GridION Q installation and configuration
GridION: Protocol
GridION Q installation and configuration V Q_GRD_revA_28Feb2020
This document will help you to install, check and configure your Q system GridION™.
FOR RESEARCH USE ONLY
Contents
Installation
GridION configuration
Shutting down
Additional information
Overview
This document will help you to install, check and configure your Q system GridION™.
1. Preparation
Preparing for installation
Before you install the device, the following must be available:
- 1x Ethernet cable (1 Gbps)
- Ethernet port providing outbound-only access to the internet over port 443, and TCP access to AWS eu-west-1 IP ranges listed here for EPI2ME analysis
- Outbound-only access over HTTPS/port 443 to 52.17.110.146, 52.31.111.95, 79.125.100.3 or DNS rule for ping.oxfordnanoportal.com for telemetry feedback
- Outbound-only access over HTTPS/port 443 to 178.79.175.200 and 96.126.99.215 or DNS rule for cdn.oxfordnanoportal.com for software updates
- 1x monitor (HDMI/DisplayPort compatible)
- 1x appropriate monitor cable
- 1x USB connected keyboard
- 1x USB connected mouse
- Optional: UPS solution with C14 cable
Technical specification
| Size and weight | 220 x 365 x 370 mm, 14.4 kg |
| Power | 650 W |
| Computer specification | 7 TB SSD Storage, 64 GB RAM, Intel i9 CPU for OS and orchestration, GridION accelerator |
| Pre-loaded software | Linux OS, GridION OS, MinKNOW |
| Environmental conditions | Designed to sequence at +18°C to +25°C Functional range of electronics +5°C to +40°C |
Recommended laboratory location
- Place the device on a strong, clean laboratory bench
- Ensure Ethernet and power connectors are in close proximity
- Ensure power socket is easily accessible should a disconnection be required in case of emergency
- Sequencing should be carried out at a room temperature of +18°C to +25°C
- Allow 30 cm clearance to rear and sides of the device
- Do not cover any ventilation grilles
- WARNING - The rear of the device will heat up during operation
What's in the box
The shipment will contain:
- a GridION Q device
- a C13 cable specific to the country of delivery
- five configuration test cells (CTCs)
- a DisplayPort to HDMI adapter
GridION Q packaging
2. Installation
CAUTION
Please note that the GridION Q device weighs approximately 11 kg, and care should be taken during lifting and moving.
Unpack the device and place it on the bench where it is to be run.
Attach all the required cables to the device using the diagram below to assist.
- 1x Ethernet
- 1x HDMI or DisplayPort to monitor*
- 1x USB for keyboard
- 1x USB for mouse
- 1x C13 cable
*1x DisplayPort to HDMI adapter is provided
IMPORTANT
Please note that on older versions of the GridION, only the USB ports on the back of the device are USB 3.0. The ports in the front of the device are USB 2.0, and are not recommended for data transfer.
Connect the power cable to your mains/UPS solution. Use the mains cord supplied, or a suitable approved and rated power cord. Ensure the device is connected to a protective earth mains supply. Turn the power source on.
Press the power button. A blue light will appear in the middle of the button. The screen will show a loading page, followed by a login screen.
When the login screen appears, enter the password "grid" and log in.
Note: Instructions on how to change the default password can be found under "Updating the device and changing the default password" in this document.
Click the Nanopore Wheel icon on the desktop to load the MinKNOW software. You will see the MinKNOW user interface appear.
Changing the default password
The default password should be changed at the earliest opportunity to ensure the security of your device. To do this, open a Terminal window and type:
passwd
Then press Enter. The following arguments will be presented in the terminal; follow the instructions to change the password:
grid@gxb02000:~$ passwd
Changing password for grid.
(current) UNIX password: grid
Enter new UNIX password: XXXX
Retype new UNIX password: XXXX
passwd: password updated successfully
Note: The new GridION/UNIX password should be in line with your local IT guidelines for device security.
You are now ready to perform the Hardware Check.
Load the five configuration test cells (CTCs) into the GridION positions X1-X5. All five positions will turn green as the CTCs are recognised.
Navigate to the Start homepage and click 'Hardware Check' option.
Select all the flow cell positions and select 'Start' to begin the checks.
Using MinION flow cells on a GridION: 
A screen will appear asking you to check that the CTCs are inserted correctly. Once confirmed, click "Start test".
The message tab on the right will show "Starting hardware check", followed by "Hardware check has completed successfully" for each flow cell.
END OF STEP
Your device is ready for sequencing once your configuration run is complete.
Please refer to the library preparation protocols in the Q channel of the Nanopore Community.
3. Configuring network parameters
CAUTION
Changing your network configuration
The network parameters for your GridION must be suited to your local network.
WARNING! Changing the network parameters on your GridION may leave your device non-functional.
