Where Is Your Second Brain?
I've been working on my second brain for years - but it's all over the place! This is a huge problem - I have notes and documents everywhere.
A second brain is a personal knowledge management system for your ideas, tasks and information.
I've got info in Office docs and OneDrive and OneNote and Google Docs and Google Keep and Amazon Photos and Raindrop and screenplay files and even Facebook. (But not X, never again X.)
Ok, so my brain was a mess. It was time to pull it all together.
This is my journey from chaos to a useful, helpful, enjoyable second brain.
TL;DR — My second brain is a set of notes and files managed by Obsidian, synchronized by OneDrive and OneSync, using Claude Code for automation and research assistance.
First Stop, Visual Studio Code
I'd seen people mention VS Code as a place to manage non-code projects. I have an (ancient) developer background, figured I could muddle through things and check it out.
And for me, it worked! VS Code is free and there are plenty of free VS Code extensions to make the environment more useful for screenplay writing, doc writing, note-taking and task management. Extensions for Kanban boards, viewing Office files and images, spelling, grammar and more.
My second brain started as a simple folder structure containing files. Markdown files, office docs, images and more. My screenplays are written with Fountain which is a great, markdown-style format for a second brain.
Markdown is a lightweight way to format plain text using standard keyboard symbols. It's an open alternative to using proprietary file formats that lock you in to specific vendors.
Markdown files are a perfect choice for creating your second brain - but start with what you have! You can create or convert files to markdown later as needed.
Now I can open VS Code and boom - there it all is! Home inventory, hobbies, finances, screenplays, world bibles and more. It opens quickly and I can view any file within in a second. You don't have to open each file in it's own program anymore. I am Speedy Gonzales.
It was humble beginning for my second brain.
OneDrive for Sync and Backup
To build my second brain, first I went through all the important projects and docs I've been storing. Moved everything I felt qualified from my hard drives, OneDrive and Google Drive.
Now my second brain is just another folder in my OneDrive. This ensures my brain backs up to the cloud and is accessible from all my devices.
OneDrive offers 5GB of storage free, Google Drive offers 15GB. My second brain is currently 3GB in size.
(I do have a OneDrive subscription though, part of a Microsoft Alumni subscription from a past job with Microsoft.)
Some people, particularly developers, prefer to use Git to manage their second brain.
Git is a versioning system for tracking file edit history in a repository.
Git works with any kind of files, not just code, but has a steep learning curve. I want my second brain to be easy to use and available to my family when needed. So, no Git for me.
Oh and although OneDrive does "back up" my files, I do like to take my own back up of it occasionally. With cloud services you just never know.
Adding The AI That Is Claude
I've been using a variety of AI tools for a while; understanding their capabilities and limitations. Copilot, Gemini, Perplexity, Ollama, and others.
I particularly enjoy finding the limitations of AI. Once, AI hallucinated a whole set of academic researchers and their (non-existent) papers when I was researching time travel for a TV series I'm working on. It was a frustrating moment that became hilarious once I realized what had happened.
It is not mandatory or required to use AI with your second brain. I find it helpful. You can skip it entirely.
Claude gradually migrated to the top of my AI tool list and stayed there for months, for a number of reasons. It became my go to AI for almost everything. Of course it still has limits, but it's been better than the rest for me.
Asking Claude to use loops and test results until they meet criteria is particularly compelling. In the developer world this is called the Ralph Wiggum Loop, but anyone can use this technique for research prompts too.
I bit the bullet and subscribed to Claude Pro; apparently Claude Code would integrate nicely with VS Code. (And Obsidian as I was to find out later.)
Claude Code is included in Claude Pro and other subscriptions.
I asked Claude to find all of my To-Dos and put them in a Kanban board, make suggestions on my active writing projects about what needs work. It did a great job of that and more.
Claude helps with my organizing, re-tagging, fixing things, connecting the dots between my notes and just generally keeping myself better organized. An incredible assistant, really.
My favorite Claude moment: I told it about my closest friends and family by name, asked it to dig deep into my notes and prepare a dossier, with links to sources, on each of them. It was amazing and eye opening what it found, the connections it made, including some insightful conclusions.
(FYI I did this later, after I had consolidated more of my second brain using the Obsidian Importer.)
The Limitations of my VS Code Second Brain
Even with Claude, I faced serious limitations using VS Code to get the full benefits of my second brain.
I desired a mobile app that works with my second brain content. In particular I wanted to take notes and images, edit my screenplays and read/add/edit tasks in my Kanban boards.
Sure I can browse my files in OneDrive, but it doesn't offer a markdown-friendly editing environment. Markdown files are just text-based, but a good markdown editor will provide many conveniences and viewing options.
There are an increasing number of Markdown-capable apps out there, but generally they aren't for working with a set of markdown files with links between, shared tags, etc.
If I'm being honest, VS Code isn't a full markdown environment either. It can edit markdowns, but has limits when you are using markdown files as a comprehensive set of documents about your life.
Plus, several of the extensions were buggy or lacked polish. The Office document viewers for example often made a mess of things when viewing simple DOCX or PPTX files. A fine experience for developers I guess but for me, this was the bulk of my second brain content so far. I was disappointed.
