag on the time ruler at the bottom to select the start and stop times of the
event. After you finish dragging, the event editor will be displayed. By
default, this will be a standalone event, not associated with the current
active thought. You can easily attach it to the active thought by clicking
Attach to “active thought” in the event editor menu.

Figure 290. Click and Drag to Create a New Event

Please see the Navigating in Timeline View section on page 235 for
information about using the Timeline and 1-click fine-tuning based on your
preferences.

Responding to Event Reminders

Reminders appear when the brain containing the event is open.

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Figure 291. TheBrain’s Event Reminder Pop-Up

From the Reminder window, you can snooze for a designated amount of time or
dismiss the reminder. Dismissing the reminder does not delete the event in your
timeline.

Editing and Deleting Events

To edit or delete an event from the Content Area:

▪ In the content area for the Thought associated with the event, right-click the
event you want to work with, then choose a command from the context menu.
Choose Properties to edit the details of the event.

Figure 292. Editing and Deleting Events in the Content Area

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To edit or delete an event from the Timeline:

▪ To edit, click the event to open the event editor pop-up.

▪ To delete, right-click the event on the Timeline, then click Delete Event. You
can also delete the event by selecting Delete Event in the event editor pop-
up.

Figure 293. Editing and Deleting an Event in the Timeline

Navigating in Timeline View

▪ Drag in the background of the timeline up and down to zoom in and out.

Figure 294. Click and Drag Up and Down to Zoom

▪ Drag left and right to scroll through time.

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▪ Buttons allow you to switch between day, week, month and year view. Or,
navigate to a specific day in the mini calendar.

Figure 295. TheBrain Timeline Buttons

Events associated with Forgotten Thoughts will only appear in the timeline if
Forgotten Thoughts are being viewed in the plex. Like the faded display in the
plex, the thought’s event will also appear as faded text.

TheBrain Icons
TheBrain includes nearly 2000 built-in icons for your thoughts, Types, and Tags.
Choose from 22 different categories such as Animals, Emojis, Food, Multimedia,
and Technology, to name a few. Here are some examples:

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To select a Brain icon to be added to a thought:

1. Right-click the thought, then click Select Stock Icon or open the
Thought Properties dialog box, click the thought icon box, then click
the Select Stock Icon command.

Figure 296. Two Ways to Access Select Stock Icon

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2. Select the Browse radio button and choose a category from the list
below. The name of the icon will appear when you hover over it. Click
on an icon to add it to the active thought.

Figure 297. The Food Category

Additionally, you may select one of the other radio buttons:

▪ Search—Type a keyword to filter all icons that match that result

▪ Suggestions—Automatically filters the icon list by using the thought name as

the search criteria

▪ Random—72 random icons will appear; click the Shuffle button to see a new
set of icons

▪ Recent—Displays all recently selected icons

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Online Menu Options

The Online menu in TheBrain toolbar provides access to your Cloud Services
settings from your desktop client and helps you share thoughts and brains
quickly.

Figure 298. Online Menu Options

Click the Online menu in TheBrain’s toolbar to access the following features:

Sync Brain—Synchronizes the current opened brain to your Cloud account.

Sync Automatically—Toggle on or off automatic synchronization, once your

brain is already synchronized to your Cloud account.

Open Thought in Web Client—Launches a Browser window and automatically

loads the current brain/thought from TheBrain Cloud.

Copy Web Thought URL—Copies the current active thought’s online URL to
your system clipboard. This saves you the hassle of launching a new browser
window to log into your Brain Cloud account and navigating to a specific thought
in order to acquire its URL.

Copy Web Thought URL and View in Browser will only work if you have
synchronized your brain to TheBrain Cloud.

Brain Access and Sharing—This is a quick way to switch a brain’s Access

Control Level (public or private), copy the brain’s online URL or grant a new
TeamBrain member access. You may also type in an email address to share a
read-only copy of your brain with someone else.

Show Account Info—Easy access to managing your external accounts and

logging out of TheBrain Cloud.

