Opentrons · ecormany · Aug 11, 2025 · Jul 31, 2025 · Jul 31, 2025 · Jul 31, 2025
diff --git a/docs/Makefile b/docs/Makefile
@@ -1,4 +1,4 @@
-FLEX_MANUAL_PREFIX ?= flex-manual
+FLEX_MANUAL_PREFIX ?= flex
 # AWS_PROFILE is intentionally left undefined by default
 BRANCH ?= edge
 SANDBOX_S3_BUCKET ?= sandbox.docs

diff --git a/docs/flex-manual/docs/images/magnetic-block.png b/docs/flex-manual/docs/images/magnetic-block.png
diff --git a/docs/flex-manual/docs/images/temperature-module.png b/docs/flex-manual/docs/images/temperature-module.png
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diff --git a/docs/flex-manual/docs/protocol-development.md b/docs/flex-manual/docs/protocol-development.md
diff --git a/docs/flex-manual/docs/software-operation.md b/docs/flex-manual/docs/software-operation.md
diff --git a/docs/flex-manual/docs/system-description.md b/docs/flex-manual/docs/system-description.md
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diff --git a/...x-manual/docs/additional-documentation.md → docs/flex/docs/additional-docs.md b/...x-manual/docs/additional-documentation.md → docs/flex/docs/additional-docs.md
diff --git a/docs/flex/docs/advanced-operation.md b/docs/flex/docs/advanced-operation.md
@@ -0,0 +1,115 @@
+---
+title: "Opentrons Flex: Advanced Operation"
+---
+
+# Advanced Operation
+
+Flex provides methods of advanced control that let you directly manipulate files on the robot and execute commands outside of protocols.
+
+## Command line operation over SSH
+
+You can work with your Flex through a Secure Shell (SSH) terminal connection. Terminal access lets you [run protocols directly from the command line](https://docs.opentrons.com/v2/new_advanced_running.html#command-line) or perform advanced tasks, such as customizing the Python environment on the robot. Protocols that reference external files on disk (apart from custom labware definition files) must be run from the command line.
+
+!!!note
+    - SSH keys are required before you can connect to Flex and issue commands from a terminal.
+    - If you're unable to use a Wi-Fi network for SSH, see [Hardwired SSH Connections][hardwired-ssh-connections] below.
+
+### Creating SSH keys
+
+Follow these steps to create SSH keys on your Mac, Windows, or Linux computer:
+
+1. Open a terminal window and type this command:
+
+    ```
+    ssh-keygen -f robot_key -t ecdsa
+    ```
+
+1. Create a passphrase when prompted. This process generates a file, `robot_key.pub`. A passphrase is not required, but you should create one.
+
+1. Copy the `robot_key.pub` file to the root of a USB-A flash drive. You will use this USB drive (and the saved key) for SSH authentication to the robot.
+
+    !!!note
+        The flash drive must have a single partition formatted with a file system readable by the embedded Linux system on Flex. FAT32, NTFS, and ext4 file systems are supported. The macOS HFS+ and APFS file systems are not. macOS can read and write to FAT-formatted drives.
+
+1. Eject the USB drive.
+
+### Making an SSH connection
+
+To make an SSH connection:
+
+1. Insert the USB drive that holds the SSH key created earlier into a USB port on your Flex.
+
+1. On your computer, open a terminal window and type the commands shown below. Replace `ROBOT_IP` with the IP address of your Flex.
+
+    ```
+    curl \
+    --location --request POST \
+    'http://ROBOT_IP:31950/server/ssh_keys/from_local'
+    ```
+    The command is successful when you see a response message that indicates a new key was added.
+
+1. After adding the key, type the command shown below. Replace `ROBOT_IP` with the IP address of your Flex.
+
+    ```
+    ssh -i robot_key root@ROBOT_IP
+    ```
+
+1. Type the passphrase you set when creating the SSH key.
+
+When an SSH connection is successful, the terminal command prompt changes to `root@` followed by the serial number of your robot (e.g., `root@FLXA1020231007001:~#`). You can now interact with the robot via the terminal window.
+
+### Hardwired SSH connections
+
+A hardwired connection uses an Ethernet cable to connect and transmit data directly between your computer and Flex. This is a secure alternative for SSH access in situations where network policies prevent you from making a wireless connection to the robot.
+
+!!!note
+    The hardwired SSH procedure requires assigning a static IP address to the robot. You may want to ask for help from your IT support team before proceeding.