Oh, and I still had tons of content distributed in several of those proprietary apps I mentioned above (OneNote, Keep, Facebook). How was I going to get all of that useful content in my brain?
The Obsidian Upgrade
I was encouraged by several acquaintances to try Obsidian with my new second brain I had built in Visual Studio Code. Not just one person, but a half dozen suggested I check it out. I looked around online and noticed a lot of happy people using it.
At first, Obsidian scared the heck out of me.
Several years ago I used OneNote for all of my notes, and made a lot of notes there, but they became big and cumbersome and took too long to navigate and use. OneNote was great for family sharing, and I do still keep information there, but Google Keep became my preferred daily note taker.
I first used Obsidian a couple years ago and it scared the heck out of me. (I dabbled with Notion as well, but that's a tale for another day.)
I installed Obsidian on my Android phone and couldn't figure out what I was supposed to do with it, or what all the little toolbar buttons do. After a few days I uninstalled it, unimpressed, and went back to Google Keep.
Start Obsidian on your desktop or laptop.
With that mobile Obsidian experience in the back of my mind I decided to install Obsidian for Windows and explore it there first.
I pointed it at my OneDrive second brain folder and called it my 'Vault', an Obsidian term.
Ok, this is not too bad. Very familiar to what I was doing with VS Code.
Wonderful Writing and Second Brain Plugins
I installed several writing plugins into Obsidian making it easier to view, edit and manage my content. Oh wow... the Office file viewers are way better than the ones I have installed in Visual Studio Code! Found a great Fountain plugin for my screenplays and another for Kanban task boards.
Then I found Claudian, which connects Claude Code to your vault! Oh this is beautiful. Claude is so helpful with second brain management.
I don't like using Claude to create content - when I see it used that way it often gives me the 'ick' - but it is great for research and helping to fix broken technical things.
I'm not sure where I got the advice, perhaps it was Claude, but I came across a recommendation to create a CLAUDE markdown file in every key folder in your vault, with instructions for Claude Code about how things work in that area. Apparently it will read all of the Claude files in the folder hierarchy above as context when you are working in a particular project/folder.
I asked Claude to create those files using all of the knowledge it could figure out from the files in each folder. Then, any time Claude and I figure out something important together in a project, I ask it to update CLAUDE so it remembers this information the next time.
Occasionally I'll add some information or context to those files myself. About my environment or preferences, things that help Claude understand my needs.
Markdown For The Win
Now I'm creating new Markdown notes and tasks with ease and when I drag and drop files between folders or rename things, Obsidian updates all of the links referencing those files.
I can focus on capturing my thoughts and putting things in an (ever-evolving) structure that works for me, and Obsidian just takes care of it. Adding links to my thoughts becomes super easy as I learn a few keyboard shortcuts.
This is great! I don't even have a mobile environment yet, but my second brain just got easier and more fun to use.
Oh and all of those plugins I installed, they go right into the vault, which is in my OneDrive folder structure.
This means if I want to use Obsidian on another laptop or desktop I simply set up OneDrive and Obsidian, sync my files and everything is ready to go.
OneSync for Android Sync
I really wanted to access my second brain on my mobile device, a Google Pixel.
I figured out that Obsidian mobile would want to have my vault on the device, not just available via a cloud service.
OneDrive doesn't really sync files onto an Android device. It's an app that lets you download or upload files, but not copy a whole tree onto your phone.
With a bit of research I discovered OneSync from MetaCtrl, which in it's free tier will sync one folder structure from OneDrive to your phone. Perfect!
Obsidian Sync will also do this, with a subscription.
It looks like Obsidian Sync offers additional capabilities as it understands the vault file/folder structure. I may look into this more deeply later.
OneSync unfortunately doesn't sync when files change, it follows a schedule.
I do a force sync in the app before using the mobile app and after, when I am switching between my laptop and my phone and want my new files to be immediately available.
I will also turn off OneSync automated sync any time I'm doing experimental work with large folder renames and moving lots of files around in my vault.
I find it faster to do large file and folder modifications on my laptop instead of on my phone, such as tag modifications or folder renames. Bigger CPU, faster disk.
Obsidian Mobile
Now that my Obsidian vault is ready-to-go on my phone, it's time to install Obsidian and see how things work.
Holding my breath, I run the app and point it my vault folder. And the first time I used the mobile app, it simply worked - there was my second brain!
Wow - I'm super excited at this point. I'm browsing my markdown notes, opening Office docs - and they all just work. I'm flabbergasted.
Remember how all of those plugins are in the vault? Well, most of them worked immediately on mobile, which is freaking awesome. Vault Lens in particular could view all my Office files without issue, and they looked far better than the extension I was using with VS Code. Very snappy! Much faster than opening files in another app.
The Fountain plugin I installed didn't work on mobile. There was another one thankfully, which worked perfectly on mobile and PC. Now I can edit my screenplays on the go!
This time I'm using the mobile environment and things make more sense to me. The desktop app helped me better understand how Obsidian works. Now with some content in my vault to browse, I understand the mobile app much better.
