WorldWideScience

Sample records for automatic workflow composition

  1. Magallanes: a web services discovery and automatic workflow composition tool

    Directory of Open Access Journals (Sweden)

    Trelles Oswaldo

    2009-10-01

    Full Text Available Abstract Background To aid in bioinformatics data processing and analysis, an increasing number of web-based applications are being deployed. Although this is a positive circumstance in general, the proliferation of tools makes it difficult to find the right tool, or more importantly, the right set of tools that can work together to solve real complex problems. Results Magallanes (Magellan is a versatile, platform-independent Java library of algorithms aimed at discovering bioinformatics web services and associated data types. A second important feature of Magallanes is its ability to connect available and compatible web services into workflows that can process data sequentially to reach a desired output given a particular input. Magallanes' capabilities can be exploited both as an API or directly accessed through a graphic user interface. The Magallanes' API is freely available for academic use, and together with Magallanes application has been tested in MS-Windows™ XP and Unix-like operating systems. Detailed implementation information, including user manuals and tutorials, is available at http://www.bitlab-es.com/magallanes. Conclusion Different implementations of the same client (web page, desktop applications, web services, etc. have been deployed and are currently in use in real installations such as the National Institute of Bioinformatics (Spain and the ACGT-EU project. This shows the potential utility and versatility of the software library, including the integration of novel tools in the domain and with strong evidences in the line of facilitate the automatic discovering and composition of workflows.

  2. Provenance-Powered Automatic Workflow Generation and Composition

    Science.gov (United States)

    Zhang, J.; Lee, S.; Pan, L.; Lee, T. J.

    2015-12-01

    In recent years, scientists have learned how to codify tools into reusable software modules that can be chained into multi-step executable workflows. Existing scientific workflow tools, created by computer scientists, require domain scientists to meticulously design their multi-step experiments before analyzing data. However, this is oftentimes contradictory to a domain scientist's daily routine of conducting research and exploration. We hope to resolve this dispute. Imagine this: An Earth scientist starts her day applying NASA Jet Propulsion Laboratory (JPL) published climate data processing algorithms over ARGO deep ocean temperature and AMSRE sea surface temperature datasets. Throughout the day, she tunes the algorithm parameters to study various aspects of the data. Suddenly, she notices some interesting results. She then turns to a computer scientist and asks, "can you reproduce my results?" By tracking and reverse engineering her activities, the computer scientist creates a workflow. The Earth scientist can now rerun the workflow to validate her findings, modify the workflow to discover further variations, or publish the workflow to share the knowledge. In this way, we aim to revolutionize computer-supported Earth science. We have developed a prototyping system to realize the aforementioned vision, in the context of service-oriented science. We have studied how Earth scientists conduct service-oriented data analytics research in their daily work, developed a provenance model to record their activities, and developed a technology to automatically generate workflow starting from user behavior and adaptability and reuse of these workflows for replicating/improving scientific studies. A data-centric repository infrastructure is established to catch richer provenance to further facilitate collaboration in the science community. We have also established a Petri nets-based verification instrument for provenance-based automatic workflow generation and recommendation.

  3. Context-aware Workflow Model for Supporting Composite Workflows

    Institute of Scientific and Technical Information of China (English)

    Jong-sun CHOI; Jae-young CHOI; Yong-yun CHO

    2010-01-01

    -In recent years,several researchers have applied workflow technologies for service automation on ubiquitous computing environments.However,most context-aware oprkflows do not offer a method to compose several workflows in order to get more large-scale or complicated workflow.They only provide a simple workflow model,not a composite workflow model.In this paper,the autorhs propose a context-aware worrkflow model to support composite workflows by expanding the patterns of the existing context-aware workflows,which support the basic workflow patterns.The suggested worklow modei offers composite workflow patterns for a context-aware workflow,which consists of various flow patterns,such as simple,split,parallel flows,and subflow.With the suggested model,the model can easily reuse few of existing workflows to make a new workflow.As a result,it can save the development efforts and time of cantext-aware workflows and increase the workflow reusability.Therefore,the suggested model is expected to make it easy to develop applications related to context-aware workflow services on ubiquitous computing environments.

  4. NGS-Trex: an automatic analysis workflow for RNA-Seq data.

    Science.gov (United States)

    Boria, Ilenia; Boatti, Lara; Saggese, Igor; Mignone, Flavio

    2015-01-01

    RNA-Seq technology allows the rapid analysis of whole transcriptomes taking advantage of next-generation sequencing platforms. Moreover with the constant decrease of the cost of NGS analysis RNA-Seq is becoming very popular and widespread. Unfortunately data analysis is quite demanding in terms of bioinformatic skills and infrastructures required, thus limiting the potential users of this method. Here we describe the complete analysis of sample data from raw sequences to data mining of results by using NGS-Trex platform, a low user interaction, fully automatic analysis workflow. Used through a web interface, NGS-Trex processes data and profiles the transcriptome of the samples identifying expressed genes, transcripts, and new and known splice variants. It also detects differentially expressed genes and transcripts across different experiments.

