According to TIGR president Claire Fraser, a strong bioinformatics infrastructure made the Institute for Genomic Research a shoo-in for its recent $25 million contract from the National Institute of Allergy and Infectious Diseases to establish a Pathogen Functional Genomics Resource Center.
“Our proposal was to build upon what we have already done and modify it as necessary for the specific needs of the resource center,” Fraser said. “The expectation is that as we get into new areas — genotyping, proteomics — that the bioinformatics efforts will keep pace.”
But Robert Fleischmann, a TIGR investigator and administrative director of the new center, said TIGR has to reinforce its IT backbone before the center meets the needs of its future users. “The first priority is to build this up from an infrastructure standpoint,” he said.
The PFGRC, which will centralize functional genomic resources for the study of pathogens, will provide researchers with microarray and genotyping technology; access to clone sets, genomic DNA, and type strains; and data analysis and storage resources. TIGR is developing a center-client web-based interface through which scientists can access and acquire these resources (http://pfgrc.tigr.org).
TIGR will have to revamp much of its current relational database structure for microarray work to serve this external client base, Fleischmann said. “What we use internally isn’t necessarily applicable to how we’re going to interact with an outside community that we’re going to be supplying.”
In addition to “pragmatic things” like graphical interfaces through which clients can design primers and order reagents, TIGR will also have to develop the client interface with the third-party supplier that will ultimately be distributing the reagents and resources that TIGR produces.
As for software, Fleischmann said that the publicly available tools that TIGR already provides for microarray analysis — MultipleExperimentViewer, ArrayViewer, and Spotfinder — would be easily adapted to the needs of the center.
“Our immediate plans are not to really dive into that area, to be honest,” Fleischmann said. By focusing on “infrastructure rather than informatics,” the center hopes to run much like a business-to-business operation within the next six months to serve the needs of the research community.
The $25 million budget for the center includes all the new IT requirements, Fleischmann said, including Sybase servers, NetApp storage space, additional switches, “and a fair amount of additional hardware and staff.”
Fleischmann said the terms of access to data stemming from research at the center have still not been finalized. It is likely, however, that the NIH will require researchers who use the center’s resources to make their data public. TIGR will create a database dedicated to information generated from the PFGRC, but researchers will not necessarily be required to deposit their work there, Fleischmann said.
The standards for that data are still under discussion as well, Fleischmann said, although the MIAME standard is under consideration for adoption.
TIGR intends to integrate data from the center’s activities with the annotation data already available through TIGR’s Comprehensive Microbial Resource. “A lot of the data that comes in will become a logical extension of the CMR,” Fleischmann said. Because the organisms that are likely to be supported by the center are organisms that have been sequenced and whose data and annotation are present in the CMR, Fleischmann said the center “would expand the scope of the CMR beyond annotation and global comparison into the area of functional genomics.”
In the first year of operation, TIGR plans to support three organisms that will be determined by a scientific advisory committee. Fleischmann said the PFGRC should be able to support around 10 researchers per pathogen for those who require microarrays, but a larger number of researchers will have access to the center’s other resources.
In the second year, the center is expected to support seven pathogens, eventually ramping up to a total of ten in the following years of the five-year contract.