'World Wide Web of cancer research' exploits human genome map

Computerworld - In June 2000, President Bill Clinton and British Prime Minister Tony Blair unveiled what amounted to a "rough draft" of the deciphered human genome, a milestone in the effort to crack the complex genetic code that shapes human development.

The work of the mapping of the human genome, whose completion was announced in April 2003, was heavily dependent on advanced computing for the data-intensive task of mapping the sequence of 3 billion base gene pairs.

Ironically, getting that genetic data into the hands of biomedical researchers has created another major computer quandary: the need for even more advanced systems that can keep up with an increasing number of disease subcategories being discovered through genetic research.

The National Cancer Institute took on that issue in 2003 by launching what it called the largest IT project in the history of biomedical research. The NCI created what is, in essence, a World Wide Web of cancer research.

The Cancer Biomedical Informatics Grid, or caBIG, promises to help researchers, physicians and patients across the country to better share more-detailed information about diseases and thus speed the development of new drugs and treatments for them.

The government-funded effort costs about $20 million a year, the NCI said.

To date, 42 of the institute's 63 national cancer centers are either linked to the caBIG grid or are installing the necessary infrastructure to participate. Many are already building applications that can be shared by members of the grid.

The need for wider data sharing became obvious as genetics research found more subcategories of cancers that would require specific treatment methods.

Traditionally, cancer researchers focused on studying a relatively small number of disease categories, such as lung cancer, breast cancer or colon cancer. But as the genome work expanded, many disease subtypes were discovered within those categories, and each may require a different treatment.

Cancer researchers quickly saw the need to assemble as much information as possible to help in the development of new disease-specific treatment options. So, to broaden the number of data sources, the NCI has begun expanding the grid to include the community hospitals and physicians that treat 80% of U.S. cancer patients.

Interoperability

Project backers said that researchers decided early on to focus on improving interoperability rather than forcing research organizations to standardize on expensive new IT systems and software.

To accomplish that, the developers used the Globus Toolkit, a set of open-source tools for building grid systems and applications that run on top of Web services that are open for anyone with a node on the system. The Globus tools are distributed by the Globus Alliance.