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Using Mobile Versions of TheBrain

Access your ideas and information on all your devices—including iOS and
Android. TheBrain for mobile devices combines the best of note-taking, file
synchronization, and mind mapping apps to give you the ultimate digital memory
everywhere you go.

The iOS and Android apps include the ability to sync your brain so you can
access it without an Internet connection. Once you download your brain locally to
your mobile device, just click the Sync button after making edits or if edits have
been made to TheBrain Cloud.

Figure 299. Syncing TheBrain on iPhone

TheBrain for iOS can be downloaded from the App Store at

https://itunes.apple.com/us/app/thebrain-tech/id835873357?mt=8

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TheBrain for Android can be downloaded from the Google Play Store at
https://play.google.com/store/apps/details?id=com.thebrain.android

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Share, Synchronize, and Back Up Your Brains

You can use TheBrain Cloud to publish and share your brain. People can view
your published brains whether or not TheBrain is installed on their machines.

To create a Brain account:

1. Go to http://www.TheBrain.com, then click the Log In button in the top-right

area of the page.

Figure 300. Sign Up Button

2. Click the Sign up button.

Figure 301. Login Button

3. Complete all fields in the Sign Up form, then click the Sign Up button. You
will see a message explaining that a confirmation notice has been sent to
the email address you provided. When you receive the message, follow its
instructions to click the link and activate your account.

Allow a few minutes for the email to be delivered. Check your spam folder if
the message doesn’t arrive within a reasonable amount of time.

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4. Now you can return to the www.thebrain.com page and click the Login
button to log in using the information you provided when you signed up.

Synchronizing Your Brain

With TheBrain and TheBrain Cloud Services you can use your brain on multiple
computers and synchronize changes. Any changes you make to your brain on
one machine will be reflected on every other machine through synchronization!

Cloud synchronization is protected using 128-bit AES Encryption. (This is the

same encryption used by the US government to protect classified information.)
Port 443 is used for encrypted syncs. If your IT staff is using a firewall, you can
ask them to add WebBrain.com and api.thebrain.com to the white list of your
company's firewall. If your IT staff is using a proxy, you will need to try setting
up a Proxy connection via TheBrain by using the options found in TheBrain’s
Preferences > System tab.

Make sure you have created an account on TheBrain.com before you begin
synchronizing. Some Cloud services require a subscription fee.

To synchronize your brain:

1. Open the brain you wish to sync. Click the cloud icon in the menu bar, or
click the Online menu, then click the Sync Brain command.

Figure 302. The Cloud Icon in the TheBrain Toolbar

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Figure 303. Sync Brain Command

2. Click the Upload button to upload this local brain.

Figure 304. Confirming Upload

3. A progress indicator shows you the upload is taking place, followed by a

brief confirmation message.

You can keep working while the synchronization process is continuing in the
background. If there is an interruption during an initial upload of your brain,
TheBrain will offer to resume from where it was stopped the next time you
synchronize.

3. When the process is complete, just go to the other computer on which you
want to access your brain. Open TheBrain application and log in. From the
list of available brains, click on TheBrain thumbnail, then click the
Download button when it appears.

Figure 305. Download for Local Use

4. To synchronize at any time, click the cloud icon in the menu bar or the
Sync Brain command in the Online menu. The active copy of your brain
will include the latest changes.

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Once your brain has been synced, your brain will be automatically set to auto-
sync. To turn this feature off, click the Sync Status button next to the Cloud icon
in the tool bar.

Figure 306. The Sync Status Button

The Sync Status will also display if local changes or online changes are available
or if the sync is up to date. The last sync date will also be displayed.

Brain thumbnails in your list of available brains will indicate if a brain is local only,
local and online (synced) or online only.

Figure 307. Brain Location Indicators

Editing Your Online Brain

The desktop application has more available features than the web client, but you
can still access and edit your online brains by performing any of the following
activities:

▪ Create and Forget Thoughts

▪ Change thought locations (child to jump)

▪ Unlink thoughts

▪ Set Pins

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▪ Edit Notes

▪ Add Attachments

You can only edit brains that YOU own.

