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application programming interface

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Michael P Cummings – 1st expert on this subject based on the ideXlab platform

  • beagle an application programming interface and high performance computing library for statistical phylogenetics
    Systematic Biology, 2012
    Co-Authors: Daniel L Ayres, Aaron E Darling, Derrick J Zwickl, Peter Beerli, Mark T Holder, Paul O Lewis, John P Huelsenbeck, Fredrik Ronquist, David L Swofford, Michael P Cummings

    Abstract:

    Phylogenetic inference is fundamental to our understanding of most aspects of the origin and evolution of life, and in recent years, there has been a concentration of interest in statistical approaches such as Bayesian inference and maximum likelihood estimation. Yet, for large data sets and realistic or interesting models of evolution, these approaches remain computationally demanding. High-throughput sequencing can yield data for thousands of taxa, but scaling to such problems using serial computing often necessitates the use of nonstatistical or approximate approaches. The recent emer- gence of graphics processing units (GPUs) provides an opportunity to leverage their excellent floating-point computational performance to accelerate statistical phylogenetic inference. A specialized library for phylogenetic calculation would allow existing software packages to make more effective use of available computer hardware, including GPUs. Adoption of a com- mon library would also make it easier for other emerging computing architectures, such as field programmable gate arrays, to be used in the future. We present BEAGLE, an application programming interface (API) and library for high-performance statistical phylogenetic inference. The API provides a uniform interface for performing phylogenetic likelihood calculations on a variety of compute hardware platforms. The library includes a set of efficient implementations and can currently ex- ploit hardware including GPUs using NVIDIA CUDA, central processing units (CPUs) with Streaming SIMD Extensions and related processor supplementary instruction sets, and multicore CPUs via OpenMP. To demonstrate the advantages of a common API, we have incorporated the library into several popular phylogenetic software packages. The BEAGLE library is free open source software licensed under the Lesser GPL and available from http://beagle-lib.googlecode.com. An example client program is available as public domain software. (Bayesian phylogenetics; GPU; maximum likelihood; parallel computing.)

  • beagle an application programming interface and high performance computing library for statistical phylogenetics
    Systematic Biology, 2012
    Co-Authors: Daniel L Ayres, Aaron E Darling, Derrick J Zwickl, Peter Beerli, Mark T Holder, Paul O Lewis, John P Huelsenbeck, Fredrik Ronquist, David L Swofford, Michael P Cummings

    Abstract:

    Phylogenetic inference is fundamental to our understanding of most aspects of the origin and evolution of life, and in recent years, there has been a concentration of interest in statistical approaches such as Bayesian inference and maximum likelihood estimation. Yet, for large data sets and realistic or interesting models of evolution, these approaches remain computationally demanding. High-throughput sequencing can yield data for thousands of taxa, but scaling to such problems using serial computing often necessitates the use of nonstatistical or approximate approaches. The recent emergence of graphics processing units (GPUs) provides an opportunity to leverage their excellent floating-point computational performance to accelerate statistical phylogenetic inference. A specialized library for phylogenetic calculation would allow existing software packages to make more effective use of available computer hardware, including GPUs. Adoption of a common library would also make it easier for other emerging computing architectures, such as field programmable gate arrays, to be used in the future. We present BEAGLE, an application programming interface (API) and library for high-performance statistical phylogenetic inference. The API provides a uniform interface for performing phylogenetic likelihood calculations on a variety of compute hardware platforms. The library includes a set of efficient implementations and can currently exploit hardware including GPUs using NVIDIA CUDA, central processing units (CPUs) with Streaming SIMD Extensions and related processor supplementary instruction sets, and multicore CPUs via OpenMP. To demonstrate the advantages of a common API, we have incorporated the library into several popular phylogenetic software packages. The BEAGLE library is free open source software licensed under the Lesser GPL and available from http://beagle-lib.googlecode.com. An example client program is available as public domain software.

  • grid services base library a high level procedural application programming interface for writing globus based grid services
    Future Generation Computer Systems, 2007
    Co-Authors: Adam L Bazinet, Daniel S Myers, John Fuetsch, Michael P Cummings

    Abstract:

    The Grid Services Base Library (GSBL) is a procedural application programming interface (API) that abstracts many of the high-level functions performed by Globus Grid services, thus dramatically lowering the barriers to writing Grid services. The library has been extensively tested and used for computational biology research in a Globus Toolkit-based Grid system, in which no fewer than twenty Grid services written with this API are deployed.

Daniel L Ayres – 2nd expert on this subject based on the ideXlab platform

  • beagle an application programming interface and high performance computing library for statistical phylogenetics
    Systematic Biology, 2012
    Co-Authors: Daniel L Ayres, Aaron E Darling, Derrick J Zwickl, Peter Beerli, Mark T Holder, Paul O Lewis, John P Huelsenbeck, Fredrik Ronquist, David L Swofford, Michael P Cummings

    Abstract:

    Phylogenetic inference is fundamental to our understanding of most aspects of the origin and evolution of life, and in recent years, there has been a concentration of interest in statistical approaches such as Bayesian inference and maximum likelihood estimation. Yet, for large data sets and realistic or interesting models of evolution, these approaches remain computationally demanding. High-throughput sequencing can yield data for thousands of taxa, but scaling to such problems using serial computing often necessitates the use of nonstatistical or approximate approaches. The recent emergence of graphics processing units (GPUs) provides an opportunity to leverage their excellent floating-point computational performance to accelerate statistical phylogenetic inference. A specialized library for phylogenetic calculation would allow existing software packages to make more effective use of available computer hardware, including GPUs. Adoption of a common library would also make it easier for other emerging computing architectures, such as field programmable gate arrays, to be used in the future. We present BEAGLE, an application programming interface (API) and library for high-performance statistical phylogenetic inference. The API provides a uniform interface for performing phylogenetic likelihood calculations on a variety of compute hardware platforms. The library includes a set of efficient implementations and can currently exploit hardware including GPUs using NVIDIA CUDA, central processing units (CPUs) with Streaming SIMD Extensions and related processor supplementary instruction sets, and multicore CPUs via OpenMP. To demonstrate the advantages of a common API, we have incorporated the library into several popular phylogenetic software packages. The BEAGLE library is free open source software licensed under the Lesser GPL and available from http://beagle-lib.googlecode.com. An example client program is available as public domain software.

  • beagle an application programming interface and high performance computing library for statistical phylogenetics
    Systematic Biology, 2012
    Co-Authors: Daniel L Ayres, Aaron E Darling, Derrick J Zwickl, Peter Beerli, Mark T Holder, Paul O Lewis, John P Huelsenbeck, Fredrik Ronquist, David L Swofford, Michael P Cummings

    Abstract:

    Phylogenetic inference is fundamental to our understanding of most aspects of the origin and evolution of life, and in recent years, there has been a concentration of interest in statistical approaches such as Bayesian inference and maximum likelihood estimation. Yet, for large data sets and realistic or interesting models of evolution, these approaches remain computationally demanding. High-throughput sequencing can yield data for thousands of taxa, but scaling to such problems using serial computing often necessitates the use of nonstatistical or approximate approaches. The recent emer- gence of graphics processing units (GPUs) provides an opportunity to leverage their excellent floating-point computational performance to accelerate statistical phylogenetic inference. A specialized library for phylogenetic calculation would allow existing software packages to make more effective use of available computer hardware, including GPUs. Adoption of a com- mon library would also make it easier for other emerging computing architectures, such as field programmable gate arrays, to be used in the future. We present BEAGLE, an application programming interface (API) and library for high-performance statistical phylogenetic inference. The API provides a uniform interface for performing phylogenetic likelihood calculations on a variety of compute hardware platforms. The library includes a set of efficient implementations and can currently ex- ploit hardware including GPUs using NVIDIA CUDA, central processing units (CPUs) with Streaming SIMD Extensions and related processor supplementary instruction sets, and multicore CPUs via OpenMP. To demonstrate the advantages of a common API, we have incorporated the library into several popular phylogenetic software packages. The BEAGLE library is free open source software licensed under the Lesser GPL and available from http://beagle-lib.googlecode.com. An example client program is available as public domain software. (Bayesian phylogenetics; GPU; maximum likelihood; parallel computing.)

B. Stiller – 3rd expert on this subject based on the ideXlab platform

  • LCN – The design of an application programming interface for QoS-based multimedia middleware
    Proceedings of 22nd Annual Conference on Local Computer Networks, 1997
    Co-Authors: C. Conrad, B. Stiller

    Abstract:

    With the advent of networked and distributed multimedia applications, requirements of middleware for providing advanced communication services changed. The needs in well suited architectures for delivering unchanged high network performance to multimedia applications and flexible communication services increased. In any case, applications have to access services of multimedia middleware and they are required to be programmed on top of these systems. Therefore, the developed application programming interface takes into account service specifications in terms of quality of service and an easy to use and intuitively programmable communication service for multimedia applications. This interface for advanced multimedia middleware hides away communication relevant information from applications and provides a minimal set of interface functions and operations.

  • Broadband Networking Technologies – QoS-based application programming interface for communication middleware
    Broadband Networking Technologies, 1997
    Co-Authors: C. Conrad, B. Stiller

    Abstract:

    Since emerging networked applications require a variety of different communication services, the number of communication subsystems and approaches to deliver flexible services has increased. Nevertheless, applications have to be programmed sufficiently on top of these communication subsystems. Providing an easy-to-use and intuitively programmable communication service for multimedia applications, an up-to- date application programming interface is needed. The developed approach offers an object-oriented interface for setting-up, accessing, and managing communication services. Moreover, these services may be of flexible nature, offering the potential to application programmers to specify communication requirements in a set of application-dependent quality-of-service (QoS) parameters. Service needs and communication demands are specified by, e.g., bandwidth requirements, delay bounds, or authentication requests. The developed and implemented application programing interface hides away communication-relevant information from applications and provides a set of efficient and stream-lined interface functions and operations.© (1997) COPYRIGHT SPIE–The International Society for Optical Engineering. Downloading of the abstract is permitted for personal use only.

  • The design of an application programming interface for QoS-based multimedia middleware
    Proceedings of 22nd Annual Conference on Local Computer Networks, 1997
    Co-Authors: C. Conrad, B. Stiller

    Abstract:

    With the advent of networked and distributed multimedia applications, requirements of middleware for providing advanced communication services changed. The needs in well suited architectures for delivering unchanged high network performance to multimedia applications and flexible communication services increased. In any case, applications have to access services of multimedia middleware and they are required to be programmed on top of these systems. Therefore, the developed application programming interface takes into account service specifications in terms of quality of service and an easy to use and intuitively programmable communication service for multimedia applications. This interface for advanced multimedia middleware hides away communication relevant information from applications and provides a minimal set of interface functions and operations.