u/IndubitablyPreMed

Hello all,

I am a fourth-year medical student in the process of creating my clinical notebook (a collection of all my medical information received over the years to help me prepare for patients). I carry this with me my whole career and add to it.

I originally built a private LLM using Claude as my guide, but every time Ollama updated, it changed my docker settings and I’m not savvy enough to constantly update it to work.

I then found Obsidian; here is my layout. Curious of your thoughts, Claude walked me through this:

• On my iMac, I have desktop Claude convert my medical PDFs to markdown files.
  • I am trying to have Claude push the .md files directly to Obsidian using the Local Rest API/MCP server. But it always times out, it only worked once. It’s become a time suck.
• Until the MCP timeout issue is resolved, I click and drag the markdown files into my obsidian vault. Claude and I developed the exact template for each folder based on my medical needs and clinical interests.
• As soon as the files are dragged into a folder in Obsidian on my iMac, it saves to my local vault folder.
• We then built a command that every 3hrs the Local vault folder backs up to my iCloud vault folder.
• I then have obsidian on my macbook, so everywhere I go my macbook/obsidian has access to my local drive on my iMac via the iCloud backup. It is essentially read only, but because it updates every three hours I have access to all the material I generate on my iMac.
• I then can use obsidian on my macbook at med school and for patient prep
• I then linked Claude desktop to my obsidian (on both iMac and macbook). That way I could query all of obsidian for a specific medical situation, Claude would be able to provide a faster response compared to searching through obsidian.
  • I’m not able to use a normal chat window or project, I must query using the code function which is fine.
• But then I stumbled upon Claudian in obsidian, got that setup and BAM!! Everything I was looking for in one place. It is working great. Still learning the specifics, but it’s really a great setup.
• Lastly, if I need to get some notes into obsidian and I’m not home. I remote access with the macbook via tailscale/screen sharing, complete it on my iMac. Click and drag the .md file into obsidian on my iMac, command a push in terminal to back up the local iMac folder to iCloud and I have the info on my macbook.

Curious of your thoughts on the setup. Did I over complicate things? Any insight into making things easier? Did I miss anything? Still a ton to learn about Obsidian, I’m kind of obsessed with it. Want to start using obsidian outside of med school to organize my brain.

Hello all,

I’m a third-year medical student in clinical rotations and preceptorships, and I’ve been trying to build a workable clinical notebook setup. I’ve gone through a few iterations and wanted to get some community input.

My first attempt was a 13B model via Ollama, with the intent of running a private local LLM + RAG pipeline to query my own clinical notes and resources. The plan was to remote into a more powerful home machine so I wasn’t bottlenecked by my laptop. It worked conceptually, but maintaining it became the bottleneck — Docker settings kept shifting with updates, and I didn’t have enough under-the-hood knowledge to manage that friction sustainably. I used ChatGPT to help build it, so my setup knowledge is pretty shallow.

I’ve since landed on a hybrid: NotebookLM for document storage and retrieval (the upload limits are much more permissive), and Claude when I need actual reasoning — differential generation, interpreting clinical patterns, that kind of thing. It’s functional but feels like a workaround. What I’d really want is Claude-level reasoning with NotebookLM-level storage capacity.

I’ve heard AnythingLLM mentioned as a more user-friendly Ollama wrapper, but reviews seem mixed. I’m also wondering if there’s a cleaner way to manage Ollama updates without needing to babysit Docker. Broadly — is there something I’m missing, or a setup that better fits low-maintenance local RAG for a clinician who isn’t a developer?

Thanks in advance.