Enhance your digital brain and integrate generative AI.

9 min readMay 27, 2024

As someone focused on productivity, structuring your notetaking flow and methodology is crucial. If you haven’t yet started using personal knowledge-base note-taking apps, which are also known as synthetic brain or digital brain, now is the perfect time to do so. Especially in today’s fast-paced world, where information overload is widespread and AI development is rapidly advancing, taking advantage of macro-trends like these can greatly enhance your productivity and organization. Additionally, implementing a digital brain enhanced with AI capabilities can help streamline processes and improve decision-making capabilities, leading to better outcomes in both your personal and professional lives as you are able to leverage the power of technology to augment your own cognitive abilities.

Here, I will focus on open-source solutions that are free from licensing restrictions or dependence on a single entity. The recommended software allows users the freedom to modify, distribute, and use it according to their preferences. The security and privacy of your data are crucial factors to consider. I won’t recommend any software if it’s unclear how and where your data is stored. I advise avoiding commercial closed-code solutions and external servers for storing user data. Regarding the selection of software, I strongly refuse to use it.

What is a digital brain?

A “digital brain” or “synthetic brain” in the context of personal knowledge base apps and note-taking software refers to a “second brain” or a “personal knowledge base” (PKB). This concept involves using an app or software to capture, organize, and store your thoughts, ideas, and information in a structured and easily retrievable manner.

The term “second brain” was popularized by Tiago Forte of Forte Labs, who created the Building a Second Brain (BASB) methodology.
A “second brain” app allows you to aggregate and curate a searchable body of knowledge, connecting bits of information to create meaningful context.
It serves as a “backup brain,” providing quick access to notes, documents, quotes, images, and videos, all in one place.
Some popular “second brain” apps include OneNote, Obsidian, Notion, Evernote, LogSeq, Trilium, and Joplin.
The concept of a “digital brain” or “synthetic brain” is about creating an external digital filing system that acts as an extension of your mind, helping you retain and apply knowledge more effectively.

Power Houses of Open Source Note-Taking

As mentioned earlier, I will focus on software that gives you freedom, privacy, and the great possibility of enriching your knowledge base with self-hosted large language models. Three apps, which I’ve chosen, are all great open-source solutions with an active community and dynamic release cycles. Those apps will significantly boost your productivity and creativity if used correctly.

Trilium, a capable beast

Trilium is a hierarchical note-taking application with a focus on building large personal knowledge bases. It offers rich WYSIWYG note editing, including tables, images, and math, with markdown auto-formatting. It supports source code editing with syntax highlighting and seamless note versioning. Trilium provides fast and easy navigation between notes, full-text search, and note hoisting. It also has a touch-optimized mobile frontend for smartphones and tablets.

Trilium allows you to arrange notes into an arbitrarily deep tree structure, and a single note can be placed in multiple places in the tree. It offers strong note encryption with per-note granularity and supports note sharing and publishing. You can sketch diagrams with the built-in Excalidraw and visualize notes and their relations with relation maps and link maps. It also has a REST API for automation.

Trilium is provided as a desktop application for Linux and Windows, with an unsupported build for macOS. It can also be hosted on your server as a web application.

LogSeq, a brain fog killer

LogSeq is an open-source, privacy-first outliner notebook that works on top of local plain-text Markdown and Org-mode files. It lets you record your notes and ideas, write, organize, and share your thoughts, and keep your to-do lists. It has a built-in functional spaced repetition system for creating flashcards.

LogSeq offers note links and backlinks, block references and block embeds, and a task management system. It has a graph view that shows all your notes as a graph, with each note acting as a node and lines showing connections. It also has a journal feature, creating a new daily note for you to empty your thoughts.

LogSeq supports Zotero integration, YouTube and Twitter integration, and an audio recorder. It also has powerful queries and whiteboards. It can be synced using GitHub or iCloud and offers native apps for iOS and Android.

Joplin, a solid companion

Joplin is an open-source, secure, and free note-taking and to-do application. It can handle a large number of notes organized into notebooks and supports images, videos, PDFs, and audio files. It offers end-to-end encryption and has a web clipper extension for Chrome and Firefox to save web pages or take screenshots as notes. Joplin also has a mobile app for Android and iOS.

Joplin can be synced across devices using Joplin Cloud or other services like Dropbox, OneDrive, Nextcloud, S3, or any WebDAV, including NextCloud. It is available on Windows, macOS, Linux, Android, and iOS. It also has a terminal app!

What happens next?

All three of the presented apps are amazing solutions to improve your methodology and quality of note-taking. Every app approaches it from a slightly different angle and style, meeting the needs of different individuals. Consider trying out each app to see which one aligns best with your personal preferences and workflow. Each app offers unique features that may enhance your overall note-taking experience. While you continue to populate your knowledge base with more information, the next exciting step can be taken, which is the use of generative AI, known as large language models, which are capable of analyzing your notes and generating summaries, insights, and even new ideas based on the content you have inputted. This advanced technology can further streamline your note-taking process and help you extract even more value from your notes.

The future must be decentralized!

