2006 Scientific Report Impact

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NA-MIC's impact on biomedical computing accelerated during this second year of its existance. The NCBC RFA stated: "The NIH NCBC will be devoted to all facets of biomedical computing, from basic research in computational science to providing the tools and resources that biomedical and behavioral researchers need to do their work." and "...the NIH NCBC will play a major role in educating and training researchers to engage in biomedical computing."

The Center's tools, resources and processes are having impact within the Center, within NIH, Nationally and Internationally. NAMIC is becoming a resource for biomedical open source software and open source software processes.

Impact within the Center

Within the Center, Core 2 has introduced the NA-MIC software process to basic researchers in Core 1. Skills such as revision control, software testing and object-oriented design are not usually part of a basic research curriculum. Good software engineering skills are critical to translate algorithims into usable, robust software for end-users. As stated in the original NA-MIC proposal, "Core 2 is the link between the innovative techniques of Core 1 and the biological questions of the Core 3 end-user practitioners. To build this link, Core 2 will establish software architectures and software processes that will empower the Core 1 algorithm developers to create robust, well-designed software and interfaces."

The Center has established a nightly build and test process for Slicer2 that has extended the number of platforms supported by slicer from two (Solaris and Windows) to six.

Although 3D Slicer is the delivery platform for the Center, there are many supporting toolkits and support tools. These have been packaged as the NA-MIC Kit. Components of the NA-MIC kit follow the NA-MIC development process or an equivalent process. Key to this is the adoption of software licenses that adher to open source rules and do not restrict usage of the software. The newly created Slicer License balances open source, access and clinical restrictions and serves as a model for future clinical oriented open source projects.

Impact within NIH Funded Research

NIH projects are starting to adopt NA-MIC pioneered processes and tools. NA-MIC hosts wikis for the Morphology Birn (mBirn) and the Function Birn (fBirn). Both of these NIH funded programs are using the wikis to organize and dissemniate the agendas of their All Hands Meetings. The word of NA-MIC's successful Programmer/Project week has reached outside the Center. The fBirn, at its recent all hands meeting in Irvine, decided to hold a similar event in June 2006 to have the Birn Coordinating Center (Birn CC) work with fBirn developers on fBirn specific adaptation of Birn CC tools. The University of Iowa has adopted CMake, CTest and Dart 2 to coordinate nightly builds and tests for the Neuroimaging Informatics Technology Initiative (NIFTI). Through outreach activities NA-MIC PI's have promoted the open, collaborative and distributed software process pioneered by NA-MIC. The outreach activities within NIH included the NIH P41 Principal Investigator's Meeting, the Wadsworth Center's P41 "Resource for the Visualization of Biological Complexity" and UConn's P41 "National Resource for Cell Analysis and Modeling". NA-MIC is becoming a resource for NIH groups interested in open sourcing biomedical software.

National and International Impact

NA-MIC software includes existing toolkits that are supported by open source software communities. ITK, the Insight Toolkit Kit, was originally funded by the National Library of Medicine. NLM funding is now limited to maintenance. NA-MIC has provided new ITK functionality to support the Center's requirements for Diffusion Tensor Imaging and Functional MRI. This new software fills the needs of NA-MIC but also provides ITK's international community with valuable new technology.

NA-MIC's software process also has national impact. Dart/Ctest has been adopted by many national and internal open software devleopment groups. For example, CMake has been adopted by the K Desktop Environment (KDE). This graphical desktop environment for Linux and Unix workstations is one of the largest open source projects in the world.

The NA-MIC All Hands Meeting welcomed attendees from outside the Center including Northwestern, U Iowa and the MIND Institute,. The Programmer/Project Weeks had participants from UIowa, SRI, and the SCI Institute

NA-MIC co-sponsored an Open Source Workshop at the 2005 MICCAI conference. The attendance was 80 people, far exceeding the expected numbers. The proceedings of the workshop were published in the electronic Insight Journal, another NIH-funded activity. A workshop on Advanced ITK and Slicer was held at the Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland.