WorkspaceOS

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A configurable single-surface workbench framework for focused, long-running creative work.

Answer 7 questions → matched extension → live config preview → apply.

You answer 7 questions about your domain. The framework generates a workbench tailored to it — advisor panel, knowledge taxonomy, prompt tone, surface layout — and you can keep customizing from there. Domain content is plug-and-play via extension folders. The framework ships two extensions today (AI research, biology research); writing your own is one folder of YAML.

The reference instance — ProjectScribe — is the maintainer's AI co-founder daily-driver, used to build WorkspaceOS itself.

Phase 1 = content extensions (personas, taxonomies, prompts). Phase 2 = capability extensions (Gmail / Calendar / Slack ingest). Phase 2 schema is already reserved so manifests authored today stay forward-compatible.

What it does

A bench with six opt-in surfaces, each driven by your domain config:

Letter	Surface	What it does
A	Advisor	Chat with a cofounder advisor panel. 3–4 advisors weigh in per message.
R	Research	Parallel critique from a research reviewer panel. 5–6 reviewers, distinct lenses.
D	Drafts	Blog and social drafts (per-project, paginated).
P	Papers	Research papers — single + portfolio. Multi-agent v2 pipeline.
K	Knowledge	Cross-project graph of decisions / claims / hypotheses extracted from chat.
W	Worklog	Weekly / monthly / quarterly progress reports.

Plus a ⌘K command palette, slide-in project inspector, and a right-side TUI log streaming every AI call, sync, and extraction in real time.

Screenshots

_{Onboarding wizard, step 1. Free-text domain answer drives extension matching.}	_{Wait state. 5-chapter SVG tutorial loops while generation runs; SSE captions update under it.}
_{Preview pane. Matched extension badge, personas, taxonomy chips, raw YAML disclosure.}	_{Research surface. Drew Endy / George Church / Jay Keasling / Doudna / Topol / Tim Lu + plant-synbio reviewers (Markus Pauly, Jenny Mortimer, Plant Methods Reviewer) after Bio Research extension applied.}

Quick start

Prerequisite: Docker. Install Docker Desktop (macOS / Windows / Linux) or OrbStack (faster on macOS). Make sure docker compose works in your terminal before continuing.

git clone https://github.com/Chesterguan/WorkspaceOS.git
cd WorkspaceOS

cp .env.example .env
# Edit .env — minimum required is GEMINI_API_KEY. Everything else has
# defaults that work for local development.

docker compose up --build -d

# Bench:        http://localhost:4000
# Backend API:  http://localhost:9000/docs

First load redirects you to /login. Register an account, then /onboarding walks you through 7 questions and generates a workbench. You can skip the wizard and use the default config at any time.

How extensions plug in

An extension is a single folder under config/extensions/<id>/:

config/extensions/bio-research/
├── manifest.yaml         # match rules + version + path refs
├── personas/
│   ├── cofounder.yaml    # 3–4 cofounder personas
│   └── research.yaml     # 5–6 research reviewers
├── taxonomies/extra.yaml # node types added to the base 7
└── prompts/worklog/
    ├── weekly.txt
    ├── monthly.txt
    └── quarterly.txt

manifest.yaml is just YAML — no Python, no JS, no build step:

id: bio-research
name: Bio Research
description: Persona panel + taxonomy for wet-lab biology and biofoundry.
version: 0.1.0
author: workspaceos
matches:
  domain_keywords: [bio, biotech, biofoundry, synthetic biology, strain, crispr]
  audience_any: [peer_researchers]
  outputs_any: [papers]
personas:
  cofounder: ./personas/cofounder.yaml
  research:  ./personas/research.yaml
taxonomy_extra: ./taxonomies/extra.yaml
worklog_templates:
  weekly:    ./prompts/worklog/weekly.txt
  monthly:   ./prompts/worklog/monthly.txt
  quarterly: ./prompts/worklog/quarterly.txt

Adding a new extension is one folder drop:

cp -r config/extensions/bio-research config/extensions/your-domain
Edit manifest.yaml — change id, name, matches.domain_keywords
Rewrite the persona / taxonomy / prompt files for your domain
Restart the backend (docker compose restart backend)

The wizard's matcher scores each extension against the user's answers:

domain_keywords substring hit = +2 each
audience_any overlap = +1 each
outputs_any overlap = +1 each

Threshold is 2. Highest-scoring extension above threshold wins. No match → falls back to Gemini synthesis → falls back to a deterministic bucket stub.

See CONTRIBUTING.md for the full extension authoring guide.

