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Migrating PacBio's Jira and Confluence Applications to Cloud for Stronger Operations


Silicon Valley-based biotech company PacBio provides cutting-edge DNA sequencers to researchers in academia and industry, powering essential biomedical research across human health, plants, animals, microbes, and gene therapy. With just over 900 employees, the firm has relied on Atlassian server products for program management, documentation, and workflow optimization.

“I rely on Atlassian tools to ensure that what we’re building aligns well with customer expectations and requirements.”


In order to set up their Atlassian platforms for long-term success to deliver this value to customers, PacBio felt that their Jira and Confluence tools would benefit from moving to Atlassian cloud. Approaching the retirement date for Atlassian’s self-managed server products in 2024, PacBio knew that cloud products were likely to receive priority support from Atlassian. PacBio also wanted to benefit from cloud-exclusive features, including plug-ins and reporting capabilities, that could help scale the use of the platform for other teams within the company.

Jira and Confluence are essentials for the software teams at PacBio, providing wide visibility into program management, resource utilization, and documentation. Though there are only about 70 people on the software team, around 250 employees have access to Jira, and around 400 have access to Confluence. Ensuring these tools functioned as efficiently as possible is crucial for the team to collaborate and deliver prime value to their customers.

PacBio engaged Contegix last summer to lead the transition process for Jira and Confluence, so internal teams could remain focused on day-to-day project execution. Now the two tools have been fully migrated, and PacBio is enjoying increased functionality and support.

Specialized support from Contegix

Specialized support from Contegix eased a tricky transition

PacBio spoke to several Platinum Solutions Providers that Atlassian recommended to support a migration. Contegix stood out thanks to a migration strategy that PacBio found to be complete, well-supported, and practical. “We were looking for pragmatism and a feeling of not being 'sold to,’” says Evans. “Cultural fit was a main deciding factor for us, and we felt our goals were understood and heard.”

Once the transition was underway, Contegix worked to migrate two different sites with two separate server instances, as PacBio had recently acquired another company whose data also needed migration. Despite delays as certain plug-in features yielded poor test executions, Contegix facilitated communication between PacBio and Atlassian, ultimately still delivering the project under budget. 

"Having Contegix manage the migration, rather than use internal resources, was fantastic," said Evans. "The team was helpful and trustworthy, which made a big difference to us, especially when trying to plan our programs and timing around the migration. We had much more confidence knowing that Contegix is specialized in this and has done lots of migrations.”

Greater observability, without greater complexity

Having Jira and Confluence on the cloud will help PacBio produce value for their customers as quickly as they can. Already, transitioning to cloud has provided new benefits at PacBio: Remote workers now have easier access to Jira and Confluence without a VPN. SumUp, a plug-in which displays real-time calculations in Jira, is now running more efficiently in cloud. Teams have regained better functionality in ScriptRunner, an indispensable automation tool that provides additional features in Jira, and even search tools offer new, more advanced capabilities. 

Greater observability

PacBio is also positioned to use roadmap tools and plug-ins on cloud to build out automated reporting, offering strategic visibility into workflows and resource allocation. Evans said that this functionality is crucial to tracking how work is laddering up to overall plans: “These tools allow us to ensure that, as a business, we stay aligned with our objectives.”

PacBio will continue to work with Contegix to onboard additional teams to Atlassian tools, as well as build out potential customizations to make sure their cloud instances are not just stood up, but optimized. For PacBio, this means greater, more efficient value delivery in alignment with company objectives—and for researchers, it means more of the essential tools that PacBio provides. 

Learn how Contegix can help you optimize your Atlassian applications by supporting your team through a cloud migration.