This document outlines the technical overview for BaseSpace Clarity LIMS v5.3 and above, including a list of required pre-installed information for setting up Clarity LIMS.
BaseSpace Clarity LIMS is a lightweight web application that provides a simple, fast, and efficient way for lab scientists to identify work they need to complete, along with the tools necessary to quickly complete and record that work.
Clarity LIMS is offered as software-as-a-service (SaaS) in the cloud and uses a PostgreSQL database to record data. For every customer, Illumina will size the system accordingly for system load. Illumina fully manages the system deployment and maintenance of the application in the cloud, and we reserve the right to archive auditing information in order to maintain system performance as the dataset grows.
The following client requirements apply:
64-bit processor (dual-core 3.0 GHz)
8GB RAM (or higher)
Note that Microsoft Surface Pro support is only for all operations where a mouse is normally used.
Touchscreen support is for read-only lab work. Running samples through steps is not supported.
Macintosh OS X (10.12.x or later)
iOS 9 or iOS 10 on iPad running Safari browser
Note that iPad support is for read-only lab work. Running samples through steps is not supported.
Supported Web Browsers
Google Chrome – Latest update
Mozilla Firefox – Latest update
Apple Safari on iPad only - Latest update
1280 x 800 or higher
A 20 Mb/s network connection speed from client to server is required. If remote access is needed for either LDAP or instrument integrations via VPN, we suggest a 100 Mb/s network connection speed between your site and your Clarity LIMS instance.
The BaseSpace Clarity LIMS Automation Worker allows specifically designed scripts to automate and extend the functionality of BaseSpace Clarity LIMS, by allowing you to integrate a wide variety of laboratory instruments and software. The Automation Worker runs as a Linux daemon.
Setting up Illumina Instrument Integrations and LDAP Integration
The Illumina instrument integrations (listed below) and the LDAP integration require a Virtual Private Network (VPN) to be setup between your network and your BaseSpace Clarity LIMS instance.
HiSeq X integration
HiSeq 4000 integration
HiSeq 3000 integration
HiSeq 2000 integration
NextSeq 500/550 integration
The NovaSeq 6000 integration (v3.0 and above), and NextSeq integration 1000/2000 (v1.0 and above) do not require a VPN to be setup.
Each instrument integration will allow you to setup your run plan. The integration will then parse information from the run interops, run parameters, and run file information back into BaseSpace Clarity LIMS. More information can be found in the user guide for each instrument integration.
To setup an integration, we will provide you with an external Amazon IP and the internal Amazon IP. You must provide the information and access below.
Open ports 500 and 4500 on your VPN to the Clarity systems for both TCP and UDP. We use IPSEC, installed directly on the Amazon instance, to establish the VPN.
The following link provides a general description of how IPSEC works:
It is suggested that you provide this information to your tech/network staff.
Configure your VPN gateway to accommodate tunnels from the Clarity systems listed above into the Network Attached Storage (NAS) server that your instruments are writing their sequencing output (run data) to.
Open your firewall to all communication from the Clarity systems listed above to ports 139 and 445 on your NAS server
Send Illumina the following information:
Public IP of the VPN gateway you are using (i.e., a Cisco router/concentrator)
Private IP of the Network Attached Storage (NAS) server your instruments are writing their output (run data) to. We will work to establish CIFS (or NFS) file sharing between this NAS server and your cloud systems.
Dimensional Query Tool
During Clarity LIMS installation, the Dimensional Query tool will be installed to help us anonymously track your interactions with Clarity LIMS. This information will help improve our product.
When each server is installed, an anonymous ID is generated for that server. This ID is used when data is sent from the server to Illumina. The server ID lets us see if there are significant differences between the profiles of our customers. As this is completely anonymous, it is impossible for Illumina to determine which customer the information comes from.
Every day, this tool wll run, package the information, and then send an encrypted package to Illumina. No private information is included in this package. This operation is lightweight and run off-hours, so it does not put any strain on the system.
What we Collect
Clarity LIMS version
Number of Pending, Open, Closed Projects
Number of Submitted Samples, Derived Samples
Number of Custom Fields, Reagents, Automations
Number of Configuration elements (workflows, protocols, steps)
What we Don't Collect
Names of any entity
Data from projects, samples, steps
MixPanel Data Collection Service
Illumina uses the MixPanel service to collect data about BaseSpace Clarity LIMS usage. This data is intended to help us improve the system, showing us which parts of the system are commonly used, and helping us to determine where we should best direct our efforts at improvements.
When each server is installed, an anonymous ID is generated for that server. This ID is used when data is sent from the server to MixPanel. The server ID lets us see if there are significant differences between the profiles of our customers. We can see if a certain ID is being used to process a lot of samples, while another server might be used less often. This gives us important information about the sizing of servers. We collect interaction information, with each username having a separate user ID. When a user clicks a button or performs a tracked action in the LIMS, a small package of data containing the MixPanel user ID, the action, and the page name is sent to MixPanel.
Each user login has a unique name, allowing us to see the difference between unique users performing various tasks in the LIMS. For example, we can see whether a large number of users are frequently activating help, or if there are other actions frequently taken by users.
The anonymous ID is generated by a combination of the server name and the user's database index. This information is not sufficient for us to pinpoint a single user.
What we Collect
Number of times a button or feature is pressed
Number of samples added to an ice bucket or completed in a workflow
Number of samples moved per action onto an output plate
Number of samples completing a step, protocol, and workflow
Number of files created in a step
General protocol types (Sample Prep, Library Prep, etc.)
Number of times help is invoked
Number of times each page is visited
Information on the browser and operating system being used
What we Don't Collect
The data we collect is about the action taken, and never contains the following:
Any of the custom fields
Required Pre-Installed Information
The information below will be collected from you prior to installing your Clarity LIMS instance:
Names of each Clarity LIMS instance
Clarity LIMS admin contact information
List of Illumina instruments to be integrated with Clarity LIMS
List of Illumina Preset Protocols that must be installed
LDAP Integration Requirement