As sequencing technologies progress, the amount of data produced grows exponentially, shifting the bottleneck of discovery towards the data analysis phase. In particular, currently available mapping ...solutions for RNA-seq leave room for improvement in terms of sensitivity and performance, hindering an efficient analysis of transcriptomes by massive sequencing. Here, we present an innovative approach that combines re-engineering, optimization and parallelization. This solution results in a significant increase of mapping sensitivity over a wide range of read lengths and substantial shorter runtimes when compared with current RNA-seq mapping methods available.
General Purpose Graphic Processing Units (GPGPUs) constitute an inexpensive resource for computing-intensive applications that could exploit an intrinsic fine-grain parallelism. This paper presents ...the design and implementation in GPGPUs of an exact alignment tool for nucleotide sequences based on the Burrows-Wheeler Transform. We compare this algorithm with state-of-the-art implementations of the same algorithm over standard CPUs, and considering the same conditions in terms of I/O. Excluding disk transfers, the implementation of the algorithm in GPUs shows a speedup larger than 12×, when compared to CPU execution. This implementation exploits the parallelism by concurrently searching different sequences on the same reference search tree, maximizing memory locality and ensuring a symmetric access to the data. The paper describes the behavior of the algorithm in GPU, showing a good scalability in the performance, only limited by the size of the GPU inner memory.
This article presents a Middleware based on Grid Technologies that addresses the problem of sharing, transferring and processing DICOM medical images in a distributed environment using an ontological ...schema to create virtual communities and to define common targets. It defines a distributed storage that builds-up virtual repositories integrating different individual image repositories providing global searching, progressive transmission, automatic encryption and pseudo-anonimisation and a link to remote processing services. Users from a Virtual Organisation can share the cases that are relevant for their communities or research areas, epidemiological studies or even deeper analysis of complex individual cases. Software architecture has been defined for solving the problems that has been exposed before. Briefly, the architecture comprises five layers (from the more physical layer to the more logical layer) based in Grid Technologies. The lowest level layers (Core Middleware Layer and Server Services sc layer) are composed of Grid Services that implement the global managing of resources. The Middleware Components Layer provides a transparent view of the Grid environment and it has been the main objective of this work. Finally, the highest layer (the Application Layer) comprises the applications, and a simple application has been implemented for testing the components developed in the Components Middleware Layer. Other side-results of this work are the services developed in the Middleware Components Layer for managing DICOM images, creating virtual DICOM storages, progressive transmission, automatic encryption and pseudo-anonimisation depending on the ontologies. Other results, such as the Grid Services developed in the lowest layers, are also described in this article. Finally a brief performance analysis and several snapshots from the applications developed are shown. The performance analysis proves that the components developed in this work provide image processing applications with new possibilities for large-scale sharing, management and processing of DICOM images. The results show that the components fulfil the objectives proposed. The extensibility of the system is achieved by the use of open methods and protocols, so new components can be easily added.
As the size and complexity of Cloud systems increase, the manual management of these solutions becomes a challenging issue as more personnel, resources and expertise are needed. Service Level ...Agreement (SLA)-aware autonomic cloud solutions enable managing large scale infrastructure management meanwhile supporting multiple dynamic requirement from users. This paper contributes to these topics by the introduction of Cloudcompaas, a SLA-aware PaaS Cloud platform that manages the complete resource lifecycle. This platform features an extension of the SLA specification WS-Agreement, tailored to the specific needs of Cloud Computing. In particular, Cloudcompaas enables Cloud providers with a generic SLA model to deal with higher-level metrics, closer to end-user perception, and with flexible composition of the requirements of multiple actors in the computational scene. Moreover, Cloudcompaas provides a framework for general Cloud computing applications that could be dynamically adapted to correct the QoS violations by using the elasticity features of Cloud infrastructures. The effectiveness of this solution is demonstrated in this paper through a simulation that considers several realistic workload profiles, where Cloudcompaas achieves minimum cost and maximum efficiency, under highly heterogeneous utilization patterns.
•A methodology for the representation of Cloud resources.•A SLA-driven architecture for the automatic scheduling of Cloud resources.•A SLA-driven architecture for the dynamic management of Cloud resources.•The resolution of a use case by a prototype implementation.
Diffusion Weighted Imaging (DWI) methods (ADC and IVIM models) extract meaningful information about the microscopic motions of water of human tissues from MRIs. This is a non invasive method which ...plays an important role in the diagnosis of ischemic strokes, high grade gliomas or tumors.
In the La Fe Polytechnic and University Hospital, the DWI methods aforementioned are used in clinical practice and Matlab is used as a development tool for his out of box performance and fast prototyping. However, each image takes hours to compute due to Matlab’s environment and interpreted functions. Because of this, its use in clinical practice is limited.
In this paper we present three compiled versions on which different parallel paradigms based on multicore (OpenMP) and GPU (CUDA) are applied. These implementations have managed to reduce the computation time to less than one minute, therefore, it allows easing their use in daily clinical practice at a cheap acquisition cost.