To edit notes in your online brain:

▪ Click in the content area and make any changes you like. The revised note
will be saved automatically as soon as you click on another thought.

Sharing Your Online Brain

All brains synced to https://app.thebrain.com are private and not accessible to
other users without your personal log in credentials. To share a Version 12 brain
with other users:

▪ Open the brain in your local desktop application

▪ Click the Online menu, then click Brain Access and Sharing…

▪ You have two different options for sharing your brain:

o Option 1: Click the Allow Public Access check box and share the Web
Link with others. This is a great option for sharing your brain with a large
group of other users or other users that do not use TheBrain software.
Anyone with the URL will be able to view your brain in read-only mode in
their web browser.
o Option 2: Leave Allow Public Access unchecked and type in an email
address to invite individual users to access your brain. This is a good
option if you want other users to be able to download a local, read-only
copy of this brain to their desktop app. The other users must have
TheBrain installed and be logged in to their Brain account with the email
address you specified.

To prepare your brain to be shared:

1. Activate the thought that you want to be the Home thought when your brain
is viewed. It will be the first thought your viewers see.

▪ Right-click the thought, then click the Set as Home Thought

command

The current wallpaper and color theme will be included in your published brain.

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Figure 308. Brain Access and Public URL

Creating a Brain Archive to Send Your Brain to Others

You can send your brain as an email attachment. To make the attachment as
small as possible, you can use TheBrain’s Backup to Brain Archive feature to
create a compact file.

To create a Brain Archive:

1. Click the File menu, then click the Backup to Brain Archive command.

2. In the Backup to Brain Archive dialog box, select either of the Access
Control options.

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Figure 309. Create Brain Archive Options

3. If necessary, click the Change button to change the file name or the folder
where the archive file will be saved. Do not change the filename extension,
which is .BRZ. Click the Backup button to create the archive file.

Make a note of where you are saving your archive file so that you can locate
it easily when needed.

A brief message will display in the toolbar area as the archive is created.

Brain Archive files are NOT .zip files. You should not use zip file utilities to
modify or access your archive files as doing so may corrupt them.

Copying Thoughts into Other Applications as an Outline

You can copy thoughts from the Selection panel into other programs such as
Microsoft Word or Excel and the thoughts will be formatted as an indented
hierarchical list.

To copy one or more thoughts into another program as an outline:

1. Select all of the thoughts you want to include in the outline (Ctrl-click on a
thought to add it to the selection or use the commands on the Edit menu to
quickly create a selection).

2. Right click in the Selection panel and then click the Copy as Text Outline
command.

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Figure 310. Copying Thoughts as an Outline

3. Open the other application and click where the outline version of the
thoughts should be inserted.

4. Right-click and then click the Paste command on the context menu (or click
the Edit menu and then click the Paste command).

Figure 311. Samples of Outlines Created by Pasting Thoughts from TheBrain

Copying Outlines with Notes

You can copy selected thoughts along with their notes and place them in a
tabbed outline.

1. Select the thoughts to be copied, then right-click in the Selection panel to

open the context menu.

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2. Click the Copy as Text Outline with Notes command.

3. Switch to Word or any other text application of your choice and press Ctrl-V
(or use the program’s command for pasting).

Pasting a Text Outline as New Thoughts

You can select tab-delineated text in another application, copy it, then paste it
into your brain. Each paragraph of text will become a child thought (and possibly
an attachment) of the active thought, based on the formatting of the text.

Pasted outlines may include labels, attachments, and notes. If a URL is included,
it is added as an attachment to the thought in the outline entry above the entry
containing the URL.

How TheBrain converts content from the source file:

▪ Each line that ends with an “Enter” or “Shift-Enter” becomes a thought

▪ A multi-line paragraph with no manual line breaks becomes a thought

▪ Indentation created using tabs show hierarchical relationships

▪ Lines starting with a hyphen (-) are added as notes

▪ Lines starting with a plus sign (+) are added as web link attachments

▪ If a pipe (|) symbol is inserted, content to the left of the pipe will be the
thought name and content to the right of the pipe will become a label (if all
content is in the same paragraph)

Example:

The following text adds a thought named “Steve Jobs” with the label “Founder of
Apple,” a link to Wikipedia, and a note containing a quotation.

