Sophosia Reference Guide
Documentssophosia-reference-guideSophosia Reference Guide is an Agent Skill for documents published in the brycewang-stanford/Auto-Empirical-Research-Skills repository on GitHub: a SKILL.md instruction file an AI agent can load to do this task.
Reference manager with PDF viewer and Markdown note support
How to use this skill
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Sophosia Reference Manager Guide
Overview
Sophosia is an open-source reference manager that combines PDF viewing, Markdown note-taking, and Excalidraw visual notes in a single application. Unlike traditional reference managers, it treats each paper as a rich workspace with typed annotations, linked notes, and visual diagrams. Built with modern web technologies (Electron + Vue), it runs on all desktop platforms.
Installation
# Download from GitHub releases (Windows/macOS/Linux)
# Or build from source:
git clone https://github.com/sophosia/sophosia.git
cd sophosia
npm install && npm run build
Features
### Core Capabilities
- **PDF Viewer**: Built-in reader with annotations
- **Markdown Notes**: Rich note editor per paper
- **Excalidraw**: Visual whiteboard for diagrams
- **Tags & Collections**: Flexible organization
- **BibTeX Support**: Import/export bibliography
- **Full-text Search**: Search across all papers
- **Citation Graph**: Visual paper relationships
### Note Types
1. **Text notes** — Markdown with LaTeX math
2. **Visual notes** — Excalidraw canvas
3. **Annotation notes** — Linked to PDF highlights
4. **Outline notes** — Structured paper summaries
Workspace Structure
### Per-Paper Workspace
Paper: "Attention Is All You Need"
├── PDF (with highlights and annotations)
├── Notes/
│ ├── summary.md (structured summary)
│ ├── ideas.md (research ideas sparked)
│ └── architecture.excalidraw (visual diagram)
├── Metadata (title, authors, year, DOI, tags)
└── Links (related papers, concept connections)
Note-Taking Features
### Markdown Notes Support
- Standard Markdown formatting
- LaTeX math: $E = mc^2$ and display equations
- Code blocks with syntax highlighting
- Tables and checklists
- Wikilinks: [[other-paper]] for cross-referencing
- Embeds: ![[figure.png]] for inline images
- Templates for consistent note structure
### Excalidraw Integration
- Draw architecture diagrams
- Mind maps for paper concepts
- Comparison charts between methods
- Hand-drawn style for informal notes
- Export as SVG/PNG for presentations
Import/Export
### Import Sources
- BibTeX (.bib)
- RIS format
- DOI lookup (auto-fetch metadata)
- PDF drag-and-drop (auto-extract metadata)
- Zotero export files
### Export Formats
- BibTeX for LaTeX
- Markdown bibliography
- CSV metadata export
- HTML reading lists
Use Cases
- Reading workflow: PDF + notes in single workspace
- Visual thinking: Excalidraw diagrams alongside papers
- Literature review: Linked notes across paper collection
- Presentation prep: Visual notes exportable as diagrams
- Research journal: Rich per-paper documentation