If you are uncertain about which parameters to use to configure your GridION network settings, please contact your IT department.
Networking requirements
GridION uses a 1x1 Gbps Copper interface for connecting to your local infrastructure. This has a single port with the IP address configured to DHCP by default (however static IPs are configurable). This connection will be used for:
- Sending telemetry* information to Oxford Nanopore Technologies.
- Receiving software and firmware updates to the device
- Streaming biological sequence data to your local storage infrastructure
To implement the GridION into the local infrastructure, all appropriate cabling must be provided by the customer.
* Telemetry contains metadata about the settings and conditions of a sequencing run. Nothing specific about the genomic content of individual reads is included - only generic information is logged, such as sequence length and q-score.
Networking options
The GridION offers 1 x 1 Gbps Copper interface. The only available option is listed below:
- Copper
- Single port with the IP address configured to DHCP by default (static IP are configurable)
Configuring your network
If you want to connect your GridION to a single network, you should use the user interface
To configure your GridION to connect to multiple networks, open a Terminal window and enter:
ont-network-settings
The options for this script are:
--dhcp - Optional - Use DCHP and removes need for all other features except for the interfaces, bond and overwrite
--address ip_address - Required - IP address of the GridION
--subnet subnet_mask - Required - Subnet mask for the GridION
--gateway gateway_address - Required- Default gateway for the GridION
--dns DNS_server1,DNS_server2 - Required - DNS servers for the GridION
--search your_domain - Required - Your domain suffix (e.g. yourcompany.local)
--overwrite - Optional
--help - Details the options above
To update the settings, you must run the suitable command from the above options with the --overwrite flag and reboot the machine.
Validate the IP address
To validate that the IP address has been set correctly using a static or DHCP address, you can use the command: ifconfig
The returned information will contain the IP address for the Ethernet link, as below:
grid@GXB03415:~$ ifconfig
docker0: flags=4099<UP,BROADCAST,MULTICAST> mtu 1500
inet 172.17.0.1 netmask 255.255.0.0 broadcast 172.17.255.255
ether 02:42:35:39:60:40 txqueuelen 0 (Ethernet)
RX packets 0 bytes 0 (0.0 B)
RX errors 0 dropped 0 overruns 0 frame 0
TX packets 0 bytes 0 (0.0 B)
TX errors 0 dropped 0 overruns 0 carrier 0 collisions 0
eno1: flags=4163<UP,BROADCAST,RUNNING,MULTICAST> mtu 1500
inet 10.150.60.13 netmask 255.255.255.0 broadcast 10.150.60.255
inet6 fe80::78cf:8a5c:26ec:4611 prefixlen 64 scopeid 0x20<link>
ether 3c:7c:3f:be:02:81 txqueuelen 1000 (Ethernet)
4. Changing the default password
Changing the default password
The default password should be changed at the earliest opportunity to ensure the security of your device. To do this, open a Terminal window and type:
passwd
Then press Enter. The following arguments will be presented in the terminal; follow the instructions to change the password:
grid@gxb02000:~$ passwd
Changing password for grid.
(current) UNIX password: grid
Enter new UNIX password: XXXX
Retype new UNIX password: XXXX
passwd: password updated successfully
Note: The new GridION/UNIX password should be in line with your local IT guidelines for device security.
5. Exiting the GUI and shutting down
Shutting down your GridION
The GridION's computer requires a stepwise, processed shut down, otherwise you may face problems e.g. when recognising flow cells.
Follow the instructions in this section to ensure you do not face errors with your GridION from incorrectly shutting down your device.
Ensure none of the flow cells are running an experiment.
An indication that no experiments are running is the lack of an Experiment status bar where the availability box is in the flow cell selection windows.
Please close the MinKNOW GUI using the "X" in the top left corner.
Select "Shut down" from the power options at the top right of the screen.
Select the "Shut down" button on the right of the pop-up window.
IMPORTANT
Do NOT select 'Reboot'. This will lead to errors in recognising the flow cells when commencing an experiment.
The screen will show the Oxford Nanopore Technologies logo on a black background. This may take several minutes to process, before the screen blacks out.
Note: Powering down will be indicated by the light on the power button switching off.
Turn off the device at the mains supply, if you are using mains power.
6. Maintenance and support
IMPORTANT
Storage of CTCs
The Configuration Test Cells (CTC)s should be stored in dry conditions at room temperature. The CTCs should not be stored in the device's flow cell positions when the platform/position is not in use.
Cleaning
Absorb excess liquid using a laboratory tissue and clean the area using an IPA wipe should any leaks/condensation develop over the course of loading a flow cell or during an experiment.
Dispose of the cleaning materials into a biohazard waste bin.
Help and support
If you experience issues with your hardware check, configuring your network or general functionality of your device, please contact Customer Support at support@nanoporetech.com