This section provides an overview of the components of Clarity LIMS. For technical requirements, refer to Technical Requirements.

Environment Overview

Clarity LIMS is built on a platform that is easy to customize and supports off-the-shelf hardware, common database systems, and industry-standard data formats.

We offer both on-premise and hosted deployment models. Both offerings use the same underlying software and security model as explained in the Clarity LIMS Security and Privacy technical note, available for download from the Illumina website.

For on-premise deployments, we provide flexibility in selecting tools that suit your needs and existing IT infrastructure. The Clarity LIMS environment includes:

• Application server

• Database

• File server

• Web client

Depending on the details of your contract with Illumina, the environment can also include:

• Automation Workers

For hosted deployments, the hardware is scaled upward by Illumina as required.

System Architecture

For on-premise deployments, you can separate application and file server functions from the database functions by installing them on discrete hardware platforms. Alternatively, you can combine them on a single server hardware platform. Base your decision on the size of your installation and how much data your laboratory processes.

Whichever solution you choose, Illumina requires that the Clarity LIMS server environment reside on dedicated hardware, free from other Illumina or third-party server products. The server environment must also be on a 1 Gbs or faster network. The network should not contain links with a capacity lower than 100 Mbps on any network-connected devices, such as routers, firewalls, and switches.

The Clarity LIMS installation installs Apache Tomcat 9.0, Apache Webserver v2 (used as a proxy), ElasticSearch and RabbitMQ to support search, and Open JDK 8.0. These software versions are the only versions that Clarity LIMS supports. The software packages are supplied by Illumina.

For hosted deployments, Illumina fully manages the system deployment and maintenance.

Application Server

Clarity LIMS uses a web application served by the Apache Tomcat server to manage the creation, collection, and retrieval of data and results. This core server is built on a Java architecture and allows for rapid deployment and custom configuration for other on-premise and hosted deployments.

For both on-premise and hosted deployments, the application requires the following standard secure ports for web and file communications:

• Web communications: Port 80, 443

• File communications: Port 22

Depending on included instrument integrations, additional open ports may be required.

Additionally, for hosted deployments, a site-to-site VPN connection, using IPSEC, might be required for instrument integrations. The most current list of required open ports is included in the preinstallation documentation that is provided during an implementation project.

Database & File Server

Clarity LIMS supports PostgreSQL database to record data generated by the client, and references to file locations on the Clarity LIMS file server.

If the system needs to export a file, it issues a call to the database to find the file location on the file server. We recommend that you store files on a server or file system separate from the Clarity LIMS application server, such as a Network Attached Storage (NAS) appliance.

When handling data, Clarity LIMS saves files in their original format. The advantages of saving files in their original format are as follows:

• The size of files is restricted only by the size of your file system.

• You benefit from the built-in error-correction and integrity-checking features included in the file system.

The amount of storage space required by Clarity LIMS depends on the following:

• The number of samples your laboratory processes each day.

• The instruments you use.

• The number of files you save to the Clarity LIMS system.

Illumina will work with you to recommend an appropriate amount of storage space.

NOTE: We do not recommend that you place the Clarity LIMS file server on a remote mount to a Windows server. We recommend you discuss other network storage devices, such as high availability NAS, with your hardware and supported operating system vendors.

Web Client

User-centric, goal-based design has become the new standard in software interfaces. Clarity LIMS has a clean, helpful, easy-to-use interface. It is a lightweight web application that provides:

• A simple, fast, and efficient way for lab scientists to identify work they need to complete.

• The tools necessary to complete and record that work quickly and efficiently.

Automation Workers

The Clarity LIMS Automation Worker allows specifically designed scripts to automate and extend the functionality of Clarity LIMS. You can integrate a wide variety of laboratory instruments and software.

The Automation Worker runs as a Windows Service or as a Linux daemon. You can install the Automation Worker on any computer with a supported OS on your Clarity LIMS network. When you install multiple copies on different machines on your network, Clarity LIMS automatically distributes work across the machines to improve system performance.

NOTE: Only one Automation Worker node can be installed on a Windows server.

Mixpanel

Mixpanel™ is a system that provides Illumina with information about how users interact with the Clarity LIMS web client. We do this by tracking which features are being used, and how often. Gathering this information allows us to determine which interactions are most common, and how our users proceed through protocol steps and tasks. We can then use this information to improve system performance and ultimately enhance the user experience.