How the wizard works

User answers 7 questions at /onboarding. Domain (free text), primary outputs, audience, dream advisor panel, what you track, cadence, stage.
Backend matches extensions. Scores each shipped extension's matches rules against the answers.
Generator builds the config:
- If an extension matches → splice its bundled files verbatim, emit "Matched extension: X (score N)" event.
- Else if GEMINI_API_KEY is set → one LLM call returns personas + taxonomy additions + tagline.
- Else → deterministic bucket stub (CS / biology / economics).
SSE streams progress captions to the wizard's wait animation (5-chapter SVG tutorial loops independently). Same events also flow into the bench's right-side TUI log so the user can see what ran after they navigate back.
Preview pane shows generated personas, taxonomy chips, worklog template sample, raw YAML disclosure. Apply writes files into config/, triggers a live reload, and marks the user as onboarded. Regenerate re-rolls.

Total wall-clock: ~15s for extension match, ~10s for Gemini, instant for the bucket stub.

Architecture

Frontend — Next.js 16 (App Router, Suspense, proxy.ts middleware), Tailwind v4, shadcn/ui, motion (Framer), React Flow + dagre for the knowledge graph. Port 4000.
Backend — FastAPI (async), PostgreSQL 15 + pgvector (768-dim IVFFlat), Server-Sent Events for the bench log + wizard generation. Port 9000.
AI — Hybrid. Local Ollama (nomic-embed-text) for embeddings when available; Gemini for generation + long-tail wizard fallback; OpenAI for paper roundtable reviewers (optional).
Deployment — Docker Compose, three services (db, backend, frontend) on the workspaceos network. Auth: JWT for users, X-API-Key for scripts and SSE query-param.

Required vs optional setup

Required	Optional
Gemini API key — chat / drafts / papers / extraction / embeddings-fallback. Free tier works for testing.	OpenAI key — only used by the paper roundtable reviewers. Papers still generate without it.
	Ollama running locally — free local embeddings. Falls back to Gemini if absent.
	GitHub token — repo sync, deep repo context, release publishing.
	LinkedIn / Dev.to / Hashnode keys — multi-platform publishing.

All API keys can be set at runtime through the Settings page (Fernet-encrypted in the DB) instead of .env.

Running AI locally with Ollama (optional)

By default WorkspaceOS sends generation/review prompts to Gemini (or whichever CLOUD_AI_PROVIDER you pick) and uses Ollama for embeddings if you've installed it. If you want everything local — no cloud calls for any AI operation — install Ollama and pull a chat model sized to your hardware.

Install:

# macOS / Linux
curl -fsSL https://ollama.com/install.sh | sh
# or download the installer from https://ollama.com/download
ollama serve   # leave running in a terminal

Pull recommended models:

# Embeddings — small, fast, used for all semantic search (~274 MB)
ollama pull nomic-embed-text

# Chat — pick ONE based on how much RAM you have:
ollama pull qwen2.5:3b        #  4–8 GB RAM, fast, decent for extraction
ollama pull qwen2.5:7b        # 16 GB RAM (recommended default)
ollama pull qwen2.5:14b       # 32 GB RAM, near cloud-quality for chat
ollama pull llama3.3:70b      # 64 GB RAM + GPU, full cloud-replacement

qwen2.5 is recommended for structured-output tasks (extraction, classification) — it follows JSON-shaped prompts more reliably than similarly-sized Llama variants. For long-form writing (drafts, papers), qwen2.5:14b and up are competitive; below that the cloud provider noticeably wins.

Point WorkspaceOS at it — set in .env:

# macOS / Windows Docker — host.docker.internal resolves to the host.
OLLAMA_BASE_URL=http://host.docker.internal:11434
# Linux — host.docker.internal doesn't resolve by default. Either use
# your host's LAN IP (typically 172.17.0.1 for the default bridge), or
# add `--add-host=host.docker.internal:host-gateway` to the backend
# service in docker-compose.yml and keep the line above.
# OLLAMA_BASE_URL=http://172.17.0.1:11434

OLLAMA_CHAT_MODEL=qwen2.5:7b                        # match what you pulled
OLLAMA_EMBED_MODEL=nomic-embed-text

# Stay local end-to-end (otherwise only embeddings/extraction are local):
LOCAL_AI_PROVIDER=ollama
CLOUD_AI_PROVIDER=ollama

Trade-offs to know:

Quality: small Ollama models (≤7B) write noticeably blander drafts than Gemini/Claude. Use qwen2.5:14b or larger if you care about prose quality on local-only.
Latency: a 7B model on an M2 Mac generates ~30–60 tokens/sec; a chat reply takes seconds, paper review takes minutes. Cloud is usually faster.
First load: each model loads into RAM on first use of a session (~10–30 seconds). Keep ollama serve running to avoid cold starts.
GPU: not strictly required, but qwen2.5:14b and up are painfully slow without one. M-series Macs use the integrated GPU automatically.

