Neuroimaging study designs, computational analyses and data provenance using the LONI pipeline.

Modern computational neuroscience employs diverse software tools and multidisciplinary expertise to analyze heterogeneous brain data. The classical problems of gathering meaningful data, fitting specific models, and discovering appropriate analysis and visualization tools give way to a new class of computational challenges--management of large and incongruous data, integration and interoperability of computational resources, and data provenance. We designed, implemented and validated a new paradigm for addressing these challenges in the neuroimaging field. Our solution is based on the LONI Pipeline environment [3], [4], a graphical workflow environment for constructing and executing complex data processing protocols. We developed study-design, database and visual language programming functionalities within the LONI Pipeline that enable the construction of complete, elaborate and robust graphical workflows for analyzing neuroimaging and other data. These workflows facilitate open sharing and communication of data and metadata, concrete processing protocols, result validation, and study replication among different investigators and research groups. The LONI Pipeline features include distributed grid-enabled infrastructure, virtualized execution environment, efficient integration, data provenance, validation and distribution of new computational tools, automated data format conversion, and an intuitive graphical user interface. We demonstrate the new LONI Pipeline features using large scale neuroimaging studies based on data from the International Consortium for Brain Mapping [5] and the Alzheimer's Disease Neuroimaging Initiative [6]. User guides, forums, instructions and downloads of the LONI Pipeline environment are available at http://pipeline.loni.ucla.edu

Grid Databases for Shared Image Analysis in the MammoGrid Project

The MammoGrid project aims to prove that Grid infrastructures can be used for collaborative clinical analysis of database-resident but geographically distributed medical images. This requires: a) the provision of a clinician-facing front-end workstation and b) the ability to service real-world clinician queries across a distributed and federated database. The MammoGrid project will prove the viability of the Grid by harnessing its power to enable radiologists from geographically dispersed hospitals to share standardized mammograms, to compare diagnoses (with and without computer aided detection of tumours) and to perform sophisticated epidemiological studies across national boundaries. This paper outlines the approach taken in MammoGrid to seamlessly connect radiologist workstations across a Grid using an "information infrastructure" and a DICOM-compliant object model residing in multiple distributed data stores in Italy and the UKComment: 10 pages, 5 figure

On the Use of XML in Medical Imaging Web-Based Applications

The rapid growth of digital technology in medical fields over recent years has increased the need for applications able to manage patient medical records, imaging data, and chart information. Web-based applications are implemented with the purpose to link digital databases, storage and transmission protocols, management of large volumes of data and security concepts, allowing the possibility to read, analyze, and even diagnose remotely from the medical center where the information was acquired. The objective of this paper is to analyze the use of the Extensible Markup Language (XML) language in web-based applications that aid in diagnosis or treatment of patients, considering how this protocol allows indexing and exchanging the huge amount of information associated with each medical case. The purpose of this paper is to point out the main advantages and drawbacks of the XML technology in order to provide key ideas for future web-based applicationsPeer ReviewedPostprint (author's final draft

DRIVER Technology Watch Report

This report is part of the Discovery Workpackage (WP4) and is the third report out of four deliverables. The objective of this report is to give an overview of the latest technical developments in the world of digital repositories, digital libraries and beyond, in order to serve as theoretical and practical input for the technical DRIVER developments, especially those focused on enhanced publications. This report consists of two main parts, one part focuses on interoperability standards for enhanced publications, the other part consists of three subchapters, which give a landscape picture of current and surfacing technologies and communities crucial to DRIVER. These three subchapters contain the GRID, CRIS and LTP communities and technologies. Every chapter contains a theoretical explanation, followed by case studies and the outcomes and opportunities for DRIVER in this field

Security-oriented data grids for microarray expression profiles

Microarray experiments are one of the key ways in which gene activity can be identified and measured thereby shedding light and understanding for example on biological processes. The BBSRC funded Grid enabled Microarray Expression Profile Search (GEMEPS) project has developed an infrastructure which allows post-genomic life science researchers to ask and answer the following questions: who has undertaken microarray experiments that are in some way similar or relevant to mine; and how similar were these relevant experiments? Given that microarray experiments are expensive to undertake and may possess crucial information for future exploitation (both academically and commercially), scientists are wary of allowing unrestricted access to their data by the wider community until fully exploited locally. A key requirement is thus to have fine grained security that is easy to establish and simple (or ideally transparent) to use across inter-institutional virtual organisations. In this paper we present an enhanced security-oriented data Grid infrastructure that supports the definition of these kinds of queries and the analysis and comparison of microarray experiment results

The Impact of Grid on Health Care Digital Repositories

Grid computing has attracted worldwide attention in a variety of applications like Health Care. In this paper we identified the Grid services that could facilitate the integration and interoperation of Health Care data and frameworks world-wide. While many of the current Health Care Grid projects address issues such as data location and description on the Grid and the security aspects, the problems connected to data storage, integrity, preservation and distribution have been neglected. We describe the currently available Grid storage services and protocols that can come in handy when dealing with those problems. We further describe a Grid infrastructure to build a cooperative Health Care environment based on currently available Grid services and a service able to validate it