+
+#### Physical connection
+
+Connect a computer to the robot using an Ethernet cable. If your computer has a built-in RJ-45 Ethernet port, plug one end into the computer and connect the other end to the Ethernet port on the robot. If you're using a computer without an Ethernet port, use an adapter with an Ethernet port to make this connection.
+
+When disconnected from a network, your Flex will assign itself an IP address and subnet mask. You'll need this information to set a static address on your computer within the same IP address range and subnet as your Flex.
+
+#### Finding the robot's IP address
+
+You can get the IP address range and subnet mask from the robot by connecting it to your computer and checking the Opentrons App:
+
+1. If the robot is connected by Ethernet cable to a switch or wall jack, disconnect it. Then establish a physical Ethernet connection to your computer, as described above.
+
+1. Launch the Opentrons App.
+
+1. Click the **Devices** tab and find your robot.
+
+    !!!note
+        If your robot appears as inactive or inaccessible in the app, wait a few moments. Flex will configure itself and eventually become available again. If this does not happen, turn the robot's power off, wait a few seconds, turn the power back on, and check the app again after the robot boots up.
+
+1. After locating your robot in the app, click the three-dot menu (⋮), select **Robot settings**, and then click the **Networking** tab.
+
+The Networking tab will show you the IP address and subnet mask of your robot. When disconnected from a network, Flex will assign itself a non-routing IP address. Here's an example of a self-assigned IP address on a Flex:
+
+- IP address: 169.254.29.160
+- Subnet mask: 255.255.0.0
+
+#### Setting a static IP address
+
+The static IP address on your computer needs to be in the same IP range and subnet that your Flex uses. Given the robot's IP address above, you could set your computer's IP address and subnet as shown here:
+
+- IP address: 169.254.29.164
+- Subnet mask: 255.255.0.0
+
+After you have a working hardwired connection, follow the instructions in [Making an SSH Connection](software-operation.md#making-an-ssh-connection) above.
+
+## Jupyter Notebook
+
+Flex runs a [Jupyter Notebook](https://jupyter.org/) server on port 48888, which you can connect to with your web browser. Use Jupyter to individually run discrete chunks of Python code, called *cells*. This is a convenient environment for writing and debugging protocols, since you can define different parts of your protocol in different notebook cells, and run a single cell at a time.
+
+Access your robot's Jupyter Notebook either:
+
+- In the Opentrons App. Go to **Devices** > your robot > **Robot Settings** > **Advanced** and then click **Launch Jupyter Notebook**.
+
+- In your web browser. Navigate directly to `http://<robot-ip>:48888`, replacing `<robot-ip>` with the local IP address of your Flex.
+
+For more details on using Jupyter, including preparing executable cells
+of code and running them on a robot, see the [Jupyter Notebook section](https://docs.opentrons.com/v2/new_advanced_running.html#jupyter-notebook) of the Python Protocol API documentation.
+
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diff --git a/docs/flex-manual/docs/index.md → docs/flex/docs/index.md b/docs/flex-manual/docs/index.md → docs/flex/docs/index.md
@@ -1,3 +1,7 @@
+---
+title: "Opentrons Flex Instruction Manual"
+---
+
 <style>
 .md-content__inner {
   text-align: center;

diff --git a/docs/flex/docs/installation/first-run.md b/docs/flex/docs/installation/first-run.md
@@ -0,0 +1,83 @@
+---
+title: "Opentrons Flex: First Run"
+---
+
+# First Run
+
+Perform basic setup on the touchscreen before connecting any other hardware to your Flex. The robot will guide you through connecting to your lab network, updating to the latest software, and personalizing Flex by giving it a name.
+
+## Power on
+
+When you power on Flex, the Opentrons logo will appear on the touchscreen. After a few moments, it will show the "Welcome to your Opentrons Flex" screen.
+
+<figure class="screenshot" markdown>
+![The Opentrons Flex welcome screen.](../images/welcome-to-flex.png "Welcome to your Opentrons Flex!")
+<figcaption>The Opentrons Flex welcome screen. You should only see this screen when you start your Flex for the first time.</<figcaption>
+</figure>
+
+## Connect to a network or computer
+
+Follow the prompts on the touchscreen to get your robot connected so it can check for software updates and receive protocol files. There are three connection methods: Wi-Fi, Ethernet, and USB.
+
+<figure class="screenshot" markdown>
+![Network connection options.](../images/choose-network-type.png "Network connection options")
+<figcaption>Network connection options. You need to have internet connectivity to set up Flex.</figcaption>
+</figure>
+
+**Wi-Fi:** Use the touchscreen to connect to Wi-Fi networks that are secured with WPA2 Personal authentication (most networks that only require a password to join fall under this category).
+
+!!! note 
+    Flex does not support captive portals (networks that don't have a password but load a webpage to authenticate users after connecting).
+
+You can also connect to an open Wi-Fi network, but this is not recommended.
+
+!!! warning
+    Connecting to an open Wi-Fi network will allow anyone in range of the network signal to control your Opentrons Flex robot without authentication.
+
+If you need to connect to a Wi-Fi network that uses enterprise authentication (including "eduroam" and similar academic networks that require a username and password), first connect to the Opentrons App by Ethernet or USB to complete initial setup. Then connect to the enterprise Wi-Fi network in the networking settings for your Flex. To access the networking settings:
+
+1.  Click **Devices** in the left sidebar of the Opentrons App.
+
+2.  Click the three-dot menu (⋮) for your Flex and choose **Robot Settings**.
+
+3.  Click the **Networking** tab.
+
+Select your network from the dropdown menu or choose "Join other network..." and enter its SSID. Choose the enterprise authentication method that your network uses. The supported methods are:
+
+- EAP-TTLS with TLS
+
+- EAP-TTLS with MS-CHAP v2
+
+- EAP-TTLS with MD5
+
+- EAP-PEAP with MS-CHAP v2
+
+- EAP-TLS
+
+Each of these methods requires a username and password, and depending on your exact network configuration may require certificate files or other options. Consult your facility's IT documentation or contact your IT manager for details of your network setup.
+
+**Ethernet:** Connect your robot to a network switch or hub with an Ethernet cable. You can also connect directly to the Ethernet port on your computer, starting in robot system version 7.1.0.
+
+**USB:** Connect the provided USB A-to-B cable to the robot's USB-B port and an open port on your computer. Use a USB B-to-C cable or a USB A-to-C adapter if your computer does not have a USB-A port.
+
+To proceed with setup, the connected computer must have the Opentrons App installed *and running*. For details on installing the Opentrons App, see the [App Installation section][app-installation] of the Software and Operation chapter.
+
+## Install software updates
+
+Now that you've connected to a network or computer, the robot can check for software and firmware updates and download them if needed. If there is an update, it may take a few minutes to install. Once the update is complete, the robot will restart.
+
+## Attach Emergency Stop Pendant
+
+Connect the included Emergency Stop Pendant (E-stop) to an auxiliary port (AUX-1 or AUX-2) on the back of the robot.
+
+<figure class="screenshot side-by-side" markdown>
+![Screen showing how to connect the E-stop.](../images/install-e-stop-before.png "Before connecting the E-stop.png")
+![Screen showing succesful E-stop connection.](../images/install-e-stop-after.png "After connecting the E-stop.png")
+<figcaption>Before and after connecting the Emergency Stop Pendant.</figcaption>
+</figure>
+
+Attaching and enabling the E-stop is *mandatory* for attaching instruments and running protocols on Flex. For more information on using the E-stop during robot operation, see the of the System Description chapter.
+
+## Give your robot a name
+
+Naming your robot lets you easily identify it in your lab environment. If you have multiple Opentrons robots on your network, make sure to give them unique names. Once you've confirmed your robot's name, you'll be taken to your Opentrons Flex Dashboard. Likely the next step you'll want to take is attaching instruments, which is covered in the next section.
diff --git a/docs/flex/docs/installation/index.md b/docs/flex/docs/installation/index.md
@@ -0,0 +1,11 @@
+---
+title: "Opentrons Flex: Installation and Relocation"
+---
+
+# Installation and Relocation
+
+This chapter describes how to prepare your lab for Opentrons Flex, how to set up the robot, and how to move it if necessary. 
+
+- Before taking delivery of your Flex, make sure that your lab or facility meets all the criteria in the [Installation Requirements](requirements.md) section. 
+- When it's time to get your Flex up and running, follow the detailed instructions in the [Unboxing](unboxing.md), [First Run](first-run.md), and [Instrument Installation and Calibration](instruments.md) sections, or use the Opentrons [On-Site Installation service](https://opentrons.com/instrument-services). 
+- If you ever need to move your Flex to a new location, near or far, follow the steps in the [Relocation](relocation.md) section.