Capability extensions (v0.2.1)

Beyond content (personas / taxonomies / prompts), extensions ship capabilities — runtime hooks that pull data, add palette entries, and put context buttons on items. Capability code lives in the framework (backend/app/capabilities/), registered by name. Manifests declare which runners to enable.

Three capability kinds are runtime-active today:

ingest_source — async runner polled on a schedule. Emits bench events + inserts knowledge graph nodes. Example: local-files-watcher watches a directory every 30s and creates a file_ingested node per new file.
slash_command — palette entry (⌘K). Two handler kinds: api_call triggers a registered backend runner; navigate pushes a route. Example: "Scan local files now" (api_call) and "Open knowledge graph" (navigate).
action_button — contextual button rendered on a target item (currently knowledge_node). visible_when filters by the item's fields. Example: "Mark as decision" shows on claim/hypothesis/ insight/question nodes; "Archive" shows on all nodes.

WorkspaceOS is the secretary, not the replacement. Benchling, Zotero, Mail, etc. stay where they are — capabilities just pull breadcrumbs into the knowledge graph so the bench has context across your tools.

Shipped extensions:

local-files-watcher — ingest_source: local_files. Walks a directory under WORKSPACE_HOST_PATH, dedups by mtime+size, caps 100 files/tick, skips dot-dirs + node_modules + .git.
macos-mail — ingest_source: macos_mail. Host-side AppleScript bridge via scripts/outlook_bridge/install.sh. Reads Apple Mail + Outlook for Mac, POSTs to /skills/local-ingest/items. No in-container code because Mail.app isn't accessible from Docker.
benchling — ingest_source: benchling_import. Pulls recent notebook entries from your Benchling tenant every 6h as benchling_entry knowledge nodes. Title + author + date + link. Body content stays in Benchling. Set api_key + tenant in the extension manifest to enable.
zotero — ingest_source: zotero_sync. Pulls top-level library items every 6h as paper_reference knowledge nodes. Title
- first author + year + DOI + venue. Set api_key + library_id
- library_type to enable.
bench-extras — utility pack: 2 slash commands + 2 action buttons. Use as the working example when authoring your own.

Added in v0.2.6 (bio-researcher build) — alongside a Knowledge-surface upgrade that links Experiment nodes to the Claim / Construct nodes they support, so the graph reflects the actual evidence trail:

preprints — ingest_source: preprint_ingest. Polls bioRxiv (and optionally medRxiv) daily for keyword-matching preprints and adds them as paper_reference nodes — same type as Zotero items, so the research panel and paper pipeline pick them up automatically. Opt-in: empty keyword list = nothing imported.
ot2-protocols — ingest_source: ot2_protocols. Walks a directory of Opentrons OT-2 Python protocols and creates one protocol node per file (name, author, API level, labware, source excerpt). Re-ingested on content change.
methods-drafter — slash_command: draft_methods. Drafts a publication-style Methods section grounded in the project's actual knowledge graph — experiments, constructs (Benchling), strains, OT-2 protocols, custom GitHub tools. Default style plant_synbio; switch via the slash payload. Saved as a Papers-surface draft tagged paper + methods_draft.
github-tools — ingest_source: github_user_tools. Syncs your public GitHub repos once a day as tool nodes (name, description, language, stars, truncated README). Citable by /draft_methods when writing Methods. PAT optional but lifts the rate limit from 60 to 5000 req/h.

Discovery + setup — where users find and configure capabilities

Where	Shows
Settings → Capabilities tab	Every declared capability grouped by kind. Each ingest source has a Configure button → modal form with field-level help, auto-fill, and a test-connection check. Encrypted at rest. No YAML editing, no restart. Link to the docs setup guide right next to each row.
⌘K command palette	Slash commands appear inline with built-in entries. Type to filter; click to fire.
In context	Action buttons render on the item they target — e.g. an "Extension actions" row on the knowledge node detail panel. Gated by `visible_when` so menus stay clean.

Configuring a capability — the easy path

Open Settings → Capabilities.
Find the ingest source you want (e.g. Zotero). Click configure.
Modal shows the fields with inline help. Paste your API key.
Click Auto-fill (where supported — e.g. Zotero introspects the key and fills library_id + library_type automatically).
Click Test — the runner fires once and reports success / the specific error if anything's off.
Click Save — the overlay is Fernet-encrypted in the DB. The next poll tick uses the new config; no restart.

For technical users the YAML path still works: edit config/extensions/<id>/manifest.yaml and restart. DB overlay wins when both are set.

