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Codifying bioinformatics processes without programming

Drug Discovery Today: BIOSILICO 2004年第4期2卷 164-169页

作者： Hudson, Thomas C. Stapleton, Ann E. Brown, Jeffrey L. Department of Computer Science Univ. of N. Carolina at Wilmington Wilmington NC 28403 601 South College Rd United States Department of Biological Sciences Univ. of N. Carolina at Wilmington Wilmington NC 28403 601 South College Rd United States Dept. of Mathematics and Statistics Univ. of N. Carolina at Wilmington Wilmington NC 28403 601 South College Rd United States

Bioinformatics is bimodal, with results gathered either from rigid pipelines, their functions encoded in programs accessible only to specialists, or from ad hoc collections of scripts or web pages, used once, then lost track of or thrown away. We discuss the possibility of developing tools to straddle this divide, in particular, tools using graphical dataflow programming, which have the potential to make bioinformatics flexible, approachable and repeatable.

关键词： Bioinformatics bioinformatics dataflow programming Drug Discovery sequence analysis Techniques & Methods

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OPTIMIZATION OF PORTABLE PARALLEL SIGNAL PROCESSING APPLICATIONS BY DESIGN SPACE EXPLORATION OF dataflow PROGRAMS

OPTIMIZATION OF PORTABLE PARALLEL SIGNAL PROCESSING APPLICAT...

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IEEE Workshop on Signal Processing Systems (SiPS)

作者： Lucarz, Christophe Mattavelli, Marco Janneck, Jorn W. Ecole Polytech Fed Lausanne CH-1015 Lausanne Switzerland Lund Inst Technol Lund Sweden

ISBN: (纸本)9781457719219

This paper describes a methodology for the optimization of portable parallel signal processing applications specified by dataflow programs. The use of dataflow as a programming model for signal processing applications targeting parallel platforms provides an important advantage versus the traditional sequential programming paradigm: the portability of parallelism. The paper introduce a design space exploration methodology for exploring alternative implementations in which abstract traces of a program, representing the actual data dependencies of its parts, are first constructed and then analyzed to guide the refactoring and mapping and of the signal processing applications to best match its intended parallel target. The methodology is demonstrated and evaluated in an at-size case study of an MPEG-4 video decoder.

关键词： dataflow programming design space exploration software synthesis multicore systems

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SCHEDULING OF DYNAMIC dataflow PROGRAMS BASED ON STATE SPACE ANALYSIS

SCHEDULING OF DYNAMIC DATAFLOW PROGRAMS BASED ON STATE SPACE...

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IEEE International Conference on Acoustics, Speech and Signal Processing

作者： Ersfolk, Johan Roquier, Ghislain Lilius, Johan Mattavelli, Marco Abo Akad Univ Turku Finland Ecole Polytech Fed Lausanne Lausanne Switzerland Turku Ctr Comp Sci Turku Finland

ISBN: (纸本)9781467300469

Compile-time scheduling of dynamic dataflow programs is still an open problem. This paper presents how scheduling of dynamic portions of asynchronous dataflow networks described using CAL language can be determined before execution by the analysis of the state space of network partitions. Experiments show that the number of run-time operations employed by dynamic schedulers is largely reduced when the schedules extracted by the state analysis are employed.

关键词： dataflow programming model checking MPEG-4 decoder

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ITKBoard: A visual dataflow language for biomedical image processing

ITKBoard: A visual dataflow language for biomedical image pr...

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2nd International Conference on Software and Data Technologies

作者： Le, Hoang D. K. Li, Rongxin Ourselin, Sebastien Potter, John M. BioMedIA Autonomous Systems Laboratory Australia Programming Languages and Compilers Group School of Computer Science and Engineering University of New South Wales Sydney Australia

ISBN: (纸本)9789898111050

Experimenters in biomedical image processing rely on software libraries to provide a large number of standard filtering and image handling algorithms. The Insight Toolkit (ITK) is an open-source library that provides a complete framework for a range of image processing tasks, and is specifically aimed at segmentation and registration tasks for both two and three dimensional images. This paper describes a visual dataflow language, ITKBoard, designed to simplify building, and more significantly, experimenting with ITK applications. The ease with which image processing experiments can be interactively modified and controlled is an important aspect of the design. The experimenter can focus on the image processing task at hand, rather than worry about the underlying software. ITKBoard incorporates composite and parameterised components, and control constructs, and relies on a novel hybrid dataflow model, combining aspects of both demand and data-driven execution.