  5. Semantics and planning based workflow composition and execution for video processing

    OpenAIRE

    Nadarajan, Gayathri

    2011-01-01

    Traditional workflow systems have several drawbacks, e.g. in their inabilities to rapidly react to changes, to construct workflow automatically (or with user involvement) and to improve performance autonomously (or with user involvement) in an incremental manner according to specified goals. Overcoming these limitations would be highly beneficial for complex domains where such adversities are exhibited. Video processing is one such domain that increasingly requires attention as...

  6. Three layered framework for automatic service composition

    Science.gov (United States)

    Liu, Xinqiong; Xia, Ping; Wan, Junli

    2009-10-01

    For automatic service composition, a planning based framework MOCIS is proposed. Planning is based on two major techniques, service reasoning and constraint satisfaction. Constraint satisfaction can be divided into quality constraint satisfaction and quantity constraint satisfaction. Contrary to traditional methods realizing upon techniques by interleaving activity, message and provider, the novelty of the framework is dividing these concerns into three layers, with activity layer majoring service reasoning, message layer for quality constraint and provider layer for quantity constraint. The layered architecture makes automatic web service composition possible for activity tree that abstract BPEL list and concrete BPEL list are achieved automatically with each layer, and users can selection proper abstract BPEL or BPEL to satisfy their request. And E-traveling composition cases have been tested, demonstrating that complex service can be achieved through three layers compositing automatically.

  7. Evaluation of an image-based tracking workflow with Kalman filtering for automatic image plane alignment in interventional MRI.

    Science.gov (United States)

    Neumann, M; Cuvillon, L; Breton, E; de Matheli, M

    2013-01-01

    Recently, a workflow for magnetic resonance (MR) image plane alignment based on tracking in real-time MR images was introduced. The workflow is based on a tracking device composed of 2 resonant micro-coils and a passive marker, and allows for tracking of the passive marker in clinical real-time images and automatic (re-)initialization using the microcoils. As the Kalman filter has proven its benefit as an estimator and predictor, it is well suited for use in tracking applications. In this paper, a Kalman filter is integrated in the previously developed workflow in order to predict position and orientation of the tracking device. Measurement noise covariances of the Kalman filter are dynamically changed in order to take into account that, according to the image plane orientation, only a subset of the 3D pose components is available. The improved tracking performance of the Kalman extended workflow could be quantified in simulation results. Also, a first experiment in the MRI scanner was performed but without quantitative results yet.

  8. An automatic protocol composition checker

    OpenAIRE

    Kojovic, Ivana

    2012-01-01

    Formal analysis is widely used to prove security properties of the protocols. There are tools to check protocols in isolation, but in fact we use many protocols in parallel or even vertically stacked, e.g. running an application protocol (like login) over a secure channel (like TLS) and in general it is unclear if that is safe. There are several works that give sufficient conditions for parallel and vertical composition, but there exists no program to check whether these conditions are actual...

  9. Automatic analysis (aa): efficient neuroimaging workflows and parallel processing using Matlab and XML

    OpenAIRE

    Rhodri Cusack; Alejandro Vicente-Grabovetsky; Daniel J Mitchell; Peelle, Jonathan E.

    2015-01-01

    Recent years have seen neuroimaging data sets becoming richer, with larger cohorts of participants, a greater variety of acquisition techniques, and increasingly complex analyses. These advances have made data analysis pipelines complicated to set up and run (increasing the risk of human error) and time consuming to execute (restricting what analyses are attempted). Here we present an open-source framework, automatic analysis (aa), to address these concerns. Human efficiency is increased by m...

  10. Workflow-centred evaluation of an automatic lesion tracking software for chemotherapy monitoring by CT

    International Nuclear Information System (INIS)

    In chemotherapy monitoring, an estimation of the change in tumour size is an important criterion for the assessment of treatment success. This requires a comparison between corresponding lesions in the baseline and follow-up computed tomography (CT) examinations. We evaluate the clinical benefits of an automatic lesion tracking tool that identifies the target lesions in the follow-up CT study and pre-computes the lesion volumes. Four radiologists performed volumetric follow-up examinations for 52 patients with and without lesion tracking. In total, 139 lung nodules, liver metastases and lymph nodes were given as target lesions. We measured reading time, inter-reader variability in lesion identification and volume measurements, and the amount of manual adjustments of the segmentation results. With lesion tracking, target lesion assessment time decreased by 38 % or 22 s per lesion. Relative volume difference between readers was reduced from 0.171 to 0.1. Segmentation quality was comparable with and without lesion tracking. Our automatic lesion tracking tool can make interpretation of follow-up CT examinations quicker and provide results that are less reader-dependent. (orig.)