Steve Jobs | Founder of Apple

+ http://en.wikipedia.org/wiki/Steve_Jobs

-"I want to put a ding in the universe."

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Figure 312. Example Thought from Text with a Pipe, Link, and Note

Importing Information into Your Brain

Importing Folders and Mind Maps

Figure 313. Importing Folders and Mind Maps

You can import folders and Mind Maps into your brain. When you import a folder,
it becomes a child thought of the active thought.

To Begin Importing:

1. Activate the thought that will receive the imported information.

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2. Click the File menu, then click the Import command.

For a Folder:

▪ Click Folders, select the Add to … button, click the Select Folder button,
navigate to the folder of your choice, then click the OK button. Click the
Import button as soon as it becomes available. Click the next Import button
to confirm that you understand this import can’t be undone. Each folder will
become a thought, every file inside the folder will become and attachment,
and any subfolders will become child thoughts.

For a Mind Map:

▪ Click MindManager (.mmap), select the Add to … button, click the Select
File button, navigate to the file of your choice, then click the Open button.
Each of the topics or ideas will become a separate child thought of the active
thought.

Importing TheBrain 8 XMLs

Version 8 brains that have been exported into an XML format (or properly-
formatted XML that has been generated outside of TheBrain) can easily be
imported back into another brain as a child of the active thought.

1. Activate the thought that will receive the imported XML.

2. Click the File menu, click the Import command, then select the Add to …
button.

3. Click TheBrain 8 XML, click the Select File button, navigate to the file of
your choice, then click the Open button.

Merging Brains
You can merge two brains together by importing a Brain Archive file (.BRZ):

1. Open the brain that you want to merge into another brain, click the File
menu, then click the Backup to Brain Archive command.

2. Note the location for the new .BRZ file, then click Backup.

3. Open the brain that will receive the merged brain, navigate to the thought
where you want the .BRZ file to be added as a child, click the File menu,
then click the Import command.

4. Select the Add to “open brain name” and link to “active thought name”
option, then click Brain Archive (brz) in the list.

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Figure 314. Merging Brains

5. Click the Select File button, then navigate to and open the initial .BRZ file
you created in the first step. Click the Import button. You will be prompted
to confirm that you want to continue, since importing a .BRZ file can’t be
undone.

The only brain that is changed is the one that is open when you begin the
merge procedure. The brain you select during step 1 is not changed at all.

Encrypting Individual File Attachments

You can encrypt individual file attachments within your brain using the Encrypt
command on an attachment’s context menu.

AES 256 bit encryption ensures that without the password, it is impossible to
recover the file contents from the encrypted file—even with administrator access
to the machine where the file is stored on a local computer or remote cloud
server.

Encrypted files cannot be searched and can only be decrypted via Windows and
macOS versions of TheBrain. These files are completely inaccessible even to
your hosting provider whether that be a private TeamBrain Enterprise Server or
TheBrain Technologies Cloud Server.

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 Encrypting Individual File Attachments

To encrypt a file:

1. Right-click the attachment, then click Encrypt in the context menu.

Figure 315. After Clicking on the Attachment’s Context Menu

2. Type in the prompt you want the user to see when they attempt to open the
file, type a password, click the check box confirming that the file cannot be
opened if the password is lost, then click the Encrypt button.

Figure 316. Example Encryption Details

3. Whenever someone attempts to open the file, they’ll see the prompt you
entered. They will have to enter the correct password, then click the
Decrypt button. After that the file can be opened by clicking on it.

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Figure 317. Decrypting and Opening the File

To modify an encrypted file, you will first need to permanently decrypt the file.
The easiest way to do this is to open the document and Save As a new
document. Make and save the new modification and return to TheBrain to
encrypt the new file.

