26,505 research outputs found

    BioWorkbench: A High-Performance Framework for Managing and Analyzing Bioinformatics Experiments

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    Advances in sequencing techniques have led to exponential growth in biological data, demanding the development of large-scale bioinformatics experiments. Because these experiments are computation- and data-intensive, they require high-performance computing (HPC) techniques and can benefit from specialized technologies such as Scientific Workflow Management Systems (SWfMS) and databases. In this work, we present BioWorkbench, a framework for managing and analyzing bioinformatics experiments. This framework automatically collects provenance data, including both performance data from workflow execution and data from the scientific domain of the workflow application. Provenance data can be analyzed through a web application that abstracts a set of queries to the provenance database, simplifying access to provenance information. We evaluate BioWorkbench using three case studies: SwiftPhylo, a phylogenetic tree assembly workflow; SwiftGECKO, a comparative genomics workflow; and RASflow, a RASopathy analysis workflow. We analyze each workflow from both computational and scientific domain perspectives, by using queries to a provenance and annotation database. Some of these queries are available as a pre-built feature of the BioWorkbench web application. Through the provenance data, we show that the framework is scalable and achieves high-performance, reducing up to 98% of the case studies execution time. We also show how the application of machine learning techniques can enrich the analysis process

    Group Communication Patterns for High Performance Computing in Scala

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    We developed a Functional object-oriented Parallel framework (FooPar) for high-level high-performance computing in Scala. Central to this framework are Distributed Memory Parallel Data structures (DPDs), i.e., collections of data distributed in a shared nothing system together with parallel operations on these data. In this paper, we first present FooPar's architecture and the idea of DPDs and group communications. Then, we show how DPDs can be implemented elegantly and efficiently in Scala based on the Traversable/Builder pattern, unifying Functional and Object-Oriented Programming. We prove the correctness and safety of one communication algorithm and show how specification testing (via ScalaCheck) can be used to bridge the gap between proof and implementation. Furthermore, we show that the group communication operations of FooPar outperform those of the MPJ Express open source MPI-bindings for Java, both asymptotically and empirically. FooPar has already been shown to be capable of achieving close-to-optimal performance for dense matrix-matrix multiplication via JNI. In this article, we present results on a parallel implementation of the Floyd-Warshall algorithm in FooPar, achieving more than 94 % efficiency compared to the serial version on a cluster using 100 cores for matrices of dimension 38000 x 38000

    A robust semantics hides fewer errors

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    In this paper we explore how formal models are interpreted and to what degree meaning is captured in the formal semantics and to what degree it remains in the informal interpretation of the semantics. By applying a robust approach to the definition of refinement and semantics, favoured by the event-based community, to state-based theory we are able to move some aspects from the informal interpretation into the formal semantics

    Specifications and programs for computer software validation

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    Three software products developed during the study are reported and include: (1) FORTRAN Automatic Code Evaluation System, (2) the Specification Language System, and (3) the Array Index Validation System

    Modularity for Security-Sensitive Workflows

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    An established trend in software engineering insists on using components (sometimes also called services or packages) to encapsulate a set of related functionalities or data. By defining interfaces specifying what functionalities they provide or use, components can be combined with others to form more complex components. In this way, IT systems can be designed by mostly re-using existing components and developing new ones to provide new functionalities. In this paper, we introduce a notion of component and a combination mechanism for an important class of software artifacts, called security-sensitive workflows. These are business processes in which execution constraints on the tasks are complemented with authorization constraints (e.g., Separation of Duty) and authorization policies (constraining which users can execute which tasks). We show how well-known workflow execution patterns can be simulated by our combination mechanism and how authorization constraints can also be imposed across components. Then, we demonstrate the usefulness of our notion of component by showing (i) the scalability of a technique for the synthesis of run-time monitors for security-sensitive workflows and (ii) the design of a plug-in for the re-use of workflows and related run-time monitors inside an editor for security-sensitive workflows
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