Skip to main content
Premium Trial:

Request an Annual Quote

Communication, Clear Goals Among Factors Necessary to Successfully Deploy caBIG Tools, Researchers Say


By Uduak Grace Thomas

At the National Cancer Institute's Cancer Biomedical Informatics Grid Initiative annual meeting this week, participants partook in several sessions aimed at providing a comprehensive overview of the factors to consider when deploying caBIG’s tools in their labs and institutions and the resources they need to navigate the waters.

In addition to strategic considerations, newcomers to caBIG as well as veterans of the systems had the opportunity to see firsthand how other researchers have used and are using the tools in their research labs and clinics and how they have addressed the challenges of deploying caBIG tools at their institutions.

Currently caBIG has more than 70 tools that members can use to share data and knowledge, as well as additional functionalities being built on top of the existing resources to meet the growing research needs of the community. In addition to being deployed in several research institutions and clinics in the US and abroad, the tools are being used in more than 50 NCI designated cancer centers.

In one conference presentation, George Komatosoulis, deputy director of the Center for Biomedical Informatics and Information Technology, noted that “deploying caBIG can mean more than just deploying tools.” He described it as a multi-step process involving things like identifying which individuals will use and provide support for the tools; conducting self assessments to identify the tools available on the ground and the additional capabilities needed; and determining broad goals for biomedical informatics and creating implementation plans based on those goals.

Potential users can also choose how to deploy the tools in their labs. For example, users can adopt software tools as they are and then build additional functionalities on the infrastructure based on their research needs, or they can use caBIG application programming interfaces and software development kits to make their existing tools interoperable with caBIG tools. For a third option, new users can work with a third party vendor to adapt existing software tools that the vendor provides to the caBIG technology.

“Deploying caBIG is an enterprise program, not simply an IT initiative,” Komatosoulis said, also noting that by connecting to the broader realm of the cancer research community, institutions wind up making decisions that impact multiple groups and users across the board and not solely in the IT space.

“You can wind up integrating new workflows … having new data requirements, perhaps new systems,” he said. “There are new complexities associated with the fact that you now have to the opportunity to share data. As a result, the team that you are going to build … has to include people from all areas of the organization.”

In her presentation, Beverly Albury, the IT program manager at the Nancy N. and J.C. Lewis Cancer and Research Pavilion, provided a detailed planning checklist and a list of questions that prospective caBIG users need to ask themselves in order to make the deployment process a bit easier. Her list took into account things like the importance of determining the infrastructural capabilities available on the ground and the kinds of research that the institute intends to perform, and then selecting tools based on these assessments.

For example, in his presentation, Joshua Mann, IT manager for the cancer center at St. Joseph's Hospital-Orange, said that prior to its adoption of some of caBIG's tools as well as support from third party vendors like Varian Medical Systems, the hospital had data stored in multiple Excel spreadsheets, Access databases, and paper charts.

He said that when the hospital was selected to participate in the NCI Community Cancer Centers Program and was made aware of the tools available through the caBIG community, it began assessing the tools it had on the ground and the kinds of clinical research data the NCCCP program required.

Then the hospital set a list of goals which, according to Mann, included things like choosing and implementing a complete electronic medical record solution; implementing a clinical trial management system, and developing a biospecimen repository. He also said they needed to find a way to integrate all the systems efficiently and "to do it all with no money."

Ken Quinn, a systems analyst at Roswell Park Cancer Institute, described how the center is currently using or planning to use caBIG resources such as caTIES, caAERS, Patient Study Calendar, and caArray to analyze and integrate clinical data which it collected and stored in disparate ways.

During his presentation, he depicted the process of deploying caBIG tools as “a very fluid type of environment, where you look into tools, you are deploying tools, [and] you think they are going to slot in here, [but] some things change, strategies change.”

Several experienced users noted that while they were able to use the tools successfully in their research, some tools presented significant challenges.

In his presentation, David Lloyd Steffen, a professor at the Baylor College of Medicine spoke about three success stories that involved using caBIG tools at the college, including the development of a caBIG-compatible clinical trials patient registration system and a biospecimen tracking software. He did note, however, that although the college had a plan in place, deploying the tools turned out to be "way more difficult that any of us ever anticipated."

One tool that came up quite regularly in several talks as proving to be something of a challenge to implement was the caTissue suite, caBIG's biorepository for managing, tracking, and annotating biospecimens. During their presentations, some researchers indicated that deploying the tool was quite difficult and time-consuming.

Sorena Nadaf, CIO of the Helen Diller Family Comprehensive Cancer Center at University of California, San Francisco, described one project at UCSF that used caTissue to track and migrate data from several thousand samples collected by the university and stored in its biospecimen bank. He noted that the team has had to put in a "significant amount of work in house" to get the tool to work for their needs.

He did note during a question and answer session following his presentation that sometimes user expectations of tools like caTissue exceed the capabilities of the original design of the tool, which may account for difficulties using them. In the case of caTissue, for example he pointed out that while the tool "is a good banking application; it's not a laboratory information management system."

During a conversation with BioInform at the conference, CBIIT Director Kenneth Buetow noted that the issues with tools like caTissue are "part of the challenges of success," pointing out that as the caBIG grows, "we have broader communities wanting to use tools originally designed for one purpose in different contexts" and that the community has to come up with ways to address these challenges.

Komatsoulis told BioInform after his presentation that the fact that several researchers indicated that deploying caTissue was challenging isn't necessarily a bad thing because it shows that the community members are actually using the resources in their research.

Researchers highlighted a third challenge during the sessions: Although the tools are free and open source, long-term maintenance and management requires the time and efforts of multiple personnel and in some cases significant financial investments.

In spite of the challenges and the complexities, several speakers noted that a key benefit of the caBIG community is that users have access to support resources such as NCI’s knowledge centers to answer questions as well as licensed third party vendors that offer client-specific caBIG support.

The Scan

Mosquitos Genetically Modified to Prevent Malaria Spread

A gene drive approach could be used to render mosquitos unable to spread malaria, researchers report in Science Advances.

Gut Microbiomes Allow Bears to Grow to Similar Sizes Despite Differing Diets

Researchers in Scientific Reports find that the makeup of brown bears' gut microbiomes allows them to reach similar sizes even when feasting on different foods.

Finding Safe Harbor in the Human Genome

In Genome Biology, researchers present a new approach to identify genomic safe harbors where transgenes can be expressed without affecting host cell function.

New Data Point to Nuanced Relationship Between Major Depression, Bipolar Disorder

Lund University researchers in JAMA Psychiatry uncover overlapping genetic liabilities for major depression and bipolar disorder.