# NEMAR

> Documentation for NEMAR (Neuroelectromagnetic Data Archive and Tools Resource) — the CLI, the platform APIs, the data plane, and the tools around them.

## The Ecosystem

- [The NEMAR ecosystem](https://docs.nemar.org/ecosystem/): How the parts of NEMAR fit together — the CLI, the backend API, the public data plane, the dataset browser, the signal viewer, and the tooling around them.
- [CLI vs the web](https://docs.nemar.org/ecosystem/cli-vs-web/): NEMAR has two surfaces, the CLI and the web app. They share one backend, accounts, and datasets. Here is when to use each.

## Web App

- [Account settings](https://docs.nemar.org/web/account-settings/): Change your email, GitHub handle, and ORCID link, choose a username and name, and what one person, one account means for you.
- [Getting started on the web](https://docs.nemar.org/web/getting-started/)
- [Managing your datasets](https://docs.nemar.org/web/managing-datasets/)
- [Publication review](https://docs.nemar.org/web/publication-review/)
- [Upload access](https://docs.nemar.org/web/upload-access/): The three account states, what each one unlocks, and how to request the one-time admin approval that lets you upload.
- [Uploading a dataset (web)](https://docs.nemar.org/web/uploading/)

## CLI

- [NEMAR CLI](https://docs.nemar.org/cli/): The command-line interface for managing NEMAR datasets. Install it, authenticate, then upload, validate, version, and download BIDS datasets.
- [Command Reference](https://docs.nemar.org/cli/commands/): Overview of the nemar CLI's top-level commands, options, and shortcuts.
- [auth](https://docs.nemar.org/cli/commands/auth/)
- [dataset](https://docs.nemar.org/cli/commands/dataset/)
- [sandbox](https://docs.nemar.org/cli/commands/sandbox/)
- [Authentication](https://docs.nemar.org/cli/getting-started/authentication/): Sign in to the NEMAR CLI with your browser, the headless case, the paste-key fallback, and managing a named key per machine.
- [Installation](https://docs.nemar.org/cli/getting-started/installation/)
- [Quick Start](https://docs.nemar.org/cli/getting-started/quickstart/): Sign in with your browser, complete sandbox training, request upload access, then validate and upload your first dataset.
- [Collaboration & the Lifecycle](https://docs.nemar.org/cli/guides/collaboration/): How a dataset moves from a private, collaborator-only draft to a public, PR-driven resource, and who can do what at each stage.
- [Downloading Datasets](https://docs.nemar.org/cli/guides/downloading/)
- [Publishing Datasets](https://docs.nemar.org/cli/guides/publishing/)
- [Uploading Datasets](https://docs.nemar.org/cli/guides/uploading/)
- [BIDS Validation](https://docs.nemar.org/cli/guides/validation/)
- [Dataset Versioning](https://docs.nemar.org/cli/guides/versioning/)
- [Account Access](https://docs.nemar.org/cli/reference/account-access/): nemar auth profile, nemar auth request-upload-access, and the Upload access line in nemar auth status.
- [Configuration](https://docs.nemar.org/cli/reference/configuration/): The config file location, the multi-account structure, the key fields a browser-minted key carries, and file permissions.
- [Debugging and Bug Reports](https://docs.nemar.org/cli/reference/debugging/): The global --debug flag and NEMAR_DEBUG=1: what the diagnostic log contains, what it redacts, where it lands, and how to attach it to a bug report.
- [Environment Variables](https://docs.nemar.org/cli/reference/environment/): NEMAR_API_KEY, NEMAR_NO_BROWSER, NEMAR_CONFIG_DIR, NEMAR_DEBUG, and NEMAR_NO_UPDATE_CHECK, plus how to authenticate a CI runner.

## Platform & APIs

- [Platform & APIs](https://docs.nemar.org/platform/): The NEMAR backend API and the public data plane — the HTTP surfaces behind the CLI and the website.
- [API Reference](https://docs.nemar.org/platform/api/): The NEMAR API: browser device sign-in, named API keys, account kinds, and the datasets/admin endpoints. For advanced users.
- [Data API: `data.nemar.org`](https://docs.nemar.org/platform/data-api/)
- [For Agents](https://docs.nemar.org/platform/for-agents/): One page to point an autonomous agent, script, or tool integration at: what NEMAR is, which host answers which question, verified request examples, and when to stream instead of download.
- [Zarr Serving Copy](https://docs.nemar.org/platform/zarr/): The derived Zarr v3 serving copy of every NEMAR recording: what it is, what it is not, and where its contract is documented.
- [Access and Hosting](https://docs.nemar.org/platform/zarr/access/): The stable URL, anonymous S3 access, the browser-versus-machine split at the edge, caching, and rate limits for the Zarr serving copy.
- [Cost Ladder and Recipes for Agents](https://docs.nemar.org/platform/zarr/cost-ladder/): Roughly how many bytes and requests each layer of the Zarr contract costs, and worked read recipes in Python and JavaScript.
- [Format Stability Policy](https://docs.nemar.org/platform/zarr/format-stability/): What format_version promises for the index and the store, what counts as additive versus breaking, and where to watch for change.
- [Index Contract](https://docs.nemar.org/platform/zarr/index-contract/): The per-dataset index.json document: format_version 3 field by field, the discovered_count invariant, failure and pending semantics, and the discovery catalog.
- [Store Contract](https://docs.nemar.org/platform/zarr/store-contract/): The Zarr v3 layout of one NEMAR recording's serving store: groups, attributes, chunk geometry, and the dequantization formula.

## Develop

- [Development Setup](https://docs.nemar.org/develop/setup/)
- [Zenodo Sandbox Testing](https://docs.nemar.org/develop/zenodo-testing/)

## Policies

- [Policies](https://docs.nemar.org/policies/): NEMAR's privacy policy, data contributor terms, submission standards, GDPR position, and takedown procedure.
- [AI-Assisted Curation](https://docs.nemar.org/policies/ai-use/): Where NEMAR uses AI in dataset curation, why its output is never final, and how to request a correction.
- [Data Contributor Terms](https://docs.nemar.org/policies/contributor-terms/): What depositors warrant when uploading a dataset to NEMAR, including de-identification, ethics approval, key handling, and licensing.
- [GDPR Position Statement](https://docs.nemar.org/policies/gdpr/): How the European Union's General Data Protection Regulation applies to NEMAR datasets, user accounts, and international transfers, with references.
- [Privacy Policy](https://docs.nemar.org/policies/privacy/): What personal information NEMAR collects from registered users, why, how long it is kept, and the rights you have over it.
- [Dataset Submission Standards](https://docs.nemar.org/policies/submission-standards/): What a dataset must include to be published on NEMAR, and what we strongly recommend beyond that minimum.
- [Takedown Procedure](https://docs.nemar.org/policies/takedown/): How to report a NEMAR dataset that should be removed, and how reports are assessed and acted on.