Information is power; the idea of centralizing that power in the hands of a few corporations is concerning. As we move towards an increasingly digital existence, our data, our privacy, and our right to knowledge should be considered fundamental human rights. By relying solely on commercial, closed-source AI tools hosted by a handful of massive corporations, we surrender control over our data and our digital freedom.

Imagine a future where we are all free to use our own self-hosted digital brains, enhanced by generative AI systems that we control, a future where we are not bound by the limitations and biases of commercial tools, where we are not locked into a specific platform or service provider. A future where we are not at the mercy of tech giants who decide what we can and cannot do with our data.

Now imagine the opposite. A future where we are dependent on a small number of companies for our digital brain needs. These companies become authoritarian hegemons, dictating the direction of global development. They control the flow of information, influence our decisions, and shape our worldviews. Our data becomes their commodity, and our privacy is sacrificed for convenience.

The choice is clear. By embracing decentralization, open-source software, and self-hosted solutions, we take back control. We ensure that our digital brains are tools of empowerment, not instruments of control. We foster innovation, creativity, and diversity. We protect our rights to privacy and knowledge.

In a future when we are free to explore, create, and innovate without compromising our fundamental rights, we can work toward a society where our digital brains are as distinct and varied as our biological ones. A decentralized future guarantees that no one entity has control over our digital lives, empowers individuals, and encourages competition.

Now is the final time to embrace the potential of decentralized, self-hosted, open-source solutions. It is time to ensure that the future of our digital brains is one of freedom, privacy, and endless possibilities.

An example from the wild

In the past few months, I’ve been working with one company to create their internal knowledge base from a myriad of unstructured, incomplete, and multiple unrelated instances of data. I’ve decided to use Trilium for that because its web interface is user-friendly, even for individuals who are new to the idea of knowledge bases and complex note-taking. Also, it can be easily self-hosted and elevated by an external tool via the REST API.

On top of the structured data collected in Trilium, we’ve been able to create a set of AI tools by using self-hosted instances of Mixtral and Llama 3 needed to implement RAG. This type of approach has a number of advantages:

Data Control and Security: With Trilium, you have complete control over your data. You don’t have to worry about your notes being stored on someone else’s server, and you can access your information offline. This ensures data security and privacy.
Self-Hosted and Customisable: Trilium is self-hosted, and you can easily set it up on your server. It is highly customizable, allowing you to modify the design to your taste and create custom templates for specific note-taking needs.
User-Friendly Interface: Trilium has an intuitive user interface, making it easy to take detailed and structured notes. Its WYSIWYG editor and easy file management features enhance the note-taking experience.
Easy Installation: Trilium is provided as a desktop application for Linux and Windows. It can also be installed and run on your server as a web application. The installation process is straightforward, and detailed instructions are provided on their GitHub page.
Scalability: Trilium scales well in both usability and performance, even with upwards of 100,000 notes. It can handle large personal knowledge bases efficiently.
Rich Feature Set: Trilium offers rich WYSIWYG note editing, including tables, images, and math, with markdown auto-formatting. It supports source code editing with syntax highlighting and seamless note versioning. It provides fast and easy navigation between notes, full-text search, and note hoisting.
Collaboration and Sharing: Trilium facilitates collaboration and sharing. It allows you to sync your notes across devices and has a web clipper for saving web content easily. You can also share and publish notes on the public internet.
Security and Privacy: Trilium offers strong note encryption with per-note granularity, ensuring the security and privacy of your data. It also has the concept of “protected notes,” requiring a password to be entered every 5 minutes, adding an extra layer of security for sensitive information.
AI Integration: Trilium has a REST API for automation, allowing you to integrate it with external tools and AI systems to enhance your knowledge base.
Diagramming and visualization Trilium lets you sketch diagrams with the built-in Excalidraw and visualize notes and their relations with relation maps and link maps.

The overall knowledge base created with Trilium and elevated with a self-hosted AI now serves as a super-knowledgeable chat assistant with a quick product and offers references, a document enhancement tool, an internal training tutor, a price update system, a social media content creation companion, and many more.

Final words

Advantages and features that Trilium supports are also mainly available in LogSeq and Joplin, not necessarily in the exact same form, but the majority of pipelines can also be implemented in those two other apps. In my article, presenting a recent use case, I wanted to introduce you to a concept and give you an insider idea of how open-source tools can be utilized to increase multiple aspects of your personal and professional life, as well as the structure of small and medium businesses. By exploring these tools, you can enhance your organization, productivity, and creativity through efficient note-taking and knowledge management. Utilizing open-source tools like Trilium, LogSeq, and Joplin can provide a flexible and customizable solution for your unique needs. Additionally, structuring your knowledge base, no matter if it’s personal or in your organization, will help you stay organized and easily access information when needed, always giving you the possibility of elevating it with large language models in the future, for yourself and for future generations.

References:

Trilium: https://github.com/zadam/trilium

LogSeq: https://logseq.com, https://github.com/logseq/logseq

Joplin: https://joplinapp.org, https://github.com/laurent22/joplin/