Links to Other Great Sites


The department is equipped with a DGX-1 and has recently acquired an DGX-A100 machine for development and we’ll be combining this with Amazon Web Services (AWS) for computer algorithm deployment.


Software Tools

The following are software tools we developed with colleagues and students over the years for outcome modeling and image analysis. These tools are available for FREE following public access license and intended for research use only, just please, cite the proper paper upon use. Enjoy!

  • Outcome modeling and bioinformatics
    • A Dose Response Explorer System (DREES)
      • The software is available for download here
      • Tutorial and sample data are found here
      • Publications:
        • I El Naqa, G Suneja, P E Lindsay, A J Hope, J R Alaly, M Vicic, J D Bradley, A Apte, and J O Deasy," Dose-response explorer: an integrated open source tool for exploring and modeling radiotherapy dose-volume-outcome relationships," Phys. Med. Biol., 51, pp. 5719–5735, 2006
        • El Naqa I., Bradley J., Blanco A., Lindsay P.E., Vicic M., Hope A., and Deasy J.O., “Multi-variable modeling of radiotherapy outcomes including dose-volume and clinical factors,” Int. J. Radiation Oncology Biol. Phys, March 2006 , Vol. 64, Issue 4, pp 1275-1286.
        • Deasy, J. Oh , A. Apte, I. El Naqa, “Tools for Extracting and Analyzing Dose-Volume Outcomes Relationships: Improvements to the Dose Response ExplorEr System (DREES), ICCR 2010, Amsterdam, 2010.
      • Editorials:
      • Ensemble Bayesian Network for Radiotherapy Outcome Modeling
        • The software is used as part of the paper below and is available for download here
        • Publications:
          • Sangkyu Lee, Norma Ybarra, Krishinima Jeyaseelan, Jan Seuntjens, and Issam El Naqa, “Bayesian Network ensemble as a multivariate strategy to predict radiation pneumonitis risk.” Medical Physics, Med. Phys. 42, 2421 (2015) (Author's Choice 2015).
        • Image Analysis
          • Multimodality Image Segmentation System (MIASYS)
            • The software is available for download zip
            • Publications:
              • Yang D, Zheng J, Nofal A, Wu Y, Deasy J, El Naqa I. Techniques and software tool for 3D multimodality medical image segmentation, Journal of radiation oncology informatics, 1:(1), 1:22, 2009
            • Deformable Image Registration for Adaptive Radiotherapy
              • The software is available for download here
              • Publications:
                • Deshan Yang, Ryan S Brame , Issam El Naqa , Aditya Apte , Yu Wu , SreeKrishna Murty Goddu , Sasa Mutic , Joseph Deasy , Daniel A Low, “DIRART - A software suite for deformable image registration and adaptive radiotherapy research", Medical Physics, 2011 Jan;38(1):67-77.
              • Image-based outcome modeling (Radiomics)
                • The software is available for download here
                • Publications:
                  • M Vallières, C R Freeman, S R Skamene and I El Naqa, “A Radiomics model from joint FDG-PET and MR texture features for prediction of lung metastases in soft-tissue sarcomas of the extremities, PMB, Jul 7;60(14):5471-96, 2015 (Editor's Choice).