| name | obsidian-second-brain |
| description | Use when the user asks to put something in the second brain, save a note to Obsidian, file research, capture a tool or reference, process inbox items, create a daily note, add a literature note, log a meeting, or interact with the Brain vault in any way. Also use when the user says "second brain", "Brain vault", "add to Obsidian", "save this", "file this", "capture this", or any variation of storing, retrieving, or organizing knowledge in their Obsidian vault. Also use for Obsidian Flavored Markdown questions: wikilinks, embeds, callouts, properties/frontmatter, tags, comments, highlights, math, Mermaid diagrams, block IDs, or any Obsidian-specific syntax when creating or editing notes. Supersedes obsidian-markdown for active Obsidian note and syntax work. |
Obsidian Second Brain
Kosta's second brain is an Obsidian vault called "Brain" synced via iCloud. It follows a structured knowledge management system organized into three main sections — Brown (PhD/academic), Tech (tools & reference), and NSFW — plus shared infrastructure (inbox, daily notes, templates).
Ask vs Act
Act immediately (no confirmation needed):
- Creating any new note (all sections)
- Appending to guide pages
- Creating/updating daily notes
- Quick-capturing to
inbox/
Pause and confirm before:
- Overwriting an existing note (
--force or equivalent)
- Deleting or archiving notes
- Moving notes between top-level sections
- Modifying template files under
templates/
Rule: if the operation is reversible locally and the destination path is deterministic, do it.
Access Methods
Two ways to interact with the vault:
- Obsidian CLI —
obsidian vault="Brain" <command> (requires Obsidian running)
- MCP proxy — via ForgeMax
obsidian_brain server (retrieve_tools, call_tool_read/write)
Prefer the CLI for direct operations. Use vault="Brain" on every command. If the CLI returns an error about Obsidian not running, fall back to MCP proxy and note which method succeeded.
Vault Structure
Brain/
├── brown/ # PhD & Academic (Brown University)
│ ├── projects/ # PhD research projects
│ │ ├── fibrosis-delivery/
│ │ ├── glp1-agonists/
│ │ └── nanoparticle-formulation/
│ ├── literature/ # Processed literature notes (papers, articles)
│ │ └── clips/ # Web clips and excerpts
│ ├── outputs/ # Academic deliverables
│ │ ├── grants/
│ │ ├── manuscripts/
│ │ └── presentations/
│ ├── meetings/ # Meeting notes (lab, committee, etc.)
│ ├── people/ # Academic contacts (advisors, collaborators)
│ ├── concepts/ # Scientific/technical concepts
│ ├── methods/ # Research methods and techniques
│ ├── areas/ # Academic life areas
│ │ ├── phd/
│ │ └── teaching/
│ └── guides/ # Lab MOC pages
│ ├── computational-methods.md
│ ├── drug-delivery.md
│ └── reading-queue.md
├── tech/ # Technology & Tools
│ ├── projects/ # Software projects
│ │ ├── openclaw/
│ │ ├── paperbanana/
│ │ └── vibenotes/
│ ├── agent-tools/ # MCP servers, skills, agent profiles, hooks, prompts
│ │ ├── mcp-servers/
│ │ ├── agent-profiles/
│ │ ├── skills/
│ │ ├── plugins-hooks/
│ │ └── prompts-templates/
│ ├── ai-tools/ # AI-powered tools and services
│ ├── docs/ # Prompting guides, API docs, config guides
│ ├── mac-tools/ # macOS tools and apps
│ ├── phone-tools/ # iOS/mobile tools
│ ├── tools/ # General-purpose tools
│ ├── extra-tools/ # Misc tools
│ ├── ui-design/ # UI/UX design resources
│ └── guides/ # Tech MOC pages
│ ├── agent-tools.md
│ ├── ai-tools.md
│ ├── design-resources.md
│ ├── mac-tools.md
│ └── phone-tools.md
├── nsfw/ # NSFW content organization
│ ├── websites/ # Sites by category
│ │ ├── tubes/
│ │ ├── niche/
│ │ ├── premium/
│ │ ├── cams/
│ │ ├── aggregators/
│ │ ├── forums/
│ │ └── creator-platforms/
│ ├── twitter/ # Twitter/X accounts
│ │ ├── models/
│ │ ├── studios/
│ │ ├── curators/
│ │ └── fitness/
│ ├── reddit/ # Subreddits and users
│ │ ├── subs-general/
│ │ ├── subs-niche/
│ │ ├── subs-fitness/
│ │ ├── subs-celebrity/
│ │ └── users/