Exporting
TheBrain features several export options. Export your brain data directly to:
▪ Folders—Exports the thoughts in your brain by converting them to a folder
hierarchy.

o Each thought becomes a folder containing the attachments and notes

within it.
o The folder structure attempts to mimic the parent-child relationships
between thoughts with parentless thoughts at the top level.
o Shortcuts on Windows and symbolic links on macOS are used to
represent thoughts that are under multiple parents.

▪ Text Outline (.txt file)—Creates a text outline of thoughts, notes and URLs.

o Indented hierarchy mimics parent-child relationships between thoughts.

o Notes are exported as lines starting with a - (dash)
o URLS are added lines starting with a + (plus)

▪ JSON Files—Exports your brain data in JSON format.

o Thoughts, links and other types of data are each exported in their own
.json file.

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o Attachments and notes are exported into folders based on the ID of the
thought or link they are attached to.
o This gives you access to 100% of your data in an open and easily parsed
modern text format.

To export your brain:

▪ Select Export from the File menu

▪ Select the output (Folders, Text or JSON) and click on Export

▪ The output location must be an empty directory

▪ To export just a portion of your brain, add thoughts first into TheBrain’s
Selection panel and then check the option to Only export the selection in
the Export window.

Figure 318. Exporting a Brain to Folders

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 TheBrain API

TheBrain API
TheBrain can now be controlled by a full-featured REST API. Designed for
experienced programmers, the API opens up a world of possibilities. Access to a
rich set of functions for querying, creating and modifying all types of data is
included. Create thoughts automatically in response to events in the real world.
Automate processes for moving thoughts through a workflow. Implement custom
import/export logic. Control your brain from your watch or with your voice. These
are just a few of the applications that are now open to pursue. Get started now at
https://api.bra.in.

Figure 319. TheBrain API

The available endpoints provide a wide array of capabilities for data access such
as: getting thoughts, links, attachments, and notes, performing searches, and
exploring the network of connections. Write access is also supported so you can

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 Glossary

programmatically create, modify, and delete thoughts, notes, links, attachments,

and more.

To assist you in getting started, we have developed a selection of example

projects in several widely-used frameworks that showcase the process of making
API calls within your program. The Blazor app contains the most example calls.
The Python and Node apps demonstrate the overall structure and creating a
thought.

Glossary
Activate To bring a thought to the center of the plex and make it
the active thought.

Active thought The thought you are working on right now. The active
thought occupies the center of the plex. The active
thought’s details are described in the Thought tab. A
thought that is not active can be activated by clicking it,
its pin, or its name in a list and pressing Enter.

Application A program such as a word processor, web browser,

game, or photo editor.

Backlinks Thoughts whose notes link to the active thought.

Backlinks appear in the content area in a footer under
the notes.

Brain A collection of associated thoughts each of which can

have content. TheBrain can create multiple brains.

Child thought A thought with at least one parent. Children of the

active thought appear in the child zone, below the
active thought. In turn, the active thought is a child of
any thought that appears above it in the parent zone.

Content Area The content area shows content attached to the active
thought or a moused-over thought, depending on the
current preference settings. Content can include notes,
attachments, links, and web pages that display in the
content area’s built-in browser. The content area also
automatically displays an area showing Mapped Links,
Backlinks, and Unlinked Mentions—related content that
has commonalities with the active thought.

Delete The complete removal of a thought and/or its content

from a brain. Deletion is permanent.

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Drag and drop To use this feature, select the item you want to drag,
click the mouse button and drag the item to where you
want it to appear.

Forget To remove a thought from TheBrain without deleting it,

its links, its content, or its note. Forgotten thoughts can
be “remembered.”

Forgotten thought A thought that is removed from TheBrain without

deleting it, its links, its content, or its note. Forgotten
thoughts can be “remembered.”

Gate The active thought and its close relatives have three
circular “gates,” each of which is used to link to a
specific relation: The parent gate is above a thought;
the child gate is below it; and the jump gate is beside it.
A gate is hollow when there are no links through it, and
solid when links exist.