  11. Characterizing chaotic melodies in automatic music composition.

    Science.gov (United States)

    Coca, Andrés E; Tost, Gerard O; Zhao, Liang

    2010-09-01

    In this paper, we initially present an algorithm for automatic composition of melodies using chaotic dynamical systems. Afterward, we characterize chaotic music in a comprehensive way as comprising three perspectives: musical discrimination, dynamical influence on musical features, and musical perception. With respect to the first perspective, the coherence between generated chaotic melodies (continuous as well as discrete chaotic melodies) and a set of classical reference melodies is characterized by statistical descriptors and melodic measures. The significant differences among the three types of melodies are determined by discriminant analysis. Regarding the second perspective, the influence of dynamical features of chaotic attractors, e.g., Lyapunov exponent, Hurst coefficient, and correlation dimension, on melodic features is determined by canonical correlation analysis. The last perspective is related to perception of originality, complexity, and degree of melodiousness (Euler's gradus suavitatis) of chaotic and classical melodies by nonparametric statistical tests.

  12. Characterizing chaotic melodies in automatic music composition

    Science.gov (United States)

    Coca, Andrés E.; Tost, Gerard O.; Zhao, Liang

    2010-09-01

    In this paper, we initially present an algorithm for automatic composition of melodies using chaotic dynamical systems. Afterward, we characterize chaotic music in a comprehensive way as comprising three perspectives: musical discrimination, dynamical influence on musical features, and musical perception. With respect to the first perspective, the coherence between generated chaotic melodies (continuous as well as discrete chaotic melodies) and a set of classical reference melodies is characterized by statistical descriptors and melodic measures. The significant differences among the three types of melodies are determined by discriminant analysis. Regarding the second perspective, the influence of dynamical features of chaotic attractors, e.g., Lyapunov exponent, Hurst coefficient, and correlation dimension, on melodic features is determined by canonical correlation analysis. The last perspective is related to perception of originality, complexity, and degree of melodiousness (Euler's gradus suavitatis) of chaotic and classical melodies by nonparametric statistical tests.

  13. Automatic analysis (aa): efficient neuroimaging workflows and parallel processing using Matlab and XML.

    Science.gov (United States)

    Cusack, Rhodri; Vicente-Grabovetsky, Alejandro; Mitchell, Daniel J; Wild, Conor J; Auer, Tibor; Linke, Annika C; Peelle, Jonathan E

    2014-01-01

    Recent years have seen neuroimaging data sets becoming richer, with larger cohorts of participants, a greater variety of acquisition techniques, and increasingly complex analyses. These advances have made data analysis pipelines complicated to set up and run (increasing the risk of human error) and time consuming to execute (restricting what analyses are attempted). Here we present an open-source framework, automatic analysis (aa), to address these concerns. Human efficiency is increased by making code modular and reusable, and managing its execution with a processing engine that tracks what has been completed and what needs to be (re)done. Analysis is accelerated by optional parallel processing of independent tasks on cluster or cloud computing resources. A pipeline comprises a series of modules that each perform a specific task. The processing engine keeps track of the data, calculating a map of upstream and downstream dependencies for each module. Existing modules are available for many analysis tasks, such as SPM-based fMRI preprocessing, individual and group level statistics, voxel-based morphometry, tractography, and multi-voxel pattern analyses (MVPA). However, aa also allows for full customization, and encourages efficient management of code: new modules may be written with only a small code overhead. aa has been used by more than 50 researchers in hundreds of neuroimaging studies comprising thousands of subjects. It has been found to be robust, fast, and efficient, for simple-single subject studies up to multimodal pipelines on hundreds of subjects. It is attractive to both novice and experienced users. aa can reduce the amount of time neuroimaging laboratories spend performing analyses and reduce errors, expanding the range of scientific questions it is practical to address.

