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Whitehead Looks to Off-the-Shelf Tools for Next-Gen Production Software


When the Whitehead Institute/MIT Center for Genome Research built its production pipeline to sequence the human genome, it relied entirely on home-grown software solutions. Now, as the center plans for the next phase of its genomics activities, some of the homemade tools are being replaced by off-the-shelf components.

The center’s current batch of production informatics software “grew up as the human sequencing effort was growing up, and we understand a lot better now what really needs to be there, and we’re moving on,” said Toby Bloom, manager of production informatics at the Whitehead Institute. “Our finishing system is moving from human to mouse, so we needed a new finishing system to try new processes there. And we have other processes that are changing over in the lab as well, so it seemed like a good time to start moving into a next generation of software.”

The production informatics team is first turning its attention to the Whitehead’s laboratory information management system. Bloom said she opted for a hybrid in-house/off-the-shelf approach that combines the flexibility and customization of a home-grown solution with the stability and reliability of a commercial software package. Bloom selected BEA Systems’ WebLogic Integration software to serve as the backbone for the new LIMS. “I was looking for something that was going to give me a very flexible way of building our processes into the software; of being able to implement our processes, change our processes, [and] run multiple processes at once,” she said.

Bloom said she evaluated several commercially available LIMS, but found they didn’t offer the kind of flexibility that the Whitehead’s high-throughput sequencing activities demand. “Some of them can’t handle our capacity, and others have a set-up stage where you set up what your process is, and that’s a fairly long stage and then it’s not easy to change things,” she said. Most laboratory processes don’t change as frequently as the Whitehead’s do, Bloom noted. In addition, she said, many of the commercial LIMS “couldn’t handle many different processes running at once on the same equipment.”

Bloom estimated that the Whitehead production pipeline has as many as a half a dozen different processes running at any given time. While “that’s not a huge number,” she remarked, “each of those processes has many, many, many steps in it, and is pretty complex. And we want to be able to run lots of real-time checking and automate a lot of pieces that aren’t currently automated.”

The BEA WebLogic backbone will also allow Bloom’s team to integrate the LIMS with other pieces of the production pipeline that require varying degrees of automated and manual work, such as the library construction workflows, finishing workflows, and project management workflows.

The migration to the new LIMS is taking place in stages, “but eventually it will probably all be re-written except for the pieces that interface directly with the robots,” Bloom said. The project is just starting now, with plans to roll out new pieces in three-month intervals.

The production informatics software team consists of 23 people, Bloom said, and around four or five are working on the development of the LIMS.

The decision to take a step into the commercial software world grew out of a desire to make the most of the Whitehead software developers’ unique expertise, Bloom said. “Off-the-shelf software has a lot of investment that can be amortized across a lot of customers, and our effort is better used in things that are specific to sequencing. That’s where our added value is, and even though off-the-shelf software can be expensive, overall I think it’s a cost savings because we can focus our efforts on what we really need to do here in the sequencing center.”

The Whitehead production informatics team has also purchased a license to enterprise analytic processing tools from Cognos to serve as the foundation for other next-generation software it is developing for a new pipeline system and a new reporting environment, Bloom said.

— BT


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