Authoring capabilities

See CONTRIBUTING.md for the full author guide. Quick shape per kind:

# config/extensions/your-id/manifest.yaml
capabilities:
  # 1. Pull external data into the bench on a schedule.
  - kind: ingest_source
    name: my_runner                   # ← key in backend/app/capabilities/registry.py
    config:
      poll_interval_seconds: 60
      # your runner's config fields

  # 2. Palette entry (⌘K).
  - kind: slash_command
    name: do_thing
    config:
      label: "Do the thing"
      keywords: [thing, do]
      icon: zap
      # handler_kind: api_call    → POSTs to handler_target
      # handler_kind: navigate    → router.push(handler_target)
      handler_kind: api_call
      handler_target: /capabilities/runners/do_thing/trigger

  # 3. Button on a specific item kind.
  - kind: action_button
    name: tag_with_x
    config:
      label: "Tag with X"
      target: knowledge_node          # which item renderer this attaches to
      handler_kind: api_call
      visible_when:                   # AND-of-ORs filter
        node_type: [claim, hypothesis]

Then register the Python runner / handler in backend/app/capabilities/registry.py (or slash.py / actions.py) and PR. Trust model = "registry as audit surface": capability code ships with the framework, manifests reference runners by name. No arbitrary file-drop, no eval, no extension-injected JSX.

Roadmap

More capability runners — Gmail (OAuth), Calendar (CalDAV / Google), Slack, Notion. Contributions welcome.
surface_widget capability kind — sub-component injected into an existing surface. Manifest schema reserves it today; runtime activation arrives next. slash_command and action_button are already shipped (see bench-extras, methods-drafter).
More content extensions — indie-founder, phd-student, engineering-manager. Contributions welcome.
Settings → "Personalize" — re-run the wizard with prefilled prior answers.
Custom surface types — not on the roadmap. The 6 surface types cover the framework's scope. Surface code stays in core.

Persona grounding (v0.2.2)

Research roundtable personas can declare a grounding hint in their YAML — at chat time, WorkspaceOS looks up the persona's recent papers via Semantic Scholar (24h-cached) and prepends the paper titles to the system prompt. "Drew Endy says X" is anchored to actual Endy publications instead of fabricated.

- id: drew_endy
  name: Drew Endy
  color: "#ef4444"
  system_prompt: |
    You are Drew Endy …
  grounding:
    source: semantic_scholar     # other sources reserved
    query: "Drew Endy synthetic biology"
    max_papers: 5

The bio-research extension's reviewers all ship with grounding set. Fails gracefully — if Semantic Scholar is down or rate-limited, the persona reverts to ungrounded behavior; the chat keeps working.

In-app feedback

The bench has a floating Feedback button (bottom-right). Click it, write what broke or what you wished it did, and the backend files a GitHub issue on Chesterguan/WorkspaceOS (configurable via FEEDBACK_REPO in .env) with auto-captured page context — current surface, project id, URL, last 10 bench events. Issue labeled user-feedback + bug / enhancement / question.

Needs GITHUB_TOKEN with issues:write scope. Disabled gracefully if the token is missing — the modal returns a clear error instead of silently failing.

Status

OSS-targeted, MIT licensed (see LICENSE). The bench, six surfaces, extension framework, onboarding wizard, knowledge graph, worklog generator, and paper pipeline v2 all work today. Multi-tenant deployment is not yet hardened — see Security notes in CONTRIBUTING.md.

Tech notes

Next.js 16 conformance — uses proxy.ts (not deprecated middleware.ts), useSearchParams wrapped in <Suspense>, dynamic params via use().
Knowledge dedup — per-user asyncio.Lock serializes concurrent advisor extractions so cosine-near nodes from one roundtable turn merge instead of duplicating.
Event SSE auth — falls back to a ?api_key= query string because EventSource can't set custom headers. Fine for single-tenant demo, not safe for shared deployment without a short-lived SSE token exchange.
Reduced motion respected — WCAG 2.3.3 honored globally.

Contributing

Pull requests welcome — especially new content extensions. See CONTRIBUTING.md for the authoring guide.

License

MIT. See LICENSE.

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WorkspaceOS

What it does

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Quick start

How extensions plug in

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Required vs optional setup

Running AI locally with Ollama (optional)

Capability extensions (v0.2.1)

Discovery + setup — where users find and configure capabilities

Configuring a capability — the easy path

Authoring capabilities

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Name		Name	Last commit message	Last commit date
Latest commit History 235 Commits
.claude/commands		.claude/commands
backend		backend
config		config
docs		docs
frontend		frontend
scripts/outlook_bridge		scripts/outlook_bridge
sidecars/datamaster		sidecars/datamaster
.env.example		.env.example
.gitignore		.gitignore
CLAUDE.md		CLAUDE.md
CONTRIBUTING.md		CONTRIBUTING.md
LICENSE		LICENSE
README.md		README.md
README.zh-CN.md		README.zh-CN.md
docker-compose.yml		docker-compose.yml

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What it does

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Quick start

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Capability extensions (v0.2.1)

Discovery + setup — where users find and configure capabilities

Configuring a capability — the easy path

Authoring capabilities

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Persona grounding (v0.2.2)

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