Home thought The Home thought is the main or top thought of your
brain. It is the thought that is activated when you click
the Home button in the Brain toolbar.

Jump thought A jump thought is linked to another thought through its

jump gate and appears in the jump zone to the left of
the active thought. Activating a jump thought produces
a more significant reconfiguration of the plex than
activating a child thought or parent thought. This is
because jump thoughts of the active thought are related
exclusively to the active thought and not to other
thoughts in the plex.

Link The act of connecting thoughts thereby establishing

close relations. Also, the line connecting two thoughts
in the plex.

Link Type A category of links that allows you to distinguish how

thoughts are related visually. For example, you could
have a Link Type called “writes” set so that links
between authors and books display brown with the
label “writes.”

Mapped Links Thoughts that are connected in the plex as parents,

children, jumps, or siblings (but do not necessarily have
text in common). Mapped links appear in the content
area in a footer under the notes.

Navigate To move from thought to thought by activating thoughts.

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Notes Every thought can have notes, which are displayed in

the content area. Notes can hold any combination of
text, images, sound, or shortcuts. The Notes editor
includes a word processor.

Parent thought A thought that has at least one child. A parent thought
is linked to its child thoughts through its child gate. The
active thought is a parent of any thought displayed in its
child zone, below it. Parent thoughts of the active
thought appear in the parent zone, above the active
thought.

Parentless A thought without a parent thought. A parentless

thought thought is often a jump thought or a thought
representing a subject heading or organizer. Usually,
the first thought in a brain (generally named after the
user) is a parentless thought.

Past Thought list The scrollable list of thoughts at the bottom of the plex,
arranged in the order activated. The most recently
activated thought is the rightmost thought in the list.

Pin An entry point to a brain. Click a pin to activate its

thought. A pin is created by dragging a thought to the
area immediately below the menu bar. The pin stays
there until it is removed by being dragged into the menu
bar or title bar. You can also create a pin of the active
thought from the thought menu.

Plex The visible portion of your brain; it includes the active

thought, its close relations, and the links between them.
It also includes the Search box, the Past Thought List,
and navigation tools.

Remember A thought that has been removed from the plex by

“forgetting” can be remembered by selecting Showing
Forgotten Thoughts on the Options menu, right-
clicking the thought, then selecting Remember thought
name on the context menu.

Search box The field in the top-right area of the plex. Type text in
this field to perform an Instant Activation search.

Siblings Two or more thoughts with a common parent. When a

thought that has siblings is active, its siblings are
displayed in the sibling zone, to the right of the active
thought.

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Template A file used as the basis for creating other files.

Template files can be added to the window of the Add
Attachment dialog box.

Thought The basic unit of a brain. A thought can represent

anything the user wants it to. A thought can have
content in the form of a file, shortcut, or web page, or it
can be devoid of content and simply act as a subject
heading or organizer.

Thought Type A way to categorize thoughts and give them distinct

colors. For example, you can have a “Person” thought
type so that all thoughts that are people display as
green.

Timeline The Timeline is the visual tool for using TheBrain’s

built-in calendar. Use it to create, edit, and view events
which can be associated with specific thoughts.

Unlinked Thoughts whose notes contain the name of the active

Mentions thought⎯even if not explicitly linked. Unlinked mentions
appear in the content area in a footer under the notes.

Styles Notes may be formatted using any of TheBrain’s built-in

Styles, which are combinations of font, color, and size.
By default, notes appear in a style called “Modern.”

Unlink Unlink thoughts that you no longer want to be related to

any other thought in your brain, or when you want to
remove a superfluous link. You cannot unlink a
thought’s only Link to the active thought.

URL Universal Resource Locator; the address of a web site.

Wander The option to step randomly through TheBrain, to let

you see thought associations.

Zones Areas in the plex devoted to specific relations of the

active thought. There are four zones: the parent zone
above the active thought, the child zone below it, the
jump zone to its left, and the sibling zone to its right.

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