JIRA in the Genomics Platform

Originally developed for tracking software development and bugs, Jira is an Atlassian application that tracks issues. It is flexible enough to be adapted to any process that follows a workflow.  It is a powerful collaboration tool that allows us to follow processes across and between platforms, enhancing information dissemination at the Broad.

Due to JIRA’s customizable nature, we’ve been able to develop different projects for multiple processes at the Broad including:

• GP software support
• Lab automation asset/request tracking
• Product order tracking
• Production sample batch tracking
• Lab notebook for development experiments

JIRA has several key objects:

• Issues – the unit of work that we want to track (ex: one library set, one flowcell, one experiment). Interchangeable with ‘ticket’. JIRA gives us the ability to create custom issue types for easier queuing in the lab.
• Project – the highest level of groups of issues in JIRA. Every issue must belong to a project. Each project must have a unique key, and this is how people most often refer to an issue. Example – “I did an experiment looking at density, which is described in DEV-905.” DEV is the key for the Process Development project.
• Fields – the areas within an issue where data is captured. For example, “Summary”, “Hypothesis”, or “Number of Samples”.
• Status – The state the issue is currently in. (e.g, "Closed", "In LC".) Super customizable based on issue type - for example an instrument has a "Down" state, and LCSETs have a "Ready For Sequencing" state.
• Transitions – the pathways to advance or return an issue to a particular status. Lab automation is increasingly transitioning tickets automatically based on deck events.
• Workflows – the predetermined (by the lab and LIMS) set of statuses and transitions an issue goes through. 
• Resolution – Issues are finalized with the ‘Closed’ status, but resolution tracks how it got there. For example in the Cell Line Factory project, one issue is one cell line. A 'Closed' CLF ticket for example could have a resolution of 'Terminated' if the cell line did not grow, or 'Validated Tumor' if the cell line was validated as a tumor.

System Architecture

We have two main JIRAs (known as instances) in use in the Genomics Platform.

• LabOpsJIRA (labopsjira.broadinstitute.org) - Our main work horse for tracking most lab production processes as well as lab automation inventory and request tracking.
• GP Informatics JIRA (gpinfojira.broadinstitute.org) - A more 'traditional' JIRA, used for requirements tracking, bug tracking, support requests and feature requests for our Informatics teams. See their confluence page here.

Each Jira has a production and a development instance. LabOpsJIRA has a special integration instance that we use for testing against LIMS changes.

Filters/Searching

Saved searches are known as filters and can be shared with other users as well as subscribed to. (for example our Illumina service team gets a daily email of all open issues.)

At the top navigation bar in Jira, click Issues → Search For Issues

There is a basic search where users can pick search criteria from dropdown fields.

TIP: It really helps search performance if you always select your relevant project/s first!

And there is a more powerful advanced search that gives many additional functions not possible in the basic search, like the ability to search within linked issues and the ability to have multiple conditions.

Queries are written with a language called JQL (JIRA Query Language) - this is very similar to SQL.

JQL is used in other analytics tools, such as our homegrown JQL -> TDE tool that allows Tableau to use a saved JIRA filter as a data source.

Dashboards/Agile Boards

Users have a couple ways of seeing their work at a glance.

Dashboards are pages that users can customize with gadgets. E.g display saved search results, show project statistics (like who has the most open assigned issues). Saved filters are a required first step for many gadgets - unfortunately JIRA doesn’t let users make up searches on the fly.

Dashboards also have activity streams where you can see what tickets others have made or commented on.

Agile Boards are interactive pages where you can drag and drop cards into relevant columns, and can also slice and dice cards based on swimlanes. Swimlanes can be configured by assignee or other customized groupings like issue type or lab protocol.

Granting access to JIRA (Admin Use)
Adding new Illumina Instruments to JIRA (Admin Use)
Updating Instrument ticket summary (Crazy Robots) (Admin Use)
Crazy Robots JIRA (General and Admin use)