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Case Study: caIntegrator2
Translational Informatics, No Programming Experience Required
Challenge: Streamlining a Robust Tool
“From bench to bedside” is the catchphrase for translational research, which aims to rapidly transform knowledge and discoveries from the lab into clinical applications for patients. If only it were as simple as a slogan – translational research studies span a wide variety of genomic, clinical and imaging data. Integrating, distributing, and analyzing these data is no small task. The National Cancer Institute (NCI) took the first step in making data integration possible for translational research when it developed caIntegrator, a novel translational informatics platform available to researchers via caBIG®, the NCI’s information network. The platform was a success, but its reach was limited to institutions possessing the technical resources required to deploy it and use it. NCI engaged 5AM to transform this robust platform into a more accessible format. The challenge was to develop a simple, web-based tool that would enable researchers with a moderate technical background to deploy a caIntegrator-like application, without requiring custom software development.
Users Lay the Groundwork
Stakeholder feedback was key in developing this user-friendly tool. 5AM met with study managers to directly capture the desired functions and features that a new version of caIntegrator could provide. We also documented use cases and developed a domain model based on the functionality of the existing caIntegrator-based applications.
Iterative Process Gives Client Flexibility
Throughout the construction phase, the system was iteratively developed to add desired functionality in an incremental manner. This process enabled the NCI to have immediate control over the functionality developed in each two-week iteration. In our Glassbox® Software Development process, each iteration produces working software, which is deployed for continual evaluation. A team of subject matter experts reviewed the functionality delivered after each iteration, provided feedback and suggested enhancements. Shortening the time required for this feedback loop enabled the team to flexibly and rapidly adapt the software to the NCI’s vision. This iterative approach was made possible by employing 5AM’s best practices in code quality, including peer reviews, continuous integration, and exhaustive automated testing.
Result: Unlocking Data from Bench to Bedside
The integration of heterogeneous clinical, microarray, and medical imaging data was once a time-intensive endeavor that required custom software development. Now, study managers can do it themselves, without needing to be software programmers.
Using caIntegrator2’s simple, web-based forms, researchers specify their studies’ configuration data, which the application uses to deploy customized web portals. The web portals allow for the query, collection, combination, and multidimensional analysis of heterogeneous clinical, genetic, and genomic data, which can be shared among research centers via caBIG®. caintegrator2 uses caGrid analytical services such as GenePattern and BioConductor to perform analysis on the study data, including clinical survival data.
This simple, web-based tool is helping translational research move ahead by making it easier for researchers to share and make use of their data. caIntegrator2 is supporting the NCI’s aim to speed discoveries and improve patient outcomes.