The biggest limitation on mobile? The Claudian plugin does not work. There are no Claude Code features or plugins compatible with Obsidian mobile that I can find.
FYI, occasionally a plugin will need to be reinstalled on the other device when I first set them up. Something about syncing plugins via OneDrive and OneSync may not be perfect, or perhaps the sync timing doesn't pick up everything.
Thankfully, reinstalling the plugin has fixed all of these kinds of issues thus far.
Grabbing Brains with Importer
Now I've got all my office documents and some markdown files in my second brain, but a ton of knowledge is still locked away in proprietary note apps.
I thought, perhaps a plugin might help? And yes it did! It's called Importer.
The Importer made it very easy to import all of my OneNote files and all of my Google Keep notes. An hour or so later, it was all done! Years of work, distributed, are consolidated in one place.
They are now a huge part of my second brain. I had over a thousand notes in Google Keep, they transferred over very nicely.
I was even able to import my Facebook posts using the Importer against a Facebook HTML export of all my stuff, but it wasn't as elegant and had linking errors afterwards. (Paths were inaccurate, video embeds weren't playing properly.) Sigh.
Plot twist: I told Claude about my troubles and shortly after the links and video embeds were all fixed!
Even though my Facebook content came through eventually, the formatting of it all leaves something to be desired - Importer just provides a generic HTML import feature. Perhaps one day there will be a Facebook importer that works a little better.
Oh and I came across another useful plugin for importing Raindrop bookmarks!
Photos are Big, Really Big
Incidentally, it is worth thinking about where photos fit into your second brain. I have many gigs of photos going back decades - around 1TB in total.
I use Amazon Photos to store them all, and my wife and I sync new photos there every day.
Do I want my second brain to be over 1TB in size? Absolutely not. Not with today's technologies. Don't even think about stashing all videos in here either.
I don't store my photos and videos in my second brain, only photos referenced by my notes and some photos and videos imported from social media posts.
Maybe one day it will all fit, but that day isn't today.
Text and audio files are nice and small and perfect for your second brain.
Improving Claude Mobile with my Second Brain
This section gets a bit technical and can be skipped if that's not for you.
Now I've got Obsidian working everywhere.
But I have this limitation, Claude mobile doesn't know about my Obsidian vault.
One of my big AI desires, since these AI apps have become prevalent, is to be able to ask my AI assistant to add a task to my task list.
In my preferred note-taking app! Is that so much to ask?
I was browsing one of my socials and came across a conversation about MCPs for Obsidian. I had never heard of these things!
An MCP (Model Context Protocol) server is a standardized bridge that connects AI models to external tools, databases, and files.
Wow - I had just started with Obsidian, quickly found out about MCPs, and then I found this one which claimed to support Claude on mobile: Obsidian-web-mcp. Could it be true?
Well, it was not easy, but eventually I set up the MCP server and got it running. Then I configured a Claude Desktop connector to talk to it.
It took a long time, and Claude Code helped me out a lot. The UIs changed since the docs were written, including important terminology. But eventually, it all WORKED!!
I went to set up the mobile app and discovered it doesn't have manual MCP Connectors, apparently a UI limitation. Claude recommended setting up the connector in the Claude web UI and that worked well with my existing Tailscale setup.
Shortly thereafter, my MCP connector to my Obsidian vault showed up in Claude Mobile! I was not expecting this to happen, it was a pleasant surprise.
It is not quite as fun or powerful as using Obsidian with Claudian on PC, but Claude mobile can now interact with my vault from my phone which is freaking awesome.
Claude on Desktop or Mobile?
Between using Claudian in Obsidian on a PC and using the MCP connector via the mobile app I much prefer Claudian. It can do much more with every file in my vault as it is basically Claude Code.
Me: Add a task to remind me to pick up flowers for Dawn.
Claude Mobile: Sure!
Using the MCP connector occasionally makes it ask a lot of follow-up questions and I'm just like go figure it out Claude why are you asking me. 
However, for capturing a note or adding tasks to my vault while I'm on the go, Claude mobile gets the job done.
Me: Could you summarize what we've discussed and learned in a new note in my vault?
Claude Mobile: Sure!
In Conclusion
I've been living and breathing Obsidian and Claude for the last week and my wife claims to be missing me. I'm very excited about the possibilities here - already I've done so much automated vault housekeeping and knowledge creation it feels crazy.
Thanks with sticking with me until the end! I hope you've learned a few things and encouraged you to try assembling your second brain.
Good luck and have fun!
Pulling It All Together, a Brainy Example
13 years ago I wrote and published an eBook called Zombies Evolved. I had to go through a huge amount of effort to understand eBook publishing formats, specialty apps and workflows to build an eBook correctly. Honestly, it was painful.
A few days ago, I asked Claude to check out my Zombies Evolved project (in my second brain) and recommend a workflow to convert my book's DOCX file into Markdown and then generate an epub and pdf version of the book.
It all looked pretty reasonable, so I asked Claude, "can you do this for me?"
The answer, of course, was yes. "I can do almost all of these steps for you. I need you to install a few apps first, but then I should be able to do everything else."
Thirty minutes later, it was done.