  14. Automatic analysis (aa: efficient neuroimaging workflows and parallel processing using Matlab and XML

    Directory of Open Access Journals (Sweden)

    Rhodri eCusack

    2015-01-01

    Full Text Available Recent years have seen neuroimaging data becoming richer, with larger cohorts of participants, a greater variety of acquisition techniques, and increasingly complex analyses. These advances have made data analysis pipelines complex to set up and run (increasing the risk of human error and time consuming to execute (restricting what analyses are attempted. Here we present an open-source framework, automatic analysis (aa, to address these concerns. Human efficiency is increased by making code modular and reusable, and managing its execution with a processing engine that tracks what has been completed and what needs to be (redone. Analysis is accelerated by optional parallel processing of independent tasks on cluster or cloud computing resources. A pipeline comprises a series of modules that each perform a specific task. The processing engine keeps track of the data, calculating a map of upstream and downstream dependencies for each module. Existing modules are available for many analysis tasks, such as SPM-based fMRI preprocessing, individual and group level statistics, voxel-based morphometry, tractography, and multi-voxel pattern analyses (MVPA. However, aa also allows for full customization, and encourages efficient management of code: new modules may be written with only a small code overhead. aa has been used by more than 50 researchers in hundreds of neuroimaging studies comprising thousands of subjects. It has been found to be robust, fast and efficient, for simple single subject studies up to multimodal pipelines on hundreds of subjects. It is attractive to both novice and experienced users. aa can reduce the amount of time neuroimaging laboratories spend performing analyses and reduce errors, expanding the range of scientific questions it is practical to address.

  15. Assessing the Performance of Automatic Speech Recognition Systems When Used by Native and Non-Native Speakers of Three Major Languages in Dictation Workflows

    DEFF Research Database (Denmark)

    Zapata, Julián; Kirkedal, Andreas Søeborg

    2015-01-01

    In this paper, we report on a two-part experiment aiming to assess and compare the performance of two types of automatic speech recognition (ASR) systems on two different computational platforms when used to augment dictation workflows. The experiment was performed with a sample of speakers...... of three major languages and with different linguistic profiles: non-native English speakers; non-native French speakers; and native Spanish speakers. The main objective of this experiment is to examine ASR performance in translation dictation (TD) and medical dictation (MD) workflows without manual...... transcription vs. with transcription. We discuss the advantages and drawbacks of a particular ASR approach in different computational platforms when used by various speakers of a given language, who may have different accents and levels of proficiency in that language, and who may have different levels...

  16. QoS measurement of workflow-based web service compositions using Colored Petri net.

    Science.gov (United States)

    Nematzadeh, Hossein; Motameni, Homayun; Mohamad, Radziah; Nematzadeh, Zahra

    2014-01-01

    Workflow-based web service compositions (WB-WSCs) is one of the main composition categories in service oriented architecture (SOA). Eflow, polymorphic process model (PPM), and business process execution language (BPEL) are the main techniques of the category of WB-WSCs. Due to maturity of web services, measuring the quality of composite web services being developed by different techniques becomes one of the most important challenges in today's web environments. Business should try to provide good quality regarding the customers' requirements to a composed web service. Thus, quality of service (QoS) which refers to nonfunctional parameters is important to be measured since the quality degree of a certain web service composition could be achieved. This paper tried to find a deterministic analytical method for dependability and performance measurement using Colored Petri net (CPN) with explicit routing constructs and application of theory of probability. A computer tool called WSET was also developed for modeling and supporting QoS measurement through simulation. PMID:25110748

  17. QoS Measurement of Workflow-Based Web Service Compositions Using Colored Petri Net

    Directory of Open Access Journals (Sweden)

    Hossein Nematzadeh

    2014-01-01

    Full Text Available Workflow-based web service compositions (WB-WSCs is one of the main composition categories in service oriented architecture (SOA. Eflow, polymorphic process model (PPM, and business process execution language (BPEL are the main techniques of the category of WB-WSCs. Due to maturity of web services, measuring the quality of composite web services being developed by different techniques becomes one of the most important challenges in today’s web environments. Business should try to provide good quality regarding the customers’ requirements to a composed web service. Thus, quality of service (QoS which refers to nonfunctional parameters is important to be measured since the quality degree of a certain web service composition could be achieved. This paper tried to find a deterministic analytical method for dependability and performance measurement using Colored Petri net (CPN with explicit routing constructs and application of theory of probability. A computer tool called WSET was also developed for modeling and supporting QoS measurement through simulation.

