Cancer is a leading cause of morbidity and mortality worldwide according to the World Health Organization [1] and it imposes a big challenge for the researchers and the scientific community. Complex problems like cancer cannot be solved by a single research institute by using traditional methods. The fight against cancer requires the collaborative efforts of multidisciplinary institutes and research labs across the countries. The collaborative efforts should be augmented with the support of high- performance computing and databases by providing a common platform for integrated research. The National Cancer Informatics Program (NCIP) [2] launched by National Institutes of Health (NIH) [3] supports biomedical informatics in cancer research. NCIP offers among other resources the NCIP Hub [4], a science gateway for helping to accelerate innovation in the cancer research community. NCIP Hub is based on the science gateway framework HUBzero® [5] and allows for creation of projects sharing data and running data analysis with different tools such as 3D Slicer [6], an open source software platform for medical image informatics, image processing, and three-dimensional visualization.
The ICTBioMed (International Consortium for Technology in Biomedicine) [7, 8] consortium applies the NCIP Hub to combine efforts of a variety of knowledge and expertise benefiting the cancer research. ICTBioMed is a consortium of domain researchers, experts in high-performance computing centers and organizations concerned with applications in health informatics.
ICTBioMed Members include:
- OHSL (Open Health Systems Laboratory), USA;
- C-DAC (Centre for Development of Advanced Computing), Pune, India;
- PSNC (Poznan Supercomputing and Networking Center), Poznan, Poland;
- the University of Notre Dame Center for Research Computing, Notre Dame, USA;
- Chalmers University Life Sciences Supercomputing Networking Center, Gothenburg, Sweden and Internet2, USA.
Additionally, experts from Arizona State University’s Computational Sciences and Complex Adaptive Systems Initiative; Duke Comprehensive Cancer Center and Tata Memorial Center in India are also involved. The ICTBioMed team is working with the HUBzero® team of Purdue University for implementing a Docker [9] execution host model, which integrates into the HUBzero® platform. ICTBioMed has created Docker containers with pre-configured workflows used by cancer researchers. Example data sets are included in the Docker container for the proof of concept and the prototype for testing these Docker containers is underway.
The enhancement will provide a seamless approach for execution of cancer-related workflows and will be available to all projects in the NCIP Hub. The science gateway opens new avenues for future collaborations across the countries to solve common problems and gives stronger opportunity to fight cancer.
References
[1] http://www.who.int/mediacentre/factsheets /fs297/en/
[2] https://cbiit.cancer.gov/ncip/ncip-home
[3] https://www.nih.gov/
[4] https://nciphub.org/
[5] McLennan, Michael, and Rick Kennell. HUBzero: A Platform for Dissemination and Collaboration in Computational Science and Engineering. Computing in Science & Engineering 12, no. 2 (2010): 48-53.
[6] Fedorov A., Beichel R., Kalpathy-Cramer J., Finet J., Fillion-Robin J-C., Pujol S., Bauer C., Jennings D., Fennessy F., Sonka M., Buatti J., Aylward S.R., Miller J.V., Pieper S., Kikinis R. 3D Slicer as an Image Computing Platform for the Quantitative Imaging Network. Magnetic Resonance Imaging. 2012 Nov;30(9):1323-41. PMID: 22770690.
[7] http://www.ictbiomed.net/
[8] Mazurek, Cezary, et al. ”Federated clouds for biomedical research: Integrating OpenStack for ICTBioMed.” Cloud Networking (CloudNet), 2014 IEEE 3rd International Conference on. IEEE, 2014.
[9] https://www.docker.com/
Adapted from a poster presentation by ICTBiomed prepared for Gateways 2017 conference, October 23-25, 2017, Ann Arbor, MI
Co-Authors
Amit Saxena, Rajendra Joshi, Hemant Darbari, C-DAC , India
Michael Zentner, Kevin Wojkivich, Purdue University, USA
Amar Bhat, Anil Srivastava, OHSL, USA
Ken Buetow, ASU, USA
Cezary Mazurek, PSNC, Poland
Sandra Gesing*, University of Notre Dame, USA
*Center for Research Computing, University of Notre Dame, Notre Dame, IN, 46556,USA; email: sandra.gesing@nd.edu