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Rediscovering Heptabase

Published: at 15:02


There’s a saying that goes, “The greatness of a horse can be seen in its long journey.” Reflecting on Heptabase, a software that I have been using and recommending for two years, I ask myself – does it still possess the unique charm it had at the beginning? Is it still the most suitable tool for me? Have I gained new insights into it? I feel it’s necessary to reassess it.

This article is for those who are interested in Heptabase, as well as current and former Heptabase users. However, if you know very little about the basic functions of Heptabase, I suggest you read the Public Wiki and PJ’s “Complete Introduction to Heptabase – The Visual Learning Software That Lets You Enter the Flow with Cards and Whiteboards” before proceeding with this article, as it may be more helpful to you.

Table of contents

Open Table of contents

Defining Heptabase

Humans have been adept at labeling or ‘defining’ things to facilitate their cognition and reduce the wear and tear on brain cells since ancient times. This is because the human brain, when processing information, tends to look for the most energy-efficient methods. By categorizing things into known and simple groups, people can understand and respond more quickly. After labeling, it not only helps individuals quickly understand things, but also guides and regulates individual behavior to a certain extent, in line with the expectations and standards implied by these labels.

Therefore, before reevaluating my understanding of Heptabase, it is necessary to define it first.

  • Make sense of complex topics.
  • Heptabase empowers you to visually make sense of your learning, research, and projects.

On the official website of Heptabase, it is defined in two ways: one, to understand complex topics; two, to visually comprehend one’s learning, research, and projects.

This seems more like a definition of a tool, i.e., a tool that can help users learn and conduct research more effectively and intuitively, enabling them to delve deeply into topics closely related to themselves.

This is also what Alan Chan, the co-founder of Heptabase, has been tirelessly proclaiming. Whether it’s in his series of articles “My Vision,” his interviews with Ness Lab, or his shared experiences.

Indeed, in the process of using Heptabase, I have profoundly felt a kind of “magic,” just as Alan has promoted.

When I first encountered Heptabase, it gave me the impression of a visual whiteboard note-taking tool that could help me manage knowledge better. At that time, due to the whirlwind of knowledge management and Zettelkasten note-taking methods brought by “How to Take Smart Notes” and Roam Research, there were tools like Notion and Obsidian dancing gracefully abroad, and tools like flomo and Siyuan leading the way in China. There were many note-taking tools for knowledge management, but only Heptabase added the visualization whiteboard into the mix. For a while, it was the center of attention, an astonishing innovation, but it also trapped me in this stereotype for nearly a year.

It was not until I began to contemplate building my own LifeOS that I woke up from this dream – Heptabase is not just a visual whiteboard note-taking tool. It subtly changed my understanding of knowledge management, connecting more links between different fields.

If I were to define Heptabase, I would say:

Heptabase is a visual note-taking tool based on cards, whiteboards, and tags that helps me build a deep understanding of complex issues from a mesoscopic perspective.

Next, let me explain why I define Heptabase in this way.

Heptabase as a Note-Taking Tool

Despite the extravagant descriptions by its official representatives or by users like myself, it’s essential to demystify Heptabase. At its core, Heptabase is a note-taking tool. But I would add that it is an adept one.

Four Key Features

Mr. Zhao mentioned in “The Modern Guide to Digital Note-Taking”:

Our note-taking tools allow us to record thoughts, establish connections, generate new ideas, and continue this cycle in what seems like an endless game.

Embedded in this idea are four features that a note-taking tool must have:

When evaluating Heptabase, it’s clear how it performs in these areas:


Besides analyzing the four features, I’d like to discuss why Heptabase is a competent note-taking tool based on its functionality.

Heptabase’s primary functions revolve around its Journal, Map (whiteboard system), Card Library, Tag system, Task management, and Highlights system, with an AI feature in redevelopment to be reintroduced later.

The Journal ensures that Heptabase has the characteristic of being ready for writing immediately upon opening. I often use it as a scratchpad and for intermittent diary entries and assisting with writing.

You might question how this differs from Evernote, Notion, or Obsidian, which also allow writing upon launch. The key difference is that Heptabase does not require you to classify your notes initially or even later during organization. With the other tools, after completing a note, you need to decide where to store it or what tags to apply for efficient retrieval later.

For instance, after jotting down a note in Notion, I have to consider which Page it should be placed on for future reference. Similarly, with Obsidian’s traditional, folder-based structure, you must think about organization post-writing.

With Heptabase, after recording something in the Journal, there is no need to immediately think about tags, attributes, or categories. When the need arises, the content naturally finds its place, whether integrated into another note through “link to block” or mentioned on a card or whiteboard. This convenience in data organization is unparalleled by other note-taking tools at this stage.

Furthermore, the complementary Map and Tag systems offer a wealth of possibilities for data organization. I can use nested whiteboards within Heptabase to structure topics internally, sections to categorize cards or text elements, mind maps for brainstorming and developing an understanding of a topic, and lines to represent the current state of my thoughts. Tags offer another dimension to organize notes, managing notes with high homogeneity, displaying massive amounts of information at once, and enabling incremental or evergreen note management.

Through this analysis, I confidently declare that Heptabase, as a note-taking tool, is comprehensive and efficient, meeting the many demands of modern digital note-taking.

This brings us to Heptabase’s mostdistinctive feature – the mesoscopic perspective, which is a unique vantage point that reshapes the way we interact with information.

The Magic of the Mesoscopic Perspective

A Multi-layered Cognitive Structure

Within Heptabase, bidirectional links, the whiteboard system, and the tagging system collectively form a multi-layered structure for knowledge management.

Bidirectional links function at the micro level, allowing users to create direct connections between individual knowledge points. These links turn isolated pieces of information into a dense network of interrelated ideas.

At the meso level, the whiteboard system provides a spatial method of organizing knowledge. Users can arrange knowledge points across a broader canvas on the whiteboard, visually exploring and defining the relationships between them. This spatial organization aids in flexible and intuitive thinking and understanding.

Similarly, the tagging system operates at the meso level. It allows users to categorize knowledge points and map out a larger structure of knowledge through the relationships between tags. By using tags, users can quickly filter, discover, and relate relevant information.

Finally, at the macro level, users utilize bidirectional links, whiteboards, and tagging systems to build a comprehensive knowledge framework. This framework involves not just the classification and hierarchy of knowledge but also a deep understanding of how different pieces of knowledge interact and generate new insights. Management at the macro level helps form a global view, allowing users to see the overall landscape of their knowledge fields and how they interconnect.

These tools, working together across different levels, allow Heptabase to transform from a simple note-taking tool into a powerful knowledge management system that adapts to different levels of thinking and organizational needs.

Features and Effects

The mesoscopic perspective is pivotal within Heptabase’s multi-layered cognitive structure. It balances between the micro view of individual knowledge points and the macro view of organized knowledge, helping users understand how discrete pieces of information can be transformed into structured knowledge and how personal actions and technology can facilitate this transformation.

The hallmark of the mesoscopic perspective is its balance between focus and context. It provides better contextual understanding, helping us to see the place of individual notes within a larger knowledge framework while understanding the causality, relevance, and importance of each piece of information.

Moreover, the mesoscopic perspective encourages the integration and connection of knowledge, aiding users in identifying and establishing links between different knowledge points. This extension from isolated notes to related concepts promotes a comprehensive and deep understanding of knowledge. Additionally, the mesoscopic view balances detail and the big picture, ensuring that our personal knowledge management is neither lost in the details nor overlooks important knowledge points, allowing for both depth and breadth in our understanding.

Based on these balances, the mesoscopic perspective naturally brings about multiple positive effects. It promotes flexible thinking, allowing us to shift easily between levels of thought, view problems from different angles, and enhance creativity and problem-solving capabilities. It also facilitates the rediscovery and reuse of knowledge, organizing it into an interconnected network for easier future retrieval and reuse.

In summary, the mesoscopic perspective helps us create a unique and personalized knowledge structure. It provides enough flexibility to organize knowledge according to our cognitive style and needs, creating a truly personal knowledge system.

The Mesoscopic Perspective as a Bridge

This analogy might seem abstract at first glance. So, let’s visualize the mesoscopic perspective as a bridge, one end anchored in the realm of minute, microscopic details and the other extending towards a comprehensive, macroscopic understanding.

  1. Enhanced Contextual Comprehension:
    • At the bridge’s ends: On one side, there are individual notes, akin to the bricks of knowledge. On the opposite end lies the overarching framework of knowledge.
    • The mesoscopic bridge: It aids users in understanding how each note not only stands alone but also fits within the entire knowledge structure.
  2. Facilitating Knowledge Connection and Integration:
    • The structure of the bridge: The bridge’s deck allows different knowledge points to cross paths, much like pedestrians meeting on a bridge.
    • The mesoscopic bridge: It enables the creation of relationships between various knowledge points, thus forming a coherent network of ideas.
  3. Balancing Detail and the Big Picture:
    • The view from the bridge: Standing on the bridge offers a view of the river’s details below and the expansive landscape in the distance.
    • The mesoscopic bridge: It assists users in paying attention to details while also keeping an eye on the larger context.
  4. Encouraging Flexible Thinking:
    • The pathway of the bridge: The bridge allows for free movement between its two ends, offering varied perspectives.
    • The mesoscopic bridge: It facilitates a flexible transition between different levels of thinking, encouraging innovative and creative thought processes.
  5. Easing Knowledge Rediscovery and Reapplication:
    • The guidance of the bridge: The bridge directs travelers, leading them to discover new routes and destinations.
    • The mesoscopic bridge: It organizes knowledge in a navigable structure, enabling users to easily rediscover and apply information when necessary.
  6. Supporting Personalized Knowledge Structures:
    • The design of the bridge: Every bridge is uniquely designed, tailored to fit its environment and the needs of its users.
    • The mesoscopic bridge: It provides the flexibility for users to craft their own approach to knowledge organization, in harmony with their cognitive preferences and requirements.

In Heptabase, the mesoscopic perspective helps users transform granular notes into logically structured, hierarchical knowledge, enhancing the efficiency of comprehension and application. This not only aids in understanding and memorization but also promotes the innovative use of knowledge, making it more conducive to users in constructing a profound understanding.

Establishing a Deep Understanding

As Alan Chan emphasized in his interview with Ness Lab and through his shared insights, Heptabase’s vision is to create a world where everyone can effectively build a deep understanding of anything.

What is “Deep Understanding”?

What then, constitutes a “deep understanding,” and what is its essence?

I believe that cultivating a deep understanding generally refers to achieving a comprehensive and in-depth grasp of a particular subject or concept. This level of understanding goes beyond a superficial acquaintance with facts, encompassing the core principles and finer details, and the ability to apply this knowledge in new contexts.

This means that to foster such depth, one must achieve the following:

  1. Principles Understanding: This is the foundation of deep understanding. Comprehending the principles of a concept means understanding how it works and why it functions the way it does. This type of understanding enables us to analyze and solve new problems fundamentally, not just apply surface-level rules or formulas.
  2. Critical Thinking: This is the ability to evaluate information and arguments, requiring us not to accept any premise as truth without scrutiny, but to form our own conclusions through analysis and evaluation. This capability is crucial for identifying misinformation, assumptions, and logical fallacies, helping us establish a more solid and reliable foundation of understanding.
  3. Application Capability: The ability to apply knowledge to new situations is a critical measure of deep understanding. This is not mere repetition of knowledge but involves adapting and applying it under different conditions and contexts.
  4. Innovation and Creation: Innovating and creating based on existing knowledge is an advanced stage of deep understanding. This requires not only an understanding of current knowledge but also the ability to generate new ideas and solutions on that basis, pushing the boundaries of knowledge further.
  5. Cross-connections: Integrating knowledge from different fields to form a comprehensive understanding can help us view problems from a broader perspective. This interdisciplinary understanding is key to solving complex issues.
  6. Communication and Expression: The ability to convey complex concepts clearly and accurately to others is a significant aspect of deep understanding. It not only helps others comprehend your ideas but also serves as a test of whether you truly understand a concept yourself.