关键词： dataflow programming visual programming languages image processing software ITK ITKBoard

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The Affinity Platform: Service-Oriented Architecture Based on Abstraction of Connection 20

The Affinity Platform: Service-Oriented Architecture Based o...

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ACM International Joint Conference on Pervasive and Ubiquitous Computing (UbiComp) / ACM International Symposium on Wearable Computers (ISWC)

作者： Ardelean, Alexandru Benta, Kuderna-Iulian IT Univ Copenhagen Copenhagen Denmark Babes Bolyai Univ Cluj Napoca Romania

ISBN: (纸本)9781450380768

The Affinity Platform is an innovative Software as a Service orchestration system designed for building Service-Oriented software solutions. It challenges the modularity of regular software frameworks and microservice architectures by abstracting the connectivity layer between two services. The main benefit of utilizing this approach is that components designed to communicate through a specific interface can be easily routed to handle this communication over a different medium. A service could extract health data from a smartwatch, use Bluetooth connectivity to send it to a smartphone for pre-processing, and the result can then be transmitted over HTTP to a server for centralization (Figure 1). All this would be possible without requiring services to agree on a specific communication protocol or data format. The capabilities of the platform were enhanced to assist the development of a multi-modal solution for monitoring patients in a constantly changing environment.

关键词： Service-Oriented Architecture dataflow programming Software Platform Language Agnostic Visual Development Platform Automatic programming

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Sampling, Splitting and Merging in Coinductive Stream Calculus

Sampling, Splitting and Merging in Coinductive Stream Calcul...

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10th International Conference on Mathematics of Program Construction

作者： Niqui, Milad Rutten, Jan Centrum Wiskunde and Informatica (CWI) Netherlands Radboud University Nijmegen Netherlands

ISBN: (纸本)9783642133206

We study various operations for partitioning, projecting and merging streams of data. These operations are motivated by their use in dataflow programming and the stream processing languages. We use the framework of stream calculus and stream circuits for defining and proving properties of such operations using behavioural differential equations and coinduction proof principles. We study the invariance of certain well patterned classes of streams, namely rational and algebraic streams, under splitting and merging. Finally we show that stream circuits extended with gates for dyadic split and merge are expressive enough to realise sonic non-rational algebraic streams, thereby going beyond ordinary stream circuits.

关键词： stream calculus dataflow programming coinduction rational stream algebraic stream stream circuit

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Calling Cards: Concrete Visual End-User programming 22

Calling Cards: Concrete Visual End-User Programming

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6th International Conference on the Art, Science, and Engineering of programming (programming)

作者： Homer, Michael Victoria Univ Wellington Sch Engn & Comp Sci Wellington New Zealand

ISBN: (纸本)9781450396561

Creating a program that performs even a simple task and shows the result is unapproachable to most people, and even trained programmers face a burden to create a new program. In this paper, we introduce a prototype system and model for live visual dataflow programming where intermediate steps are visible and all components are tangible and manifest. Our system aims to allow a user to dive in and immediately have a working program that can be incrementally extended.

关键词： end-user programming exploratory programming visual programming dataflow programming

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METHODOLOGY FOR THE HARDWARE/SOFTWARE CO-DESIGN OF dataflow PROGRAMS

METHODOLOGY FOR THE HARDWARE/SOFTWARE CO-DESIGN OF DATAFLOW ...

