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
概览
This document will help you to install, check and configure your Q system GridION™.
1. Preparation
准备安装
在安装测序仪之前，请确保您配置好：
- 1 x 宽带网线（1 Gbps）
- 对EPI2ME分析：宽带端口——对互联网上的443端口进行出站访问，并通过TCP访问此处列出的AWS eu-west-1 IP地址范围。
- 对遥测反馈：能够通过HTTPS/443端口出站访问52.17.110.146、52.31.111.95、79.125.100.3，或访问域名ping.oxfordnanoportal.com
- 对软件更新：能够通过HTTPS/443端口出站访问178.79.175.200 及 96.126.99.215，或访问域名cdn.oxfordnanoportal.com
- 1x 显示器（兼容 HDMI/DisplayPort ）
- 1X 适配的显示器电线
- 1x 通过USB连接的键盘
- 1x 通过USB连接的鼠标
- 可选：连接C14电线的不间断电源
技术规格
| 尺寸和重量 | 220 x 365 x 370 mm, 14.4 kg |
| 功率 | 650 W |
| 计算规格 | 7 TB 固态硬盘存储、64 GB 内存、用于操作系统及流程编排的英特尔i7-10700K 处理器、GridION 加速器 |
| 预装软件 | Linux OS, GridION OS, MinKNOW |
| 环境条件 | 请在+18℃至+25℃的环境温度范围内使用本测序仪 储存环境温度为+5℃至+40℃ |
推荐的实验室摆放位置
- 请将仪器至于一张稳固、清洁的实验台上。
- 请确保宽带网接口靠近电源。
- 请确保电源插头处在方便插拔的位置，以便在紧急情况下将测序仪断开。
- 测序应在+18℃至+25℃的室温下进行。
- 请确保仪器四周均留有30厘米的空间。
- 请勿覆盖任何通风口。
- 警告 - 操作过程中仪器后部会发热。
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
注意
Please note that the GridION Q device weighs approximately 11 kg, and care should be taken during lifting and moving.
打开测序设备包装，将设备置于操作台上计划的摆放位置。
请参照下图，将所需线缆与测序设备连接。
- 1x 宽带网
- 1x 用于连接显示器的HDMI/DisplayPort*
- 1x 键盘USB
- 1x 鼠标USB
- 1x C13电线
*包装中提供1 x DisplayPort转HDMI适配器
重要
请注意：旧版测序设备背面的USB接口为USB 3.0。设备正面的接口为USB 2.0，因此不推荐用于数据传输。
请将电源线与主电源/不间断电源连接。请使用我们提供的电源线，或符合认可标准的额定电源线，并确保设备已连接至保护接地电源。打开电源开关。
按下电源按钮。按钮中心应亮起蓝光。屏幕将显示加载页面，然后是登录界面。
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.
将五张配置测试芯片（CTC）插入GridION的X1至X5芯片卡槽。当五张配置测试芯片均被识别后，五个卡槽将亮起绿灯。
Navigate to the Start homepage and click 'Hardware Check' option.
选择所有测序芯片卡槽并选择“Start”（开始）以启动检测。
在GridION上使用 MinION 测序芯片：
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.
步骤结束
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
注意
更改您的网络配置
GridION的网络参数配置须适合您当地的网络环境。
警告! 更改 GridION 网络参数可能导致设备无法正常工作。
如您对GridION网络设置的配置参数存疑，请联系本地IT部门。
网络要求
GridION 使用 1x1 Gbps 铜线接口与您本地网络设施连接。该端口唯一，且默认使用DHCP配置IP地址（也可手动配置IP地址）。
连接将用于：
- 向 Oxford Nanopore Technologies 发送遥测* 信息
- 接收设备的软件和固件更新
- 将生物测序数据传输至您本地的存储基础设施
用户须自备网线进行配置。
* 遥测仅发送有关测序运行条件和设置的源数据，如序列长度和质量值等信息，而不会记录具体基因组序列信息。
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)
配置您的网络
如果您希望将GridION连接至单个网络，请使用用户界面。
如需配置GridION与多个网络连接，请打开终端窗口并输入以下命令：
ont-network-settings
此脚本的选项包括：
--dhcp - 非必需 - 使用DCHP，并仅保留接口、绑定和覆盖这三项属性
--address ip_address - 必需 - GridION的IP地址
--subnet subnet_mask - 必需 - GridION的子网掩码
--gateway gateway_address - 必需- GridION的默认网关
--dns DNS_server1,DNS_server2 - 必需 - GridION的DNS服务器
--search your_domain - 必需 - 您的域名后缀（例如，公司名.地域）
--overwrite - 非必需
--help - 详细说明上述选项
如需重置设置，请务必在上述命令选项前使用--overwrite 标志，再关闭设备、然后重新启动。
验证 IP 地址
如需验证静态或动态（DHCP）IP地址的配置是否正确，请使用命令：ifconfig
返回信息将包含宽带网络的IP地址，示例如下：
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.
重要
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
重要
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