  18. QoS Measurement of Workflow-Based Web Service Compositions Using Colored Petri Net

    Science.gov (United States)

    Nematzadeh, Hossein; Motameni, Homayun; Nematzadeh, Zahra

    2014-01-01

    Workflow-based web service compositions (WB-WSCs) is one of the main composition categories in service oriented architecture (SOA). Eflow, polymorphic process model (PPM), and business process execution language (BPEL) are the main techniques of the category of WB-WSCs. Due to maturity of web services, measuring the quality of composite web services being developed by different techniques becomes one of the most important challenges in today's web environments. Business should try to provide good quality regarding the customers' requirements to a composed web service. Thus, quality of service (QoS) which refers to nonfunctional parameters is important to be measured since the quality degree of a certain web service composition could be achieved. This paper tried to find a deterministic analytical method for dependability and performance measurement using Colored Petri net (CPN) with explicit routing constructs and application of theory of probability. A computer tool called WSET was also developed for modeling and supporting QoS measurement through simulation. PMID:25110748

  19. Automatic page composition with combined image crop and layout metrics

    Science.gov (United States)

    Hunter, Andrew; Greig, Darryl

    2012-03-01

    Automatic layout algorithms simplify the composition of image-rich documents, but they still require users to have sufficient artistry to supply well cropped and composed imagery. Combining an automatic cropping technology with a document layout system enables better results to be produced faster by less-skilled users. This paper reviews prior work in automatic image cropping and automatic page layout and presents a case for a combined crop and layout technology. We describe one such technology in a system for interactive publication design by amateur self-publishers and show that providing an automatic cropping system with additional information about the layout context can enable it to generate a more appropriate set of ranked crop options for a given image. Furthermore, we show that providing an automatic layout system with sets of ranked crop options for images can enable it to compose more appropriate page layouts.

  20. An Approach to Design Reusable Workflow Engine

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    Developers still need design workflow system according to users' specific needs, though workflow management coalition standardized the five kinds of abstract interfaces in workflow reference model. Specific business process characteristics are still supported by specific workflow system. A set of common functionalities of workflow engine are abstracted from business component, so the reusability of business component is extended into workflow engine and composition method is proposed. Needs of different business requirements and characteristics are met by reusing the workflow engine.

  1. Managing and Documenting Legacy Scientific Workflows.

    Science.gov (United States)

    Acuña, Ruben; Chomilier, Jacques; Lacroix, Zoé

    2015-01-01

    Scientific legacy workflows are often developed over many years, poorly documented and implemented with scripting languages. In the context of our cross-disciplinary projects we face the problem of maintaining such scientific workflows. This paper presents the Workflow Instrumentation for Structure Extraction (WISE) method used to process several ad-hoc legacy workflows written in Python and automatically produce their workflow structural skeleton. Unlike many existing methods, WISE does not assume input workflows to be preprocessed in a known workflow formalism. It is also able to identify and analyze calls to external tools. We present the method and report its results on several scientific workflows. PMID:26673793

  2. Managing and Documenting Legacy Scientific Workflows.

    Science.gov (United States)

    Acuña, Ruben; Chomilier, Jacques; Lacroix, Zoé

    2015-10-06

    Scientific legacy workflows are often developed over many years, poorly documented and implemented with scripting languages. In the context of our cross-disciplinary projects we face the problem of maintaining such scientific workflows. This paper presents the Workflow Instrumentation for Structure Extraction (WISE) method used to process several ad-hoc legacy workflows written in Python and automatically produce their workflow structural skeleton. Unlike many existing methods, WISE does not assume input workflows to be preprocessed in a known workflow formalism. It is also able to identify and analyze calls to external tools. We present the method and report its results on several scientific workflows.

  3. Automatic Music Composition using Answer Set Programming

    CERN Document Server

    Boenn, Georg; De Vos, Marina; ffitch, John

    2010-01-01

    Music composition used to be a pen and paper activity. These these days music is often composed with the aid of computer software, even to the point where the computer compose parts of the score autonomously. The composition of most styles of music is governed by rules. We show that by approaching the automation, analysis and verification of composition as a knowledge representation task and formalising these rules in a suitable logical language, powerful and expressive intelligent composition tools can be easily built. This application paper describes the use of answer set programming to construct an automated system, named ANTON, that can compose melodic, harmonic and rhythmic music, diagnose errors in human compositions and serve as a computer-aided composition tool. The combination of harmonic, rhythmic and melodic composition in a single framework makes ANTON unique in the growing area of algorithmic composition. With near real-time composition, ANTON reaches the point where it can not only be used as a ...

  4. Structured Composition of Dataflow and Control-Flow for Reusable and Robust Scientific Workflows

    Energy Technology Data Exchange (ETDEWEB)

