Heptabase vs SiYuan
Heptabase is a visual learning tool where notes are cards you arrange and connect on infinite whiteboards; SiYuan is a free, open-source, block-based knowledge base with Notion-style databases and local storage. Here’s how they compare on pricing, platforms, linking, search, capture and collaboration — and how to decide between them.
What is Heptabase?
Heptabase is for people who think spatially. Notes are cards; understanding happens by laying them out on infinite whiteboards, drawing connections, grouping into sections and mindmaps, and annotating PDFs alongside. It’s a deliberate take on learning deeply — less “capture everything” and more “make sense of what you’re studying” — and nothing else in this list matches its canvas experience.
Cards support Markdown, backlinks, tags with table views, and journals, so it still functions as a complete note system off the whiteboard. It runs on desktop, web and mobile with offline support and cloud sync. There’s no free plan (7-day trial); 2026 pricing is AI-credit-tiered — Pro at $8.99/month (annual) with Premium tiers above it for heavier AI use.
What is SiYuan?
SiYuan packs a remarkable amount into an open-source (AGPL) package: block-level bidirectional links, WYSIWYG Markdown, Notion-like database and attribute views, spaced-repetition flashcards, a graph, PDF annotation and a plugin marketplace — all stored locally, with the option to self-host the whole thing in Docker. It’s free for personal and commercial use.
Sync is where money changes hands, modestly: a one-time PRO license (~$64) unlocks third-party S3/WebDAV sync, or you can subscribe to the official encrypted cloud service. The developer is China-based with a very active GitHub, and the app is fully usable in English. It’s single-player — no real-time collaboration — but as a personal all-in-one it rivals tools costing $100+/year.
Heptabase vs SiYuan at a glance
| Heptabase | SiYuan | |
|---|---|---|
| Price | Pro $8.99/mo (annual); Premium tiers for more AI credits | Free; PRO one-time ~$64; optional paid official cloud sync |
| Free plan | No — 7-day trial | Yes — full core app, commercial use included |
| Platforms | Web, macOS, Windows, Linux, iOS, Android | Windows, macOS, Linux, iOS, Android, Docker (self-host) |
| Storage model | Cloud-synced with strong offline support | Local-first; encrypted sync via official cloud or your own S3/WebDAV |
| Editing model | Cards on infinite whiteboards; Markdown, mindmaps, sections | Block-based WYSIWYG Markdown with database views |
| Backlinks & wiki links | Yes — card links and backlinks | Yes — block-level bidirectional links |
| Graph view | Whiteboards serve as the visual map | Yes — graph view |
| Search | Full-text | Full-text, including SQL-style queries |
| Web capture | Limited — no first-party clipper | Browser clipping extension |
| Email-in capture | No | No |
| RSS / feeds | No | No |
| Team collaboration | Limited — shared whiteboards | No |
| Publishing & sharing | Read-only whiteboard sharing | Export or self-hosted sharing |
| AI assistant access | Built-in AI (credit-metered); no MCP | Configurable OpenAI-compatible integration |
| Offline access | Yes | Yes — fully offline |
| Open source | No | Yes — AGPL-3.0 |
| End-to-end encryption | No | Yes — encrypted sync |
| Data export | Markdown, PDF | Markdown, PDF, and more |
Pricing and features as of mid-2026 — check each product’s site for current details.
Where Heptabase shines
- The best whiteboard-native note experience available — cards, sections, mindmaps and connections feel built-in, not bolted on.
- PDF annotation on the same canvas as your notes suits deep study workflows.
- Tags double as tables, giving light database views over cards.
- Solid offline support with sync across desktop, web and mobile.
Worth knowing: No free plan — only a 7-day trial. Collaboration is limited to shared whiteboards; it’s primarily single-player. Spatial organization is the point — if you don’t think in maps, the canvas is overhead rather than insight.
Where SiYuan shines
- An unusually complete free feature set: block refs, databases, flashcards, PDF annotation, graph — no plugins required.
- Open source (AGPL) with local-first storage and Docker self-hosting.
- Sync your own way — one-time license for S3/WebDAV, or the official encrypted cloud.
- Very active development with a plugin bazaar on top.
Worth knowing: No collaboration and no first-party hosted sharing beyond exports and self-hosting. The interface is denser and less polished than Western commercial rivals, and documentation can be rough in translation. Capture from the web, email or feeds isn’t a focus.
Which should you choose?
Choose Heptabase if:
- You learn by arranging ideas spatially and drawing the connections yourself.
- You study from PDFs and want annotation living next to your notes.
- A visual overview of a topic matters more to you than fast capture.
Choose SiYuan if:
- You want maximum capability for minimum (or zero) money, as open source.
- Self-hosting on your own infrastructure appeals to you.
- You want Notion-style databases and flashcards in a local-first app.
A third option: Dexi
If what you actually want is one searchable place for notes, bookmarks, newsletters and RSS — with tags, @mentions and [[wiki links]] that organize themselves as you write, semantic search that finds ideas even when the words don’t match, and an MCP server so Claude and other AI assistants can work with your notes directly — take a look at Dexi. It’s free for up to 1,000 notes, with no app to install.
Frequently asked questions
What is the main difference between Heptabase and SiYuan?
Heptabase is a visual learning tool where notes are cards you arrange and connect on infinite whiteboards, while SiYuan is a free, open-source, block-based knowledge base with Notion-style databases and local storage. In practice, Heptabase is best for students, researchers and visual thinkers who understand topics by mapping them out spatially; SiYuan is best for self-hosters and open-source enthusiasts who want Notion-grade blocks and databases on their own disk.
Which is cheaper, Heptabase or SiYuan?
Heptabase: Pro $8.99/mo (annual); Premium tiers for more AI credits (free plan: no — 7-day trial). SiYuan: Free; PRO one-time ~$64; optional paid official cloud sync (free plan: yes — full core app, commercial use included). Prices as of mid-2026 — check each product's site for current rates.
Is Heptabase or SiYuan better for teams?
Heptabase — team collaboration: limited — shared whiteboards. SiYuan — team collaboration: no. If neither fits, Dexi's Team plan ($10/member/month) offers per-note sharing with team-wide search.
Can I switch between Heptabase and SiYuan?
Both tools let you get your data out — Heptabase exports via markdown, pdf, and SiYuan via markdown, pdf, and more. Markdown is the common ground for most migrations, though block references, properties and other tool-specific structure typically need manual cleanup after import.
Collect, connect and search everything you read — free, no credit card required.
Try Dexi free