Skip to main content
Premium Trial:

Request an Annual Quote

Celera Works with Bioinformatics and IT Partners to Expand CDS Capabilities


A number of agreements announced last week between Celera Genomics and third-party tool and service providers highlighted some aspects of the company’s “buy versus build” bioinformatics strategy.

In one partnership, Celera and Spotfire said they would work together to integrate Spotfire’s DecisionSite analytical software with the Celera Discovery System. Other partnerships include Swedish bioinformatics company Virtual Genetics, which said that Celera has agreed to evaluate its VirtualAdapt information retrieval software and services; IconMedialab, which is assisting Celera with development of the CDS Genome Browser; and Celerent, which announced that it has been awarded follow-on contracts to assist Celera’s technical team with computing projects.

Of the Spotfire agreement, Tony Kerlavage, senior director of bioinformatics and product strategy at Celera, said, “When there are tools that already have a large market penetration, such as Spotfire does, our customers are already using them and it makes perfect sense to help our customers by allowing them to use the tools that they’re familiar with in conjunction with the CDS.”

Kerlavage said that the Spotfire deal is only one example of several third-party toolmakers that Celera will be working with.

“It doesn’t mean that we won’t be developing our own tools,” he added, “but people have developed very good tools for that purpose already. We don’t feel the need to reinvent them.”

DecisionSite enables visual analysis of product, process, and customer information from a variety of sources. Celera and Spotfire will work together on a module that will allow users to move seamlessly between DecisionSite and CDS in order to add genomic and biomedical information from CDS to their own data and experiment results.

Separately, Spotfire also announced that Biogen has licensed DecisionSite to assist in its drug discovery and development process.

Kerlavage said that the DecisionSite integration is a component of Celera’s broader mRNA expression strategy, which also involves recent agreements with Genzyme and Lynx to add gene expression data to the CDS. “If customers have their own mRNA expression data from whatever source, or if they’re downloading data from Celera’s site, they’ll be able to do their clustering and analysis within the Spotfire tool and then they’ll be able to link back into the CDS and get access to the wealth of annotation that we have on those sets of genes,” he said.

Bill Ladd, director of bioinformatics at Spotfire, sees the deal as a bit of a coup for both companies.

“You can look at Celera as one of the premier distributors of genomic information and you can look at Spotfire as one of the premier tools for integrating and understanding information. And I see it as a very natural fit to both their customers and our customers. It expands the utility for both customer bases,” Ladd said.

While the partnership with Spotfire eliminates the need to develop specialized data analysis and integration tools for CDS, Celera also eases the burden of developing and updating the CDS architecture through outsourced IT services.

Russell Turner, head of the visualization team at Celera, said that the IconMedialab team, which comprises approximately one-fifth of the overall CDS Genome Browser development team, has helped with “analyzing the application domain, gathering and defining software requirements, designing the client and server software architecture, and supervising development of the software implementation.”

Peter Davies, project manager at IconMedialab, said that five IconMedialab employees have worked with Celera over the past two years on the visualization software. The team has developed three-tiered object-oriented software to allow focused retrieval of Celera data into a client application. The client also reads data from multiple XML files and retrieves XML data from an HTTP server based on servlet technology. All three sources of data are integrated into a single client model and displayed for the user, Davies said.

The Genome Browser has been available for over a year to Celera’s pharmaceutical customers. Frank Mayberry, director of delivery systems for Celera, said the development team is continually adding capabilities to the product based on customer feedback.

Celerent of Manchester, NH, is another IT firm Celera has chosen to partner with. The company previously assisted Celera’s technical team with reconfiguring and consolidating its archiving and database systems to optimize their performance.

Under the follow-on contract, Celerent said it will continue to supply technical consulting and implementation services, and will also assist with scaling of existing servers and an operating system upgrade rollout for hundreds of Celera’s systems.

“By outsourcing some of their implementation and project management to Celerent, Celera is able to concentrate on their core business,” said Tony Dancona, Celerent’s president and chief executive officer.

But Celera isn’t the only winner in these IT relationships. Tool and service providers portray their association with Celera — one of the few genomics companies recognized beyond the industry — as validation of their technology. Virtual Genetics, for example, which began its feasibility study at Celera in October, is counting on the company’s endorsement of its technology and services.

“We are excited and optimistic that VirtualAdapt will meet Celera’s requirement and this will form the basis of collaboration between the companies. It is an important indication of our future commercial strength and potential,” said Göran Häss, president of Virtual Genetics.

And of course, it doesn’t hurt to be associated with the company known for sequencing the human genome — and perhaps claiming a little piece of the credit.

Lou Hawn, managing director of IconMedialab’s Washington office, noted, “We are extremely proud to have made a major contribution to Celera Genomics’ history-making undertaking to sequence and analyze, for the first time ever, the entire human genome.”

“Knowing that our efforts contribute towards Celera’s goals inspires us to do more, faster,” said Celerent’s Dancona.

— BT

Filed under

The Scan

Rett Syndrome Mouse Model Study Points to RNA Editing Possibilities

Investigators targeted MECP2 in mutant mouse models of Rett syndrome, showing in PNAS that they could restore its expression and dial down symptoms.

Investigators Find Shared, Distinct Genetic Contributors to Childhood Hodgkin Lymphoma

An association study in JAMA Network Open uncovers risk variants within and beyond the human leukocyte antigen locus.

Transcriptomic, Epigenetic Study Appears to Explain Anti-Viral Effects of TB Vaccine

Researchers report in Science Advances on an interferon signature and long-term shifts in monocyte cell DNA methylation in Bacille Calmette-Guérin-vaccinated infant samples.

DNA Storage Method Taps Into Gene Editing Technology

With a dual-plasmid system informed by gene editing, researchers re-wrote DNA sequences in E. coli to store Charles Dickens prose over hundreds of generations, as they recount in Science Advances.