The GridION is a compact benchtop device designed to run up to five MinION or Flongle flow cells. Each flow cell is independently addressable, meaning that experiments can be run concurrently or individually. Integrated compute in the GridION enables real-time data streaming and analysis.

Our GridION FAQs are located here.

The shipment will contain:

• GridION device
• C13 cable specific to the country of delivery
• Five configuration test cells (CTCs)
• DisplayPort to HDMI adapter
• Quick Start Guide

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

• 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

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.

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.

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)

• If you need to update the hostname of the device, run the following command and replace the <new_hostname> portion with your desired hostname (omitting the angle bracket characters <>):

sudo -S hostnamectl set-hostname <new_hostname>

• Power cycle the device by shutting down with the following command, then press the physical power button to turn the device back on:

sudo shutdown -h now

First find the correct timezone name by typing the command:

sudo timedatectl list-timezones

Then change the timezone using the following commands:

sudo su -
Timezone="Europe/London"
timedatectl set-timezone $Timezone
systemctl restart systemd-timesyncd

Note: this requires NTP/port 123 access if using an external internet time server.

Enter the following commands:

NTPserver="ntp.ubuntu.com" timedatectl set-ntp false cat << EOF > /etc/systemd/timesyncd.conf # See timesyncd.conf(5) for details.[Time] NTP=$NTPserver EOF systemctl stop ntp ntpdate $NTPserver systemctl disable ntp timedatectl set-ntp true hwclock --systohc timedatectl set-local-rtc 0

Some error messages may appear, however these can be ignored. You can check that the process has worked by typing:

timedatectl status

Note: it may take several minutes to sync with the NTP server.

A loading bar appears under the flow cell during the checks.

This example is a Flongle CTC (loading bar highlighted in red).

We strongly recommend performing a flow cell check before loading a DNA or RNA library to assess the number of pores available.

Oxford Nanopore Technologies will replace any flow cell that falls below the warranty number of active pores within three months of purchase, provided that you report the results within two days of performing the flow cell check and you have followed the storage recommendations.

When a flow cell is inserted into a device, the flow cell position indicator LED will light up a colour depending on the condition of the ASIC on the flow cell. The application-specific integrated circuit (ASIC) is connected to the sensor array and measures the ionic current flow across the nanopores.

• Blue: No ASIC is detected on the flow cell
• Green: ASIC is detected
• Red: There is a problem with the ASIC

A loading bar appears under the flow cell during the checks.

This example is a Flongle CTC (loading bar highlighted in red).

The quality of the flow cell will be shown as one of the three outcomes:

1. Yellow exclamation mark (Flongle flow cell): The number of sequencing pores is below warranty. Take the flow cell out of the device, re-insert it and run a flow cell check again. If the flow cell is still below warranty, contact support@nanoporetech.com

2. Green tick (MinION flow cell): The number of sequencing pores is above warranty.

3. Question mark (PromethION flow cell): A flow cell check has not been run on the flow cell during this MinKNOW session.

Note: The indicator of quality will only remain visible during a MinKNOW session. Once the MinKNOW session has ended, the status of the flow cell will be erased.

To run a sequencing experiment, you will need your DNA or RNA sample purified and a sequencing library prepared. For more information about sample preparation, refer to the Prepare section of our Documentation.

You can access the MinKNOW protocol by following this link.

GridION: Data offload to remote storage

Our device FAQs are located here.

Data can be managed and transferred from the file manager tab on the host settings.

Navigate through the tabs to view the data stored:

• Internal tab: Data stored on the connected sequencing device (MinION Mk1C, GridION, PromethION)
• Removable tab: Data stored on a connected removable storage device e.g. USB drive
• Network tab: Data stored on a connected network drive. The network drive must be mounted prior.

Click the icon in the bottom right corner to open Create New Directory and type in a directory name. Click Create.

Navigate to Device Settings to view available disk space on the device. Any peripherals plugged in, including USB, can be ejected using the Eject option.

A network drive can also be connected to the device by selecting Add Network Drive and filling in the required credentials for connecting using a Samba (SMB) server or a Network File System (NFS).

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.

MinKNOW is the software used on nanopore sequencing devices. The software is described in more detail in the MinKNOW Technical Document. The MinKNOW Protocol provides instructions on how to use the software.

