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Scientific research has become very data and compute intensive because of the progress in data acquisition and measurement devices, which is particularly true in Life Sciences. To cope with this deluge of data, scientists use distributed computing and storage infrastructures. The use of such infrastructures introduces by itself new challenges to the scientists in terms of proper and efficient use. Scientific workflow management systems play an important role in facilitating the use of the infrastructure by hiding some of its complexity. Althought most scientific workflow management systems are provenance-aware, not all of them come with provenance functionality out of the box. In this paper we describe the improvement and integration of a provenance system into an e-infrastructure for biomedical research based on the MOTEUR workflow management system. The main contributions of the paper are: presenting an OPM implementation using relational database backend for the provenance store, providing an e-infrastructure with a comprehensive provenance system, defining a generic approach to provenance implementation, potentially suitable for other workflow systems and application domains and demonstrating the value of this system based on use cases presenting the provenance data through a user-friendly web interface. [ABSTRACT FROM AUTHOR]

In this paper we present the architecture of a framework for building Science Gateways supporting official standards both for user authentication and authorization and for middleware-independent job and data management. Two use cases of the customization of the Science Gateway framework for Semantic-Web-based life science applications are also described. [ABSTRACT FROM AUTHOR]

Massively-parallel sequencing (MPS) technologies and their diverse applications in genomics and epigenomics research have yielded enormous new insights into the physiology and pathophysiology of the human genome. The biggest hurdle remains the magnitude and diversity of the datasets generated, compromising our ability to manage, organize, process and ultimately analyse data. The Wiki-based Automated Sequence Processor (WASP), developed at the Albert Einstein College of Medicine (hereafter Einstein), uniquely manages to tightly couple the sequencing platform, the sequencing assay, sample metadata and the automated workflows deployed on a heterogeneous high performance computing cluster infrastructure that yield sequenced, quality-controlled and 'mapped' sequence data, all within the one operating environment accessible by a web-based GUI interface. WASP at Einstein processes 4-6 TB of data per week and since its production cycle commenced it has processed ~ 1 PB of data overall and has revolutionized user interactivity with these new genomic technologies, who remain blissfully unaware of the data storage, management and most importantly processing services they request. The abstraction of such computational complexity for the user in effect makes WASP an ideal middleware solution, and an appropriate basis for the development of a grid-enabled resource - the Einstein Genome Gateway - as part of the Extreme Science and Engineering Discovery Environment (XSEDE) program. In this paper we discuss the existing WASP system, its proposed middleware role, and its planned interaction with XSEDE to form the Einstein Genome Gateway. [ABSTRACT FROM AUTHOR]

Recent developments in MRI contrast agents give new perspectives in radiological diagnosis and therapy planning, but require specific image analysis methods. By employment of an academic research grid, we are currently validating and optimizing a recently developed fully automatic method for liver segmentation in Gd-EOB enhanced MRI. The grid enables extensive parameter scans and evaluation against expert's reference segmentation. The implementation layout and so far reached results are presented. Furthermore, experiences made in the production phase and consequences resulting for the exploitation of publicly funded research grids for Healthgrid applications are given. [ABSTRACT FROM AUTHOR]

Tensor analysis of diffusion weighted magnetic resonance images is increasingly used for non-invasive tracking of nerve fibers in the human brain. Diffusion-tensor imaging (DTI) enables in-vivo research on the internal structure of the central nervous system, encompassing interconnection of functional areas, correlation between fiber deformations and certain desease patterns, as well as brain tumor localization. But the modeling of the local diffusion parameters is a computationally expensive part of the processing pipeline, resulting to run times up to days on standard desktop computers. A grid implementation of the algorithm with slice based parallelization reduces the processing down to 10% compared to a local cluster and 20% compared to sequential processing on the grid. A workflow implementation enables fault-tolerant handling of temporary failures within the grid. Furthermore, pure web-based access to the grid application allows for collaborative utilitzation even from protected infrastructures, as they are typically found in clinical environments. [ABSTRACT FROM AUTHOR]

Grid computing, the collaboration of distributed re- sources across institutional borders, is an emerging technology to meet the rising demand on computing power and storage capacity in fields such as high-energy physics, climate modeling, or more recently, life sciences. A secure, reliable, and highly efficient data transport plays an integral role in such grid environments and even more so in medical grids. Unfortunately, many grid middleware distributions, such as the well-known Globus Toolkit, lack the integration of the world-wide medical image communication standard Digital Imaging and Communication in Medicine (DICOM). Currently, the DICOM protocol first needs to be converted to the file transfer protocol (FTP) that is offered by the grid middleware. This effectively reduces most of the advantages and security an integrated network of DICOM devices offers. In this paper, a solution is proposed that adapts the DICOM protocol to the Globus grid security infrastructure and utilizes routers to transparently route traffic to and from DICOM systems. Thus, all legacy DICOM devices can be seamlessly integrated into the grid without modifications. A prototype of the grid routers with the most important DICOM functionality has been developed and successfully tested in the MediGRID test bed, the German grid project for life sciences. [ABSTRACT FROM AUTHOR]