9,474 research outputs found

    COEL: A Web-based Chemistry Simulation Framework

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    The chemical reaction network (CRN) is a widely used formalism to describe macroscopic behavior of chemical systems. Available tools for CRN modelling and simulation require local access, installation, and often involve local file storage, which is susceptible to loss, lacks searchable structure, and does not support concurrency. Furthermore, simulations are often single-threaded, and user interfaces are non-trivial to use. Therefore there are significant hurdles to conducting efficient and collaborative chemical research. In this paper, we introduce a new enterprise chemistry simulation framework, COEL, which addresses these issues. COEL is the first web-based framework of its kind. A visually pleasing and intuitive user interface, simulations that run on a large computational grid, reliable database storage, and transactional services make COEL ideal for collaborative research and education. COEL's most prominent features include ODE-based simulations of chemical reaction networks and multicompartment reaction networks, with rich options for user interactions with those networks. COEL provides DNA-strand displacement transformations and visualization (and is to our knowledge the first CRN framework to do so), GA optimization of rate constants, expression validation, an application-wide plotting engine, and SBML/Octave/Matlab export. We also present an overview of the underlying software and technologies employed and describe the main architectural decisions driving our development. COEL is available at http://coel-sim.org for selected research teams only. We plan to provide a part of COEL's functionality to the general public in the near future.Comment: 23 pages, 12 figures, 1 tabl

    Data Provenance and Management in Radio Astronomy: A Stream Computing Approach

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    New approaches for data provenance and data management (DPDM) are required for mega science projects like the Square Kilometer Array, characterized by extremely large data volume and intense data rates, therefore demanding innovative and highly efficient computational paradigms. In this context, we explore a stream-computing approach with the emphasis on the use of accelerators. In particular, we make use of a new generation of high performance stream-based parallelization middleware known as InfoSphere Streams. Its viability for managing and ensuring interoperability and integrity of signal processing data pipelines is demonstrated in radio astronomy. IBM InfoSphere Streams embraces the stream-computing paradigm. It is a shift from conventional data mining techniques (involving analysis of existing data from databases) towards real-time analytic processing. We discuss using InfoSphere Streams for effective DPDM in radio astronomy and propose a way in which InfoSphere Streams can be utilized for large antennae arrays. We present a case-study: the InfoSphere Streams implementation of an autocorrelating spectrometer, and using this example we discuss the advantages of the stream-computing approach and the utilization of hardware accelerators

    Stochastic Query Covering for Fast Approximate Document Retrieval

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    We design algorithms that, given a collection of documents and a distribution over user queries, return a small subset of the document collection in such a way that we can efficiently provide high-quality answers to user queries using only the selected subset. This approach has applications when space is a constraint or when the query-processing time increases significantly with the size of the collection. We study our algorithms through the lens of stochastic analysis and prove that even though they use only a small fraction of the entire collection, they can provide answers to most user queries, achieving a performance close to the optimal. To complement our theoretical findings, we experimentally show the versatility of our approach by considering two important cases in the context of Web search. In the first case, we favor the retrieval of documents that are relevant to the query, whereas in the second case we aim for document diversification. Both the theoretical and the experimental analysis provide strong evidence of the potential value of query covering in diverse application scenarios
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