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Get Started Free →Reference manager with PDF viewer and Markdown note support
.claude/skills/brycewang-stanford-sophosia-reference-guide/SKILL.md| Test case | Without → With | Effect | Δ tokens | Δ turns |
|---|---|---|---|---|
| case-01 | ✗→✓ | ▲ Improved | 33% | 0% |
| case-02 | ✗→✓ | ▲ Improved | -15% | 0% |
| case-10 | ✗→✓ | ▲ Improved | -22% | 0% |
| case-11 | ✗→✓ | ▲ Improved | -37% | 0% |
| case-12 | ✗→✓ | ▲ Improved | 8% | 0% |
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.
bash# 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
markdown### 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
markdown### 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)
markdown### 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
markdown### 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
| Case | Status | Duration (ms) | Turns | Tokens | Tool calls | ||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Without | With | Δ | Without | With | Δ | Without | With | Δ | Without | With | Δ | ||
case-01 | fail→pass | 11,470 | 16,226 | +41% | 1 | 1 | 0% | 1,870 | 2,491 | +33% | 0 | 0 | — |
case-02 | fail→pass | 12,887 | 6,370 | -51% | 1 | 1 | 0% | 2,171 | 1,849 | -15% | 0 | 0 | — |
case-03 | pass→pass | 12,568 | 4,425 | -65% | 1 | 1 | 0% | 1,830 | 1,296 | -29% | 0 | 0 | — |
case-04 | pass→pass | 18,455 | 5,391 | -71% | 1 | 1 | 0% | 2,694 | 1,641 | -39% | 0 | 0 | — |
case-05 | pass→pass | 9,539 | 3,573 | -63% | 1 | 1 | 0% | 1,347 | 1,188 | -12% | 0 | 0 | — |
case-06 | pass→pass | 14,748 | 5,809 | -61% | 1 | 1 | 0% | 2,087 | 1,531 | -27% | 0 | 0 | — |
case-07 | pass→pass | 10,984 | 10,715 | -2% | 1 | 1 | 0% | 1,781 | 1,967 | +10% | 0 | 0 | — |
case-08 | pass→pass | 15,317 | 5,873 | -62% | 1 | 1 | 0% | 2,176 | 1,511 | -31% | 0 | 0 | — |
case-09 | pass→pass | 13,436 | 5,214 | -61% | 1 | 1 | 0% | 2,172 | 1,451 | -33% | 0 | 0 | — |
case-10 | fail→pass | 10,024 | 2,980 | -70% | 1 | 1 | 0% | 1,542 | 1,198 | -22% | 0 | 0 | — |
case-11 | fail→pass | 13,727 | 3,823 | -72% | 1 | 1 | 0% | 2,092 | 1,326 | -37% | 0 | 0 | — |
case-12 | fail→pass | 7,151 | 4,047 | -43% | 1 | 1 | 0% | 1,217 | 1,316 | +8% | 0 | 0 | — |
case-13 | pass→pass | 7,603 | 2,613 | -66% | 1 | 1 | 0% | 1,045 | 1,142 | +9% | 0 | 0 | — |
case-14 | pass→pass | 9,558 | 2,555 | -73% | 1 | 1 | 0% | 1,365 | 1,071 | -22% | 0 | 0 | — |
case-15 | fail→pass | 9,813 | 4,218 | -57% | 1 | 1 | 0% | 1,477 | 1,210 | -18% | 0 | 0 | — |
case-16 | pass→pass | 24,237 | 2,342 | -90% | 1 | 1 | 0% | 3,482 | 991 | -72% | 0 | 0 | — |
case-17 | fail→pass | 9,277 | 2,976 | -68% | 1 | 1 | 0% | 1,712 | 1,165 | -32% | 0 | 0 | — |
case-18 | fail→pass | 12,123 | 2,812 | -77% | 1 | 1 | 0% | 1,647 | 1,153 | -30% | 0 | 0 | — |
case-19 | fail→pass | 9,585 | 2,140 | -78% | 1 | 1 | 0% | 1,504 | 1,024 | -32% | 0 | 0 | — |
case-20 | pass→pass | 13,890 | 7,421 | -47% | 1 | 1 | 0% | 1,905 | 1,809 | -5% | 0 | 0 | — |
case-21 | pass→pass | 7,887 | 1,877 | -76% | 1 | 1 | 0% | 1,068 | 1,018 | -5% | 0 | 0 | — |
case-22 | fail→fail | 14,437 | 9,593 | -34% | 1 | 1 | 0% | 2,047 | 2,294 | +12% | 0 | 0 | — |
case-23 | pass→fail | 23,998 | 15,685 | -35% | 1 | 1 | 0% | 3,593 | 3,559 | -1% | 0 | 0 | — |
case-24 | pass→pass | 5,795 | 6,345 | +9% | 1 | 1 | 0% | 1,033 | 1,605 | +55% | 0 | 0 | — |
DecimalAI ran this skill against gemini-3.6-flash twice over the same eval suite — once with the skill loaded and once without — and compared the two runs case by case. 24 cases were attempted. The headline lift of +33 percentage points is the difference between those two pass rates over the 24 comparable cases. 1 case got worse with the skill loaded, and it is included in that figure.
Without the skill loaded, the model failed this case. With it loaded, the same prompt on the same model passed. This is one improved case from the latest verified run; every case, including any that regressed, is in the table above.
Other measured skills in the registry, with their headline benchmark lift.