13c-metabolic-flux
Estimates intracellular metabolic fluxes from steady-state carbon-13 isotope-tracing measurements using validated atom maps,โฆ
Instance password used as the Bearer token when auth is enabled.
Claude Code
$ npx -y skills add K-Dense-AI/scientific-agent-skills --skill open-notebook --agent claude-code
Codex
$ npx skills add K-Dense-AI/scientific-agent-skills --skill open-notebook -a codex -y
Cursor
$ npx skills add K-Dense-AI/scientific-agent-skills --skill open-notebook -a cursor -y
Gemini CLI
$ npx skills add K-Dense-AI/scientific-agent-skills --skill open-notebook -a gemini-cli -y
GitHub Copilot
$ npx skills add K-Dense-AI/scientific-agent-skills --skill open-notebook -a github-copilot -y
OpenCode
$ npx skills add K-Dense-AI/scientific-agent-skills --skill open-notebook -a opencode -y
Windsurf
$ npx skills add K-Dense-AI/scientific-agent-skills --skill open-notebook -a windsurf -y
name: open-notebook
description: Organizes research with the self-hosted Open Notebook alternative to NotebookLM. Supports source ingestion (PDFs, web pages, audio, video, and Office documents), cited document chat, text and vector search, notes, custom transformations, and multi-speaker podcasts. Use when automating Open Notebook through its REST API or configuring its local or cloud AI providers, including OpenAI, Anthropic, Google, Ollama, Groq, and Mistral.
license: MIT
compatibility: Requires a running Open Notebook backend and worker; Python 3.11+ with requests for bundled helpers. Docker Compose is the documented deployment option. Network access to the instance and any configured providers is required.
metadata:
version: "1.5"
skill-author: K-Dense Inc.
last-reviewed: "2026-09-30"
upstream-version: "1.14.0"
openclaw:
envVars:
- name: OPEN_NOTEBOOK_URL
required: false
description: Backend origin, default http://localhost:5055, not the web UI URL.
- name: OPEN_NOTEBOOK_PASSWORD
required: false
description: Instance password used as the Bearer token when auth is enabled.Open Notebook organizes sources, notes, and AI conversations into research notebooks. It supports several AI providers through Esperanto, full-text and vector search, custom transformations, and podcast generation with speaker profiles. Application storage is self-hosted; content sent to configured cloud models is not local-only.
This skill targets the latest published release observed on 2026-09-30, [v1.14.0](https://github.com/lfnovo/open-notebook/releases/tag/v1.14.0). Request/response contracts were checked against its official source and current main commit `3127f14ea9dbb519f0e4ddc64a0742ca644ba6ef`. Bundled helpers have mocked HTTP regression tests; deployment, ingestion, and paid AI calls were not run against a live instance. Deployment and remote workflow examples are illustrative.
Use Docker Desktop/Engine with Compose. The upstream docker-compose file configures SurrealDB v2 and the `lfnovo/open_notebook:v1-latest` application image. It mounts `./notebook_data` at `/app/data` and `./surreal_data` at `/mydata`.
curl --fail --location --output docker-compose.yml \ https://raw.githubusercontent.com/lfnovo/open-notebook/v1.14.0/docker-compose.yml
Before starting, edit the downloaded Compose file: replace the literal `OPEN_NOTEBOOK_ENCRYPTION_KEY=change-me-to-a-secret-string` value, or change it to `${OPEN_NOTEBOOK_ENCRYPTION_KEY:?Set OPEN_NOTEBOOK_ENCRYPTION_KEY}` and supply that variable. Exporting a shell variable alone does **not** replace the upstream literal. Retain the key across restarts; it encrypts provider credentials, not source documents. Set `OPEN_NOTEBOOK_PASSWORD` in the application's container environment when password protection is wanted; clients then send `Authorization: Bearer <instance-password>`. For a reproducible deployment, resolve and record an image digest; `v1-latest` moves.
docker compose up -d docker compose logs --tail=100 open_notebook
Source installation is also supported; it needs a separate processing worker. See [configuration](references/configuration.md) for persistence and provider setup.
In **Manage โ Models**, add a configuration/credential, test it, discover models, and register the particular models needed. Assign chat and embedding defaults; assign speech models separately for transcription/podcasts. OpenAI, Anthropic, Google, Ollama, Groq, and Mistral have different modalities. Discover support from the instance's `/api/models/providers`; do not infer speech support from LLM support.
Credential discovery returns `discovered[]` with `name` and `provider`, often without a usable `model_type`. Registration requires `models[]` containing `name`, `provider`, and an explicitly chosen `model_type`. The four types are `language`, `embedding`, `speech_to_text`, and `text_to_speech`. They are not `llm`, `stt`, or `tts`. See the [API reference](references/api_reference.md) and [credential example](references/configuration.md).
Resolve this skill's directory and run from its `scripts/` directory, or add that directory to the Python import path. Install requests in a dedicated environment, for example `uv run --isolated --with requests python notebook_management.py --help`. Each CLI only lists records; creation, AI calls, and deletion are explicit functions. Set `OPEN_NOTEBOOK_URL` to the backend origin (an existing `/api` suffix is also accepted). Set `OPEN_NOTEBOOK_PASSWORD` only if the instance requires authentication.
from notebook_management import create_notebook
from source_ingestion import add_text_source, wait_for_processing
from chat_interaction import build_context, create_chat_session, send_chat_message
notebook = create_notebook("Methods review", "Compare reported experimental designs")
source = add_text_source(
notebook["id"], "Pilot study excerpt",
"Illustrative study: 24 samples were randomized to two treatments.",
process_async=True, embed=False,
)
wait_for_processing(source["id"])
built = build_context(notebook["id"], source_ids=[source["id"]], note_ids=[])
if not built["context"]["sources"]:
raise RuntimeError("No source content was included")
session = create_chat_session(notebook["id"], "Methods discussion")
answer = send_chat_message(
session["id"], "What design was reported? Cite the source and identify gaps.",
built["context"],
)
ai_messages = [m for m in answer["messages"] if m["type"] == "ai"]Create a notebook with `POST /api/notebooks` and JSON `name`, `description`. Use `PO
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