│ ├── instagram/ # Instagram accounts
│ │ ├── models/
│ │ ├── fitness/
│ │ └── photographers/
│ ├── lpsg/ # LPSG threads
│ │ ├── celebrity/
│ │ ├── verified/
│ │ ├── amateur/
│ │ └── discussion/
│ ├── bodybuilders/ # Bodybuilders & fitness
│ │ ├── pro/
│ │ ├── classic/
│ │ ├── physique/
│ │ ├── influencers/
│ │ └── powerlifting/
│ └── onlyfans/ # OnlyFans/Fansly creators
│ ├── of/
│ ├── fansly/
│ └── other/
├── inbox/ # Unsorted captures (shared across all sections)
│ ├── quick/ # Quick captures from Stik, shortcuts, or agent drops
│ ├── agent/ # Agent-deposited items (automated captures)
│ └── literature/ # Papers/articles to be processed into literature notes
├── daily/ # Daily notes (YYYY-MM-DD.md)
├── areas/ # Personal life areas (non-academic)
│ ├── fitness/
│ └── personal/
├── guides/ # Personal MOC pages
│ └── weekly-dashboard.md
├── templates/ # Note templates (used by Templater plugin)
├── assets/ # Binary assets
│ ├── images/
│ └── pdfs/
└── archive/ # Retired/processed items
└── inbox-processed/
Note Types and Templates
Every note has a type property in frontmatter. Use the matching template when creating notes.
| Type | Template | Where it goes | When to use |
|---|
daily | Daily note | daily/ | Daily journal, tasks, captures |
tool | Tool note | tech/{subcategory}/ | New tool, app, CLI, service |
reference | Reference note | tech/{subcategory}/ or brown/concepts/ | Concept, technique, general reference |
knowledge | Knowledge doc | tech/docs/ | Guides, prompt docs, API references |
literature | Literature note | brown/literature/ | Academic paper or article |
meeting | Meeting note | brown/meetings/ | Meeting minutes and action items |
project | Project note | brown/projects/{name}/ or tech/projects/{name}/ | New project tracker |
person | Person note | brown/people/ | Contact, advisor, collaborator |
output | Output note | brown/outputs/{type}/ | Manuscript, grant, presentation |
mcp-server | MCP server | tech/agent-tools/mcp-servers/ | MCP server configuration |
skill-ref | Skill reference | tech/agent-tools/skills/ | Documenting an installed skill |
agent-profile | Agent profile | tech/agent-tools/agent-profiles/ | Specialized agent documentation |
nsfw-website | NSFW website | nsfw/websites/{category}/ | NSFW website |
nsfw-creator | NSFW creator | nsfw/{platform}/{category}/ | NSFW creator/account |
nsfw-subreddit | NSFW subreddit | nsfw/reddit/{category}/ | NSFW subreddit |
nsfw-bodybuilder | NSFW bodybuilder | nsfw/bodybuilders/{category}/ | Bodybuilder/fitness model |
nsfw-lpsg | NSFW LPSG thread | nsfw/lpsg/{category}/ | LPSG forum thread |
Frontmatter Conventions
All notes use these common properties:
type: <note-type>
status: <status>
tags:
- type/<type-tag>
- domain/<domain>
created: YYYY-MM-DD
updated: YYYY-MM-DD
Status values by type
| Type | Statuses |
|---|
tool | active, inactive, evaluating |
reference | draft, stable, outdated |
knowledge | current, outdated, archived |
literature | to_read, reading, done |
meeting | raw, processed |
project | active, paused, completed, archived |
output | draft, in_review, submitted, published |
Tag Taxonomy
Tags follow a hierarchical namespace pattern:
#type/* — Note classification: type/reference, type/catalog, type/config, type/daily, type/skill, type/agent-profile#domain/* — Knowledge domain: domain/research, domain/prompting, domain/academia, domain/mcp, domain/macos, domain/design, domain/infrastructure, domain/drug-delivery#topic/* — Specific topics: topic/tools, topic/ai-tools, topic/claude, topic/openai, topic/github#tier/* — Quality/importance tier: tier/s, tier/a#project/* — Project association: project/paperbanana, project/openclaw
Workflow: Adding Something to the Second Brain
Determine section first:
- Academic/research/lab-related →
brown/
- Tool, app, service, or tech reference →
tech/
- NSFW content →
nsfw/
- Not sure →
inbox/quick/ (sort later)
Then create the note and verify. No confirmation needed for new notes.
