Grid Analysis of Radiological Data

IGI-Global Medical Information Science Discoveries Research Award 2009International audienceGrid technologies and infrastructures can contribute to harnessing the full power of computer-aided image analysis into clinical research and practice. Given the volume of data, the sensitivity of medical information, and the joint complexity of medical datasets and computations expected in clinical practice, the challenge is to fill the gap between the grid middleware and the requirements of clinical applications. This chapter reports on the goals, achievements and lessons learned from the AGIR (Grid Analysis of Radiological Data) project. AGIR addresses this challenge through a combined approach. On one hand, leveraging the grid middleware through core grid medical services (data management, responsiveness, compression, and workflows) targets the requirements of medical data processing applications. On the other hand, grid-enabling a panel of applications ranging from algorithmic research to clinical use cases both exploits and drives the development of the services

DCMS: A data analytics and management system for molecular simulation

Molecular Simulation (MS) is a powerful tool for studying physical/chemical features of large systems and has seen applications in many scientific and engineering domains. During the simulation process, the experiments generate a very large number of atoms and intend to observe their spatial and temporal relationships for scientific analysis. The sheer data volumes and their intensive interactions impose significant challenges for data accessing, managing, and analysis. To date, existing MS software systems fall short on storage and handling of MS data, mainly because of the missing of a platform to support applications that involve intensive data access and analytical process. In this paper, we present the database-centric molecular simulation (DCMS) system our team developed in the past few years. The main idea behind DCMS is to store MS data in a relational database management system (DBMS) to take advantage of the declarative query interface (i.e., SQL), data access methods, query processing, and optimization mechanisms of modern DBMSs. A unique challenge is to handle the analytical queries that are often compute-intensive. For that, we developed novel indexing and query processing strategies (including algorithms running on modern co-processors) as integrated components of the DBMS. As a result, researchers can upload and analyze their data using efficient functions implemented inside the DBMS. Index structures are generated to store analysis results that may be interesting to other users, so that the results are readily available without duplicating the analysis. We have developed a prototype of DCMS based on the PostgreSQL system and experiments using real MS data and workload show that DCMS significantly outperforms existing MS software systems. We also used it as a platform to test other data management issues such as security and compression