HPC AND GRID COMPUTING FOR INTEGRATIVE BIOMEDICAL RESEARCH

Integrative biomedical research projects query, analyze, and integrate many different data types and make use of datasets obtained from measurements or simulations of structure and function at multiple biological scales. With the increasing availability of high-throughput and high-resolution instruments, the integrative biomedical research imposes many challenging requirements on software middleware systems. In this paper, we look at some of these requirements using example research pattern templates. We then discuss how middleware systems, which incorporate Grid and high-performance computing, could be employed to address the requirements.

e-Science, caGrid, and Translational Biomedical Research

Translational research projects target a wide variety of diseases, test many different kinds of biomedical hypotheses, and employ a large assortment of experimental methodologies. Diverse data, complex execution environments, and demanding security and reliability requirements make the implementation of these projects extremely challenging and require novel e-Science technologies.

Translational Research Design Templates, Grid Computing, and HPC

Design templates that involve discovery, analysis, and integration of information resources commonly occur in many scientific research projects. In this paper we present examples of design templates from the biomedical translational research domain and discuss the requirements imposed on Grid middleware infrastructures by them. Using caGrid, which is a Grid middleware system based on the model driven architecture (MDA) and the service oriented architecture (SOA) paradigms, as a starting point, we discuss architecture directions for MDA and SOA based systems like caGrid to support common design templates.

Sharing data and analytical resources securely in a biomedical research Grid environment

OBJECTIVES

To develop a security infrastructure to support controlled and secure access to data and analytical resources in a biomedical research Grid environment, while facilitating resource sharing among collaborators.

DESIGN

A Grid security infrastructure, called Grid Authentication and Authorization with Reliably Distributed Services (GAARDS), is developed as a key architecture component of the NCI-funded cancer Biomedical Informatics Grid (caBIG). The GAARDS is designed to support in a distributed environment 1) efficient provisioning and federation of user identities and credentials; 2) group-based access control support with which resource providers can enforce policies based on community accepted groups and local groups; and 3) management of a trust fabric so that policies can be enforced based on required levels of assurance.

MEASUREMENTS

GAARDS is implemented as a suite of Grid services and administrative tools. It provides three core services: Dorian for management and federation of user identities, Grid Trust Service for maintaining and provisioning a federated trust fabric within the Grid environment, and Grid Grouper for enforcing authorization policies based on both local and Grid-level groups.

RESULTS

The GAARDS infrastructure is available as a stand-alone system and as a component of the caGrid infrastructure. More information about GAARDS can be accessed at http://www.cagrid.org.

CONCLUSIONS

GAARDS provides a comprehensive system to address the security challenges associated with environments in which resources may be located at different sites, requests to access the resources may cross institutional boundaries, and user credentials are created, managed, revoked dynamically in a de-centralized manner.

A roadmap for caGrid, an enterprise Grid architecture for biomedical research

caGrid is a middleware system which combines the Grid computing, the service oriented architecture, and the model driven architecture paradigms to support development of interoperable data and analytical resources and federation of such resources in a Grid environment. The functionality provided by caGrid is an essential and integral component of the cancer Biomedical Informatics Grid (caBIG) program. This program is established by the National Cancer Institute as a nationwide effort to develop enabling informatics technologies for collaborative, multi-institutional biomedical research with the overarching goal of accelerating translational cancer research. Although the main application domain for caGrid is cancer research, the infrastructure provides a generic framework that can be employed in other biomedical research and healthcare domains. The development of caGrid is an ongoing effort, adding new functionality and improvements based on feedback and use cases from the community. This paper provides an overview of potential future architecture and tooling directions and areas of improvement for caGrid and caGrid-like systems. This summary is based on discussions at a roadmap workshop held in February with participants from biomedical research, Grid computing, and high performance computing communities.

The Cancer Biomedical Informatics Grid (caBIG) Security Infrastructure

Security is a high priority issue in medical domain, because many institutions performing biomedical research work with sensitive medical data regularly. This issue becomes more complicated, when it is desirable or needed to access and analyze data in a multi-institutional setting. In the NCI cancer Biomedical Informatics Grid (caBIG) program, several security issues were raised that existing security technologies could not address. Considering caBIG is envisioned to span a large number of cancer centers and investigator laboratories, these issues pose considerable challenge. In this paper we present these issues and the infrastructure, referred to as GAARDS, which has been developed to address them.