All data are collected anonymously. We collect data on Clarity LIMS usage only. We do not collect specific sample names, projects, or values entered. We do track total usage (number of samples selected, how many protocol steps executed, and so on). Data are collected across all customers for analysis in one group. We do not directly track which site is doing which work. If you require more information about Mixpanel, contact the Illumina Support team.

Security

All client traffic is encrypted over secure HTTP (HTTPS). To ensure the security of the transactions between Clarity LIMS and clients, on-premise deployments require a purchased certificate. The certificate should be from a well-known vendor such as DigiCert, Entrust, or QuoVadis. For information on the policies, processes, and controls enacted for security and privacy of data in hosted deployments, see the Clarity LIMS Security and Privacy Technical Note, available for download from the Illumina website.

The following information is a summary of the technical requirements for an on-premise or based deployment of Clarity LIMS v6 and later. To install and use Clarity LIMS, the client and server systems must meet these requirements. Clarity LIMS is designed to run on standard commodity hardware. The requirements provide general guidelines for your hardware configuration. You can obtain specific configuration quotes from the hardware vendor of your choice.

Allow enough time for the procurement of your hardware and software. Make sure that all components are installed and configured before proceeding with the installation of Clarity LIMS.

Production Server Requirements

For on-premise deployments, Clarity LIMS has two levels of recommended hardware. For larger labs in full production, we strongly suggest the high-throughput requirements.

The production server must be configured in US locale.

Recommended

• Server class 64-bit CPU with at least eight cores at 2.9 GHz

• 20 MB shared cache (L3) memory

• 32 GB RAM

  • 6 GB allocated to Tomcat

  • 6 GB allocated to the database

  • 2 GB allocated to ElasticSearch

• 100 GB hard disk drive space for the operating system, application, and log storage

• 1 Gbps Ethernet network or faster

High-throughput:

• Server class 64-bit CPU with at least 16 cores at 2.9 GHz

• 20 MB shared cache (L3) memory

• 64 GB RAM

  • 12 GB allocated to Tomcat

  • 12 GB allocated to the database

  • 4 GB allocated to ElasticSearch

• 100 GB hard disk drive space for the operating system, application, and log storage

• 1 Gbps Ethernet network or faster

For hosted deployments, Illumina sizes the system accordingly for system load. We reserve the right to archive auditing information to maintain system performance as the data set grows.

If your subscription is not renewed for your hosted deployment, at your request, we will supply you with an export of all user data. In practice, we will provide a database dump and details on the database schema for you to pull out any data you need going forward.

Server Operating System Requirements

For on-premise deployments, Clarity LIMS has been qualified to run with the following server operating systems versions:

• RedHat Enterprise Linux v8.10 (64-bit)

• Oracle Linux v8.10 (64-bit)

For hosted deployments, Illumina uses the latest qualified Oracle Linux version.

Database Requirements

For on-premise deployments, Clarity LIMS has been qualified to run with PostgreSQL 15.7.

For hosted deployments, Illumina uses the latest qualified PostgreSQL version.

Web Client Requirements

The following client requirements apply to both on-premise and hosted deployments.

Hardware

• 64-bit processor (dual-core 3.0 GHz)

• 8 GB RAM

Operating Systems

• Windows (10 or later)

• Linux (restricted to the server-supported versions listed previously)

• Macintosh OS (13 Venture or later)

• iOS (17 or later) on iPad running Safari browser

Web Browsers

• Google Chrome (latest update)

• Mozilla Firefox (latest update)

• Apple Safari on iPad only (latest update)

Other Requirements

• 1280 x 800 or higher

• Cookies and JavaScript must be enabled

For both on-premise and hosted deployments, a 20 Mbs network connection speed from client to server is required. If remote access via VPN is needed for LDAP or instrument integrations, we recommend 100 Mb/s network connection speed between your site and the hosted instance.

Automation Worker Requirements

The following requirements apply to automation workers installed on premise, for both on premise deployments and hosted deployments, to support instrument integrations.

Hardware

• 64-bit processor

• 2 Gb RAM

• Hard disk drive space equivalent to twice the size of the largest file you are planning to transfer

Operating Systems

• Windows 10 (or Windows Server 2016/2022)

• RedHat Enterprise Linux v8.10

• Oracle Linux v8.10

Applications

• Linux – Illumina installs Java Open JDK 8.0 update 362 (1.8.0_362)

• Windows – Clients must install Java Open JDK 8.0 update 362 (1.8.0_292)