NEW YORK (GenomeWeb) – The National Cancer Informatics Program (NCIP) at the National Cancer Institute's Center for Biomedical Informatics and Information Technology has developed and made available a virtual platform called NCIP Hub that provides an avenue for communal resource sharing and research collaboration.
It's a place where members of the cancer research community can share and use resources such as tools, seminars, teaching materials, workshops, blogposts, research publications, and so on, Ishwar Chandramouliswaran, a program manager in the NCIP and one of the website's developers, told BioInform. It is intended, he said, to provide a sustainable medium for resource sharing and collaboration; to "democratize" access to community-generated data tools and standards; and to foster scientific collaboration and open innovation.
The Hub makes use of HubZero infrastructure, an open-source software platform developed by Purdue University — with grants from the National Science Foundation — for building websites that can support scientific discovery and collaboration as well as education. Chandramouliswaran said that NCIP selected this particular platform because it offered broad and generic features that could support the needs of different kinds of users, for example, biologists versus bioinformaticians, and at the same time connected users allowing them to take advantage of each other's resources. HubZero can also handle large user bases; offers good tracking mechanisms and metrics; and is open source, which aligns well with NCIP's goals, he said.
NCIP has launched a pilot version of the Hub that is already being used or evaluated for potential use by several early-access researchers including one group that is developing algorithms for imaging. They are using the system, Chandramouliswaran said, to exchange information with their collaborators. A second group within the NCI is using the Hub to coordinate their program activities, he added.
The system is also open to the cancer research community, and members can begin contributing content now. Interested parties who want to become active contributors can reach out to Chandramouliswaran. There are no restrictions on membership, and content submissions don't have to meet specific criteria, he said. The Hub does have a system of checks and balances in place including an administrative review process to ensure that contributed content is sound.
NCIP Hub is just one of several resources that the NCI's informatics arm is pushing forward to address the perceived bioinformatics needs of the cancer research community. According to Chandramouliswaran, it fits in well with other informatics-focused NCI initiatives that all aim to provide better, more efficient access to cancer data and tools that have come from the projects that the agency has funded over the years. Recent initiatives include efforts to migrate code from the cancer biomedical informatics grid (caBIG) program to GitHub to make it more broadly available to the community. The NCI also adopted a new open-source license that would make it easier for academic institutions and commercial firms to download and makes changes to the caBIG software and code.
The NCI has also invested in larger-scale informatics projects like the Cancer Genomics Cloud Pilots, an ongoing initiative to build a cloud-computing environment — or multiple environments — that provide access to co-located computing resources and storage and pre-loaded data from the Cancer Genome Atlas. Last year, the NCI's Board of Scientific Advisors and the National Cancer Advisory Board approved a proposal to launch three pilot clouds capable of handling up to 2.5 petabytes of core TCGA data with at least one additional data type and the ability to support large numbers of users simultaneously. That was followed early this year by the NCI officially launching the proposal-collection phase of the pilots giving potential respondents six weeks to submit their applications. Winning proposals are expected to receive awards in September this year.
A separate but related component of the NCI's informatics strategy is the Cancer Genomics Hub, a petabyte-scale data repository that will provide access to genomic and clinical data from NCI's cancer genome research programs. In 2012, the agency awarded a $10.3 million contract to a team at the University of California, Santa Cruz, to develop and maintain that resource — the project is expected to wrap this year.
The NCI is also funding a larger resource — which will be tied to both CGHub and the genomic cloud pilots — called the Genomics Data Commons, a portal to the diverse cancer datasets that NCI-funded projects have generated. The agency began accepting applications to build the commons last November.