MindWiki vs Heptabase.
Honest, side-by-side comparison so you can pick the right tool — and so we can point out where Heptabase is still the better fit.
The short version
Heptabase is a whiteboard-first knowledge tool — you arrange cards on infinite canvases to make sense of complex topics visually. MindWikiis a text-first markdown vault with a knowledge graph view over wikilinks. They're both about "making sense of complex thinking," but they take very different visual shapes. Use Heptabase when the canvas itself is the artifact. Use MindWiki when the writing is the artifact and you want AI clients reading it directly.
Best for
MindWiki is best for: long-form thinkers who write in pages and want AI clients connected to the same vault.
Heptabase is best for: visual thinkers who arrange cards on whiteboards as their primary sense-making surface.
Where MindWiki is different from Heptabase
- Text-first vault, not a canvas-first product.
- Native macOS app + web vault that share plain markdown files.
- Knowledge graph is a navigation view over real pages, not a free-canvas drawing surface.
- Built-in MCP endpoint and REST API for AI clients.
- Pro automation does scheduled vault maintenance (linking, classifying, summaries).
Feature comparison
| Feature | MindWiki | Heptabase |
|---|---|---|
| Primary surface | Pages + graph navigation | Whiteboard canvases |
| Storage | Markdown on disk + cloud | Cloud-hosted with offline cache |
| Knowledge graph | Wikilink graph view | Per-whiteboard card relations |
| Long-form writing | Primary use case | Cards typically short |
| AI access | MCP + REST API | Built-in AI; limited external access |
| Pricing | Free + Pro | Paid plans |
Migration reality
Heptabase exports cards as markdown. Cards become pages; the whiteboard layout doesn't come over. Migration steps:
- Export your Heptabase space.
- Each card becomes a markdown page in your MindWiki vault.
- Whiteboard relationships translate to wikilinks where the original cards referenced each other. Spatial arrangement itself doesn't transfer.
- If you used Heptabase mainly for whiteboards, expect to keep using Heptabase for that and use MindWiki as the long-form companion.
When Heptabase wins
- The whiteboard is your primary thinking surface.
- You arrange a few canvases per topic and treat each as a research artifact.
- You want spatial layout to be a durable, exportable part of the work.
- You don't need AI clients connecting to your knowledge base directly.
Frequently asked questions
Does MindWiki have whiteboards?
No. MindWiki is text-first. The graph view is a navigation surface over real pages, not a free-canvas drawing tool.
Can I use Heptabase and MindWiki together?
Yes — many people do. Use Heptabase for visual sense-making and MindWiki as the long-form notes layer your AI reads.