Quick capture (unsorted)
obsidian vault="Brain" create name="<descriptive-name>" path="inbox/quick/<name>.md" content="<content>" silent
Verify:
obsidian vault="Brain" open path="inbox/quick/<name>.md"
If the CLI returns a not-found error, retry with MCP proxy: call_tool_write(obsidian_brain, create, {...}).
Example: Adding a new tool
obsidian vault="Brain" create name="my-tool" path="tech/mac-tools/my-tool.md" content="---
type: tool
status: active
tool_category: cli
install_method: homebrew
install_command: brew install my-tool
url: https://example.com
tags:
- type/catalog
- domain/macos
created: 2026-03-08
updated: 2026-03-08
---
# My Tool
Description of what it does.
## Install
\`\`\`bash
brew install my-tool
\`\`\`
## Usage
## Links
- [GitHub](https://example.com)" silent
Then update the relevant guide (append, not overwrite — safe):
obsidian vault="Brain" append file="mac-tools" content="- [[my-tool]] — Short description"
Verify both steps succeeded:
obsidian vault="Brain" read path="tech/mac-tools/my-tool.md" | head -5
obsidian vault="Brain" search query="[[my-tool]]" limit=1
If guide append fails (file not found), check the guide path matches tech/guides/mac-tools.md and retry with full path.
Example: Adding a literature note
obsidian vault="Brain" create name="smith2025-hydrogel" path="brown/literature/smith2025-hydrogel.md" content="---
type: literature
status: to_read
citekey: smith2025-hydrogel
title: 'Hydrogel-Based Drug Delivery Systems'
authors:
- 'Smith, J.'
year: 2025
venue: 'Nature Materials'
doi: '10.1038/...'
url: ''
projects:
- fibrosis-delivery
tags:
- type/reference
- domain/research
created: 2026-03-08
updated: 2026-03-08
---
# Hydrogel-Based Drug Delivery Systems
## Key findings
## Methods
## Relevance to my work
## Questions / follow-ups
## Raw notes" silent
Then append to reading queue:
obsidian vault="Brain" append file="reading-queue" content="- [[smith2025-hydrogel]] — Hydrogel-Based Drug Delivery Systems (2025)"
Verify:
obsidian vault="Brain" read path="brown/literature/smith2025-hydrogel.md" | head -3
Handling conflicts (existing note at target path)
Before overwriting, check:
obsidian vault="Brain" read path="<target-path>" 2>/dev/null | head -5
If the note exists and Kosta didn't explicitly say to overwrite it, stop and report what's there. Do not silently clobber.
Guide Pages (MOCs)
Guide pages are curated index notes with Dataview queries. When adding a new note that fits a guide's scope, append a link to the guide's "Recent Additions" section. Append is always safe; never rewrite a guide page wholesale without being asked.
Tech guides (in tech/guides/)
agent-tools.md — MCP servers, skills, agent profilesai-tools.md — AI-powered tools and servicesmac-tools.md — macOS tools and appsphone-tools.md — iOS/mobile toolsdesign-resources.md — UI/UX design resources
Brown guides (in brown/guides/)
computational-methods.md — Lab computational methodsdrug-delivery.md — Drug delivery researchreading-queue.md — Papers to read
Personal guides (in guides/)
weekly-dashboard.md — Weekly overview
Enabled Plugins
- Templater — Template engine (use
template="Template Name" when creating notes)
- Dataview — Query engine for dynamic lists and tables
- Tasks — Task management with due dates and recurrence
- Omnisearch — Full-text search
- QuickAdd — Quick capture macros
- Metadata Menu — Frontmatter management
- Obsidian Linter — Auto-formatting
- BRAT — Beta plugin manager
Reference Files
For detailed information on specific topics, see:
Obsidian Flavored Markdown syntax (consult when creating or editing notes):
- obsidian-syntax.md — Full OFM syntax: wikilinks, embeds, callouts, properties, tags, comments, math, Mermaid, footnotes
- CALLOUTS.md — Full callout type list with aliases, nesting, and custom CSS callouts
- EMBEDS.md — All embed types: audio, video, search embeds, external images
- PROPERTIES.md — All property types, tag syntax rules, and advanced frontmatter usage
