Upload Data to EMBER-DANDI page

docs/user-guide/uploading-data.md

@@ -0,0 +1,89 @@
+# Uploading Data
+
+These instructions will guide you on how to upload data to EMBER-DANDI. 
+
+Please follow the instructions for the option that best fits your needs:
+
+**My files are all in NWB and BIDS:**
+
+Below, we have provided one set of instructions for users that new to EMBER-DANDI, and one set for experienced users.
+
+1. [I've used DANDI or CLI tools before](#instructions-for-experienced-users)
+2. [I'm new to Python, CLI, and/or DANDI](#instructions-for-new-users)
+    - Learn how to set up Python, install the DANDI CLI, and use NWB
+
+**My files are in a mix of standards or I have not used standards:**
+
+Please contact the EMBER team at [help@emberarchive.org](mailto:help@emberarchive.org) to facilitate data ingestion into EMBER-DANDI. We are also happy to add you to our Slack workspace.
+
+
+## Instructions for Experienced Users
+
+The following is a quick reference of the steps for uploading data using the DANDI CLI:
+```
+dandi download https://dandi.emberarchive.org/dandiset/<dandiset_id>/draft
+cd <dandiset_id>
+dandi organize <source_folder> -f dry
+dandi organize <source_folder>
+dandi validate .
+dandi upload -i ember-dandi
+```
+
+## Instructions for New Users
+
+### Install Python
+
+If you're new to Python, it may be useful to start by checking out (Python's Getting Started page)[https://www.python.org/about/gettingstarted/]. There are many ways to install and use Python, so we've highlighted a few common ways to get started below.
+- [Install Anaconda](https://www.anaconda.com/docs/getting-started/getting-started)
+- [Install uv](https://docs.astral.sh/uv/#installation)
+
+### Install the [DANDI Client](https://pypi.org/project/dandi/)
+
+Once you've gotten up and running with Python, the following command will install the DANDI CLI:
+```bash
+pip install -U dandi
+```
+
+### Register for an EMBER-DANDI Account
+
+The steps for registering for an EMBER-DANDI account can found on our [Getting Started](../getting-started/index.md#account-creation) page.
+
+### Getting Started with NWB
+
+For the latest information on NWB (Neurodata Without Borders), we recommend referring to their documentation at [nwb.org](https://nwb.org)!
+
+Below, you will find a brief set of steps to help you quickly get started with NWB.
+
+1. We recommended installing the [NWB Guide](https://nwb-guide.readthedocs.io/en/stable/installation.html), a desktop application that converts common neuroscience data formats into NWB to enable uploading to EMBER-DANDI.
+2. Complete key tutorials for NWB GUIDE:
+    - [Generate a dataset](https://nwb-guide.readthedocs.io/en/stable/tutorials/dataset.html)
+    - Convert a [single session of data](https://nwb-guide.readthedocs.io/en/stable/tutorials/single_session.html)
+    - Convert a [multi-session of data](https://nwb-guide.readthedocs.io/en/stable/tutorials/multiple_sessions.html)
+3. Repeat steps with your own your data
+    - Important Note: All data formats are not currently supported! Ensure your data is supported by checking the [ecosystem compatibility](https://nwb-guide.readthedocs.io/en/stable/format_support.html)
+
+### Create an EMBER-DANDI dandiset
+
+1. Log in to EMBER-DANDI with your approved GitHub account
+2. Select the "New Dandiset" button in the top right corner
+3. Fill out basic metadata and hit "Register Dandiset"
+
+### Upload data to your dandiset
+
+1. Validate your converted files, replacing `<source_folder>` with the path to your .nwb files:  
+
+    ```bash
+    dandi validate --ignore DANDI.NO_DANDISET_FOUND <source_folder>
+    ```
+
+2. Navigate to your dataset in the EMBER-DANDI archive and copy the dandiset ID number
+3. Upload your validated .nwb files using the following commands, replacing `<dandiset_id>` and `<source_folder>` with your specific information:  
+
+    ```bash
+    dandi download https://dandi.emberarchive.org/dandiset/<dandiset_id>/draft
+    cd <dandiset_id>
+    dandi organize <source_folder> -f dry
+    dandi organize <source_folder>
+    dandi validate .
+    dandi upload -i ember-dandi
+    ```

mkdocs.yml

@@ -27,11 +27,15 @@ theme:
 extra_css:
   - stylesheets/extra.css
 
+markdown_extensions:
+  - pymdownx.superfences
+  - pymdownx.highlight
+
 nav:
   - Home: index.md
   - Getting Started:
     - Overview: getting-started/index.md
   - User Guide:
     - Overview: user-guide/index.md
-    # - user-guide/uploading-data.md
+    - user-guide/uploading-data.md
     # - user-guide/downloading-data.md

pyproject.toml

@@ -7,4 +7,5 @@ requires-python = ">=3.12"
 dependencies = [
     "mkdocs>=1.6.1",
     "mkdocs-material>=9.7.0",
+    "pymdown-extensions>=10.17.1",
 ]