    Bowers, S; Ludaescher, B; Ngu, A; Critchlow, T

    2005-09-07

    Data-centric scientific workflows are often modeled as dataflow process networks. The simplicity of the dataflow framework facilitates workflow design, analysis, and optimization. However, some workflow tasks are particularly ''control-flow intensive'', e.g., procedures to make workflows more fault-tolerant and adaptive in an unreliable, distributed computing environment. Modeling complex control-flow directly within a dataflow framework often leads to overly complicated workflows that are hard to comprehend, reuse, schedule, and maintain. In this paper, we develop a framework that allows a structured embedding of control-flow intensive subtasks within dataflow process networks. In this way, we can seamlessly handle complex control-flows without sacrificing the benefits of dataflow. We build upon a flexible actor-oriented modeling and design approach and extend it with (actor) frames and (workflow) templates. A frame is a placeholder for an (existing or planned) collection of components with similar function and signature. A template partially specifies the behavior of a subworkflow by leaving ''holes'' (i.e., frames) in the subworkflow definition. Taken together, these abstraction mechanisms facilitate the separation and structured re-combination of control-flow and dataflow in scientific workflow applications. We illustrate our approach with a real-world scientific workflow from the astrophysics domain. This data-intensive workflow requires remote execution and file transfer in a semi-reliable environment. For such work-flows, we propose a 3-layered architecture: The top-level, typically a dataflow process network, includes Generic Data Transfer (GDT) frames and Generic remote eXecution (GX) frames. At the second level, the user can specialize the behavior of these generic components by embedding a suitable template (here: transducer templates for control-flow intensive tasks). At the third level, frames inside the

  5. Concentrate composition for Automatic Milking Systems - Effect on milking frequency

    DEFF Research Database (Denmark)

    Madsen, J; Weisbjerg, Martin Riis; Hvelplund, Torben

    2010-01-01

    The purpose of this study was to investigate the potential of affecting milking frequency in an Automatic Milking System (AMS) by changing ingredient composition of the concentrate fed in the AMS. In six experiments, six experimental concentrates were tested against a Standard concentrate all...... the Standard concentrate. A marked effect was found on the number of visits of the cows in the AMS and the subsequent milk production in relation to composition of the concentrate. The composition of the concentrates also influenced the composition of the milk and the MR intake. Based on the overall responses...

  6. Distributed Behavioural Adaptation for the Automatic Composition of Semantic Services

    OpenAIRE

    Melliti, Tarek; Poizat, Pascal; Ben Mokhtar, Sonia

    2008-01-01

    International audience Services are developed separately and without knowledge of all possible use contexts. They often mismatch or do not correspond exactly to the end-user needs, making direct composition without mediation impossible. In such a case, software adaptation can support composition by producing semi-automatically new software pieces called adaptors. Adaptation proposals have addressed the signature and behavioural service interface levels. Yet, taking also into account the se...

  7. QoS-Aware Automatic Service Composition: A Graph View

    Institute of Scientific and Technical Information of China (English)

    Wei Jiang; Tian Wu; Song-Lin Hu; Zhi-Yong Liu

    2011-01-01

    In the research of service composition,it demands efficient algorithms that not only retrieve correct service compositions automatically from thousands of services but also satisfy the quality requirements of different service users.However,most approaches treat these two aspects as two separate problems,automatic service composition and service selection.Although the latest researches realize the restriction of this separate view and some specific methods are proposed,they still suffer from serious limitations in scalability and accuracy when addressing both requirements simultaneously.In order to cope with these limitations and efficiently solve the combined problem which is known as QoS-aware or QoS-driven automatic service composition problem,we propose a new graph search problem,single-source optimal directed acyclic graphs (DAGs),for the first time.This novel single-source optimal DAGs (SSOD) problem is similar to,but more general than the classical single-source shortest paths (SSSP) problem.In this paper,a new graph model of SSOD problem is proposed and a Sim-Dijkstra algorithm is presented to address the SSOD problem with the time complexity of O(n log n +m) (n and m are the number of nodes and edges in the graph respectively),and the proofs of its soundness.It is also directly applied to solve the QoS-aware automatic service composition problem,and a service composition tool named QSynth is implemented.Evaluations show that Sim-Dijkstra algorithm achieves superior scalability and efficiency with respect to a large variety of composition scenarios,even more efficient than our worklist algorithm that won the performance championship of Web Services Challenge 2009.

  8. Using UML to Model Web Services for Automatic Composition

    Directory of Open Access Journals (Sweden)

    Amal Elgammal

    2010-07-01

    Full Text Available There is a great interest paid to the web services paradigm nowadays. One of the most important problems related to the web service paradigm is the automatic composition of web services. Several frameworks have been proposed to achieve this novel goal. The most recent and richest framework (model is the Colombo model. However, even for experienced developers, working with Colombo formalisms is low-level, very complex and timeconsuming. We propose to use UML (Unified Modeling Language to model services and service composition in Colombo. By using UML, the web service developer will deal with the high level graphical models of UML avoiding the difficulties of working with the low-level and complex details of Colombo. To be able to use Colombo automatic composition algorithm, we propose to represent Colombo by a set of related XML document types that can be a base for a Colombo language. Moreover, we propose the transformation rules between UML and Colombo proposed XML documents. Next Colombo automatic composition algorithm can be applied to build a composite service that satisfies a given user request. A prototypical implementation of the proposed approach is developed using Visual Paradigm for UML.

