The ability to track changes in tumors and organs at risk over a course of radiotherapy is essential for successful adaptive radiation therapy (ART). To that end, we have developed a software suite that helps with tracking geometric and dosimetric changes of organs and targets within the clinical setting. The core engine, denoted as ART engine, is fully autonomous and consists of several modules, including data import/export, dose calculation, deformable image registration (DIR), interactive review graphical user interfaces, and messaging. The system has been successfully used for various research projects and is currently being thoroughly tested as part of our institutional software validation and quality assurance process. We have crossvalidated our DIR algorithm against four commercially available DIR algorithms using images from H&N radiotherapy. The estimated accuracy of our system was equivalent or better.