The Oxford Nanopore Technologies software will require access to the AWS IP ranges currently listed here:

http://docs.aws.amazon.com/general/latest/gr/aws-ip-ranges.html

Access to the following IP addresses is also needed:

              178.79.175.200  
               96.126.99.215  

After successfully checking the hardware you should update to the latest software release. This can be completed by entering the following into the terminal:

sudo apt clean
sudo apt update
sudo apt install ont-gridion-release

The default sudo password is grid, this should be changed to ensure the security of your device. Once these commands have completed successfully without errors please turn off the device using the command before turning on again to complete a full power cycle:

sudo poweroff

Oxford Nanopore Technologies will post a release note in the Nanopore Community when new software or updates to the device go out.

We urge users to update as soon as reasonably possible after the release has been made available.

Keep the device up-to-date with Linux security updates, in line with advice from your local IT department.

Note: It is specifically required that you make outbound-only access to the internet over port 443 to enable updates through your network Firewall.

The below instructions can be used to create a bootable USB drive that can be used to rebuild the OS on your device.

These instructions are for users who did not receive a USB drive with the ISO image. If you have received a USB drive, proceed to the next step: "How to boot from USB".

https://nanoporetech.box.com/s/i7c2itn6sro0mhumi3lxefpp0yddh3y6

Appropriate software for burning the ISO image is:

• Rufus on Windows

Note: The alternate ISO burning tool balenaEtcher does not work for our ISO image. You will need access to a computer running Windows and may need Administrator rights to install the Rufus software.

When burning the ISO image, use the below settings (it must use an EFI/GPT boot):

• Partition scheme: GPT
• Target system: UEFI

The USB drive should have the below specification:

• Must be 32 GB or larger
• USB 3.0 recommended
• UEFI boot option must be used

Note: We recommend flashing two USB drives with a different vendor as a backup. Common USB drives can fail to reimage devices with no obvious root cause.

Note: It is normal for the system to restart multiple times.

Press Enter once the UEFI option is chosen, then ensure Format disks and lose /data is highlighted. This option will reset all disks and rebuild your whole system, and will require you to manually set the hostname once building is complete.

The rebuild process will now blank all of the system’s disks and then reboot. Proceed with the installation as described from step 4 selecting “Customer factory reset”.

During the process to blank all of the system’s disks, the following screen will be visible showing either ASRock or ASUS with a scrolling circle. This process may take time to complete and be following by a reboot.

The final "secure wipe" option will lose data and wipe the hard drives completely to a known state. If your GridION is unable to boot up even after "secure wipe" and a subsequent customer factory reset, contact Support (support@nanoporetech.com) as this may indicate a hardware failure.

To find our most common FAQs, please see the support section for MinKNOW here.

In most cases where troubleshooting is required, we recommend exporting your logs and sending them to Technical Services.

The Nanopore support hub can also be accessed directly from your MinKNOW UI.

In the top right of MinKNOW you will see the "Help" option:

Clicking this option will bring you to a page with a link and a QR code:

On larger devices such as the GridION and PromethION 24/48, and devices such as the MinION Mk1b and P2 Solo, clicking the link will directly bring you to the Nanopore support page.

On devices such as the P2 Integrated and MinION Mk1C, you will be able to scan the QR code with another device, or type in the shortened URL on another device to quickly reach the support hub.

For the PromethION 24/48, PromethION 2i, GridION and PromethION 2 Solo connected to a GridION:

• Click Export in the Export Logs section.

When you have successfully exported the logs, you will be notified of where they are located below the button. The logs will be downloaded as a TGZ file in the logs directory.

You can change the location of the logs by using the file manager, where you can easily retrieve them without needing SSH:

• Click on the file next to Logs exported to: in the Export Logs panel. This will open where the logs are located in the File Manager of MinKNOW.
• Use the control panel in the lower right corner of the File Manager to move the log files.

If the PromethION 2 Solo is connected to a stand-alone computer

Log files for each sequencing experiment can be found in:

• Windows C:\data\logs

• Mac OS X /private/var/log/MinKNOW

• Linux /var/log/minknow

In the "Help" page, click Clean up in the Clean Up Files section and confirm in the in the pop-up.

Note: Run data will not be deleted. Logs and temporary data will be removed.

Click Run repair in the troubleshooting section of the Help page and confirm in the pop-up. MinKNOW will attempt to repair the following issues:

• Ensure required directories under "/data" exist and have the correct ownership and permissions
• Ensure required files under "/data" have the correct ownership and permissions
• Ensure the GPU is working at maximum performance
• Ensure that Bluetooth is disabled