  9. A prototype of workflow management system for construction design projects

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    A great deal of benefits can be achieved if information and process are integrated within the building design project. This paper aims to establish a prototype of workflow management system for construction design project through the application of workflow technology. The composition and function of prototype is presented to satisfy the needs of information share and process integration. By integrating all subsystems and modules of the prototype, the whole system can deal with design information-flow modeling, emulating and optimizing, task planning and distributing, automatic tracking and monitoring, as well as network service, etc. In this way, the collaborative design environment of building design project is brought into being.

  10. Automatic Discovery of Non-Compositional Compounds in Parallel Data

    CERN Document Server

    Melamed, I D

    1997-01-01

    Automatic segmentation of text into minimal content-bearing units is an unsolved problem even for languages like English. Spaces between words offer an easy first approximation, but this approximation is not good enough for machine translation (MT), where many word sequences are not translated word-for-word. This paper presents an efficient automatic method for discovering sequences of words that are translated as a unit. The method proceeds by comparing pairs of statistical translation models induced from parallel texts in two languages. It can discover hundreds of non-compositional compounds on each iteration, and constructs longer compounds out of shorter ones. Objective evaluation on a simple machine translation task has shown the method's potential to improve the quality of MT output. The method makes few assumptions about the data, so it can be applied to parallel data other than parallel texts, such as word spellings and pronunciations.

  11. Data Exchange in Grid Workflow

    Institute of Scientific and Technical Information of China (English)

    ZENG Hongwei; MIAO Huaikou

    2006-01-01

    In existing web services-based workflow, data exchanging across the web services is centralized, the workflow engine intermediates at each step of the application sequence.However, many grid applications, especially data intensive scientific applications, require exchanging large amount of data across the grid services.Having a central workfiow engine relay the data between the services would results in a bottleneck in these cases.This paper proposes a data exchange model for individual grid workflow and multiworkflows composition respectively.The model enables direct communication for large amounts of data between two grid services.To enable data to exchange among multiple workflows, the bridge data service is used.

  12. Automatic page composition with nested sub-layouts

    Science.gov (United States)

    Hunter, Andrew

    2013-03-01

    This paper provides an overview of a system for the automatic composition of publications. The system first composes nested hierarchies of contents, then applies layout engines at branch points in the hierarchies to explore layout options, and finally selects the best overall options for the finished publications. Although the system has been developed as a general platform for automated publishing, this paper describes its application to the composition and layout of a magazine-like publication for social content from Facebook. The composition process works by assembling design fragments that have been populated with text and images from the Facebook social network. The fragments constitute a design language for a publication. Each design fragment is a nested mutable sub-layout that has no specific size or shape until after it has been laid-out. The layout process balances the space requirements of the fragment's internal contents with its external context in the publication. The mutability of sub-layouts requires that their layout options must be kept open until all the other contents that share the same space have been considered. Coping with large numbers of options is one of the greatest challenges in layout automation. Most existing layout methods work by rapidly elimination design options rather than by keeping options open. A further goal of this publishing system is to confirm that a custom publication can be generated quickly by the described methods. In general, the faster that publications can be created, the greater the opportunities for the technology.

  13. On A Semi-Automatic Method for Generating Composition Tables

    CERN Document Server

    Liu, Weiming

    2011-01-01

    Originating from Allen's Interval Algebra, composition-based reasoning has been widely acknowledged as the most popular reasoning technique in qualitative spatial and temporal reasoning. Given a qualitative calculus (i.e. a relation model), the first thing we should do is to establish its composition table (CT). In the past three decades, such work is usually done manually. This is undesirable and error-prone, given that the calculus may contain tens or hundreds of basic relations. Computing the correct CT has been identified by Tony Cohn as a challenge for computer scientists in 1995. This paper addresses this problem and introduces a semi-automatic method to compute the CT by randomly generating triples of elements. For several important qualitative calculi, our method can establish the correct CT in a reasonable short time. This is illustrated by applications to the Interval Algebra, the Region Connection Calculus RCC-8, the INDU calculus, and the Oriented Point Relation Algebras. Our method can also be us...

  14. Linked-OWL: A new approach for dynamic linked data service workflow composition

    Directory of Open Access Journals (Sweden)

    Hussien Ahmad

    2013-06-01

    Full Text Available The shift from Web of Document into Web of Data based on Linked Data principles defined by Tim Berners-Lee posed a big challenge to build and develop applications to work in Web of Data environment. There are several attempts to build service and application models for Linked Data Cloud. In this paper, we propose a new service model for linked data "Linked-OWL" which is based on RESTful services and OWL-S and copes with linked data principles. This new model shifts the service concept from functions into linked data things and opens the road for Linked Oriented Architecture (LOA and Web of Services as part and on top of Web of Data. This model also provides high level of dynamic service composition capabilities for more accurate dynamic composition and execution of complex business processes in Web of Data environment.