HPG Aligner applies suffix arrays for DNA read mapping. This implementation produces a highly sensitive and extremely fast mapping of DNA reads that scales up almost linearly with read length. The ...approach presented here is faster (over 20× for long reads) and more sensitive (over 98% in a wide range of read lengths) than the current state-of-the-art mappers. HPG Aligner is not only an optimal alternative for current sequencers but also the only solution available to cope with longer reads and growing throughputs produced by forthcoming sequencing technologies.
https://github.com/opencb/hpg-aligner.
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► We designed a prototype to share DICOM studies in a distributed environment. ► We designed a prototype using DICOM-SR to federate data leveraging research interest. ► We deploy a ...real infrastructure, creating a knowledge database on breast cancer. ► Systematization of use cases improving diagnosis and follow-on of breast cancer.
An important effort has been invested on improving the image diagnosis process in different medical areas using information technologies. The field of medical imaging involves two main data types: medical imaging and reports. Developments based on the DICOM standard have demonstrated to be a convenient and widespread solution among the medical community. The main objective of this work is to design a Web application prototype that will be able to improve diagnosis and follow-on of breast cancer patients. It is based on TRENCADIS middleware, which provides a knowledge-oriented storage model composed by federated repositories of DICOM image studies and DICOM-SR medical reports. The full structure and contents of the diagnosis reports are used as metadata for indexing images. The TRENCADIS infrastructure takes full advantage of Grid technologies by deploying multi-resource grid services that enable multiple views (reports schemes) of the knowledge database. The paper presents a real deployment of such Web application prototype in the Dr. Peset Hospital providing radiologists with a tool to create, store and search diagnostic reports based on breast cancer explorations (mammography, magnetic resonance, ultrasound, pre-surgery biopsy and post-surgery biopsy), improving support for diagnostics decisions. A technical details for use cases (outlining enhanced multi-resource grid services communication and processing steps) and interactions between actors and the deployed prototype are described. As a result, information is more structured, the logic is clearer, network messages have been reduced and, in general, the system is more resistant to failures.
This paper describes a methodology for redesigning the clinical processes to manage diagnosis, follow-up, and response to treatment episodes of breast cancer. This methodology includes three ...fundamental elements: (1) identification of similar and contrasting cases that may be of clinical relevance based upon a target study, (2) codification of reports with standard medical terminologies, and (3) linking and indexing the structured reports obtained with different techniques in a common system. The combination of these elements should lead to improvements in the clinical management of breast cancer patients. The motivation for this work is the adaptation of the clinical processes for breast cancer created by the Valencian Community health authorities to the new techniques available for data processing. To achieve this adaptation, it was necessary to design nine Digital Imaging and Communications in Medicine (DICOM) structured report templates: six diagnosis templates and three summary templates that combine reports from clinical episodes. A prototype system is also described that links the lesion to the reports. Preliminary tests of the prototype have shown that the interoperability among the report templates allows correlating parameters from different reports. Further work is in progress to improve the methodology in order that it can be applied to clinical practice.
The integration of multi-centre medical image data to create knowledge repositories for research and training activities has been an aim targeted since long ago. This paper presents an environment to ...share, to process and to organise medical imaging data according to a structured framework in which the image reports play a key role. This environment has been validated on a clinical environment, facing problems such as firewalls and security restrictions, in the frame of the CVIMO (Valencian Cyberinfrastructure of Medical Imaging in Oncology) project. The environment uses a middleware called TRENCADIS (Towards a Grid Environment for Processing and Sharing DICOM Objects) that provides users with the management of multiple administrative domains, data encryption and decryption on the fly and semantic indexation of images. Data is structured into four levels: Global data available, virtual federated storages of studies shared across a vertical domain, subsets for projects or experiments on the virtual storage and individual searches on these subsets. This structure of levels gives the needed flexibility for organising authorisation, and hides data that are not relevant for a given experiment. The main components and interactions are shown in the document, outlining the workflows and explaining the different approaches considered, including the protocols used and the difficulties met.
COMP Superscalar (COMPSs) is a programming framework that provides an easy-to-use programming model and a runtime to ease the development of applications for distributed environments. Thanks to its ...modular architecture COMPSs can use a wide range of computational infrastructures providing a uniform interface for job submission and file transfer operations through adapters for different middlewares. In the context of the VENUS-C project the COMPSs framework has been extended through the development of a programming model enactment service that allows researcher to transparently port and execute scientific applications in the Cloud.
This paper presents the implementation of a bioinformatics workflow (using BLAST as core program), the porting to the COMPSs framework and its deployment on the VENUS-C platform. The proposed approach has been evaluated on a Cloud testbed using virtual machines managed by EMOTIVE Cloud and compared to a similar approach on the Azure platform and to other implementations on HPC infrastructures.
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