In short, the essence of “deep understanding” means not just remembering facts and information, but understanding the reasons, processes, and connections behind them.

To build a deep understanding using Heptabase, PJ suggests the following:

  1. Breaking downcomplex knowledge into many atomic concepts is crucial for establishing deep understanding.
  2. ”Atomic” concept cards should not be limited to having just concise content; rather, it’s about each card supporting a single concept thoroughly.
  3. Each atomic card and its corresponding Section group must be thoughtfully named. The goal is to convey the core concept of the card in a phrase so that your future self can instantly grasp what the card or group is about.

Based on PJ’s suggestions, I’ve come to understand that cultivating deep understanding with Heptabase can be broken down into six actionable steps.

Step One: Decomposing Complex Knowledge

The journey to deep understanding begins with breaking down complex knowledge into smaller, more digestible parts. This makes it easier to comprehend the meaning and interrelation of each part. Heptabase’s card system is perfectly suited for this method as it allows you to articulate each concept or knowledge point on an individual card.

Step Two: Crafting Concept Cards

At this stage, you create a card for each atomic concept and tag it accordingly. Tags can include definitions, attributes, examples, or connections to other concepts, aiding in future retrieval and review.

Step Three: Organizing Cards

Using Heptabase’s whiteboard feature, you can organize related cards together into knowledge blocks (sections). This visualizes the logical relationships and promotes understanding of the overall structure.

Step Four: Naming Groups and Inductive Summarization

For each knowledge block (section), give a descriptive name and create an inductive card or mind map. This helps summarize the core ideas of the block and deepens your understanding of its content.

Step Five: Review and Iteration

Regularly reviewing and iterating on your cards and sections is key to solidifying deep understanding and long-term memory. Continuously deepening your understanding through this process allows for adjustments based on new insights.

Step Six: Linking and Expanding

Finally, by identifying and establishing connections between different cards and sections, you integrate new knowledge into your existing framework. This helps form a coherent and comprehensive knowledge network.

Subtle Achievement Through These Steps

Through these six steps, users gradually achieve the following:

  1. Knowledge Accumulation: Step by step, you build a comprehensive and detailed knowledge repository through decomposing complex knowledge and creating concept cards.
  2. Internalization of Knowledge: By naming groups, creating summaries, and regular review, you deepen your understanding and incorporate the knowledge into your thought process.
  3. Formation of Wisdom: Through iterative expansion and integration of knowledge, you not only deepen your understanding of existing knowledge but also assimilate new information and perspectives, leading to more complete and profound insights. This process fosters innovative thinking, aiding you in applying your knowledge flexibly when facing practical problems.
  4. Dynamic Learning Process: Heptabase’s design, with its flexibility and interactivity, provides a platform conducive to continuous learning and exploration. You can adjust and optimize your knowledge system according to your learning pace and interests, making the learning process a dynamic and ongoing journey of discovery.


My understanding of Heptabase may still be incomplete or even one-sided. Nevertheless, it is undeniable that as I reevaluate it from the current standpoint, Heptabase, with its unique visualization of cards, whiteboards, and tags, offers me a mesoscopic perspective that allows me to discern connections amid a sea of information, construct knowledge systems, and achieve deep learning and understanding.

Heptabase is not just a tool; it’s a methodology, a way of thinking, a force for personal growth and development.

I hope that my renewed understanding of Heptabase can provide some inspiration and assistance to friends and users interested in it.

If you wish to try Heptabase, you can claim a 7-day free trial via this link.