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IEEE Workshop on Signal Processing Systems (SiPS)

作者： Roquier, Ghislain Thavot, Richard Mattavelli, Marco Ecole Polytech Fed Lausanne CH-1015 Lausanne Switzerland

ISBN: (纸本)9781457719219

New generations of multi-core processors and reconfigurable hardware platforms are expected to provide a dramatic increase of processing capabilities. However, one obstacle for exploiting all the promises of such new platforms is the legacy of current applications and the development methodologies used, which is deeply rooted in a sequential way of thinking. A paradigm shift is necessary at all levels of application development to yield portable and efficient implementations, capable of exploiting the full potential of such platforms. dataflow programming is an alternative approach that address the problem of providing portable and scalable parallel applications. dataflow programming is able to explicitly expose the intrinsic parallelism of applications. This paper presents a hardware/software co-design methodology that starting from a unique dataflow program enables, by the direct synthesis of both hardware (HDL) and software components (C/C++), to map a signal processing application onto heterogeneous systems architectures composed by reconfigurable hardware and multi-core processors. Experimental results based on the implementation of the MPEG-4 Simple Profile decoder onto an heterogeneous platform are also provided to show the capabilities and flexibility of the approach.

关键词： dataflow programming hardware/software co-design reconfigurable hardware multi-core processor

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Virtual Systolic Array for QR Decomposition

Virtual Systolic Array for QR Decomposition

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IEEE 27th International Parallel and Distributed Processing Symposium (IPDPS)

作者： Kurzak, Jakub Luszczek, Piotr Gates, Mark Yamazaki, Ichitaro Dongarra, Jack Univ Tennessee Knoxville TN 37996 USA Univ Manchester Manchester M13 9PL Lancs England Oak Ridge Natl Lab Oak Ridge TN 37831 USA Univ Tennessee Knoxville TN 37996 USA

ISBN: (纸本)9780769549712

Systolic arrays offer a very attractive, data-centric, execution model as an alternative to the von Neumann architecture. Hardware implementations of systolic arrays turned out not to be viable solutions in the past. This article shows how the systolic design principles can be applied to a software solution to deliver an algorithm with unprecedented strong scaling capabilities. Systolic array for the QR decomposition is developed and a virtualization layer is used for mapping of the algorithm to a large distributed memory system. Strong scaling properties are discovered, superior to existing solutions.

关键词： systolic array QR decomposition multi-core message passing dataflow programming roofline model

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Parsl+CWL: Towards Combining the Python and CWL Ecosystems

Parsl+CWL: Towards Combining the Python and CWL Ecosystems

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2024 Workshops of the International Conference for High Performance Computing, Networking, Storage and Analysis, SC Workshops 2024

作者： Karle, Nishchay Clifford, Ben Babuji, Yadu Chard, Ryan Katz, Daniel S. Chard, Kyle University of Chicago Department of Computer Science Chicago United States Argonne National Laboratory Lemont United States University of Illinois Urbana-Champaign NCSA & CS & iSchool UrbanaIL United States

ISBN: (纸本)9798350355543

The Common Workflow Language (CWL) is a widely adopted language for defining and sharing computational workflows. It is designed to be independent of the execution engine on which workflows are executed. In this paper, we describe our experiences integrating CWL with Parsl, a Python-based parallel programming library designed to manage execution of workflows across diverse computing environments. We propose a new method that converts CWL CommandLineTool definitions into Parsl apps, enabling Parsl scripts to easily import and use tools represented in CWL. We describe a Parsl runner that is capable of executing a CWL CommandLineTool directly. We also describe a proof-of-concept extension to support inline Python in a CWL workflow definition, enabling seamless use in Parsl's Python ecosystem. We demonstrate the benefits of this integration by presenting example CWL CommandLineTool definitions that show how they can be used in Parsl, and comparing performance of executing an image processing workflow using the Parsl integration and other CWL runners. © 2024 IEEE.

关键词： commandlinetool common workflow language common workflow language (cwl) computational reproducibility cross-platform execution cwl dataflow programming dynamic workflows high performance computing (hpc) inline expressions parallel computing parsl python programming resource management scalability scientific workflows workflow workflow automation workflow ecosystem workflow execution workflow integration workflow management systems workflow portability

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