  15. Automated data reduction workflows for astronomy

    CERN Document Server

    Freudling, W; Bramich, D M; Ballester, P; Forchi, V; Garcia-Dablo, C E; Moehler, S; Neeser, M J

    2013-01-01

    Data from complex modern astronomical instruments often consist of a large number of different science and calibration files, and their reduction requires a variety of software tools. The execution chain of the tools represents a complex workflow that needs to be tuned and supervised, often by individual researchers that are not necessarily experts for any specific instrument. The efficiency of data reduction can be improved by using automatic workflows to organise data and execute the sequence of data reduction steps. To realize such efficiency gains, we designed a system that allows intuitive representation, execution and modification of the data reduction workflow, and has facilities for inspection and interaction with the data. The European Southern Observatory (ESO) has developed Reflex, an environment to automate data reduction workflows. Reflex is implemented as a package of customized components for the Kepler workflow engine. Kepler provides the graphical user interface to create an executable flowch...

  16. Lattice QCD workflows

    Energy Technology Data Exchange (ETDEWEB)

    Piccoli, Luciano; /Fermilab /IIT, Chicago; Kowalkowski, James B.; Simone, James N.; /Fermilab; Sun, Xian-He; Jin, Hui; /IIT, Chicago; Holmgren, Donald J.; Seenu, Nirmal; Singh, Amitoj G.; /Fermilab

    2008-12-01

    This paper discusses the application of existing workflow management systems to a real world science application (LQCD). Typical workflows and execution environment used in production are described. Requirements for the LQCD production system are discussed. The workflow management systems Askalon and Swift were tested by implementing the LQCD workflows and evaluated against the requirements. We report our findings and future work.

  17. Unidirectional high fiber content composites: Automatic 3D FE model generation and damage simulation

    DEFF Research Database (Denmark)

    Qing, Hai; Mishnaevsky, Leon

    2009-01-01

    A new method and a software code for the automatic generation of 3D micromechanical FE models of unidirectional long-fiber-reinforced composite (LFRC) with high fiber volume fraction with random fiber arrangement are presented. The fiber arrangement in the cross-section is generated through random...

  18. Covariance among milking frequency, milk yield, and milk composition from automatically milked cows

    DEFF Research Database (Denmark)

    Løvendahl, Peter; Chagunda, G G

    2011-01-01

    Automatic milking systems allow cows voluntary access to milking and concentrates within set limits. This leads to large variation in milking intervals, both within and between cows, which further affects yield per milking and composition of milk. This study aimed to describe the degree to which ...

  19. Workflow automation architecture standard

    Energy Technology Data Exchange (ETDEWEB)

    Moshofsky, R.P.; Rohen, W.T. [Boeing Computer Services Co., Richland, WA (United States)

    1994-11-14

    This document presents an architectural standard for application of workflow automation technology. The standard includes a functional architecture, process for developing an automated workflow system for a work group, functional and collateral specifications for workflow automation, and results of a proof of concept prototype.

  20. Professional Windows Workflow Foundation

    CERN Document Server

    Kitta, Todd

    2007-01-01

    If you want to gain the skills to build Windows Workflow Foundation solutions, then this is the book for you. It provides you with a clear, practical guide on how to develop workflow-based software and integrate it into existing technology landscapes. Throughout the pages, you'll also find numerous real-world examples and sample code that will help you to get started quickly.Each major area of Windows Workflow Foundation is explored in depth along with some of the fundamentals operations related to generic workflow applications. You'll also find detailed coverage on how to develop workflow in

  1. AUTOMATIC WEB SERVICE SELECTION BY OPTIMIZING COST OF COMPOSITION IN SLAKY COMPOSER USING ASSIGNMENT MINIMIZATION APPROACH

    Directory of Open Access Journals (Sweden)

    P. Sandhya

    2012-12-01

    Full Text Available Web service composition is a means of building enterprises virtually by knitting relevant web services on the fly. Automatic web service composition is done dynamically at runtime. Extensive research has been done in the field of automatic web service composition. However all the works focus on providing client oriented results and hence there is less industry adoption of composition technology. In this paper we have proposed a new service collaboration stack that composes with realistic business metrics of a provider in addition to client metrics. Some of the service provider metrics include time planning, profit management, native intelligence, user adoption, environment, market scenario, vision and industry adoption. In this paper we focus on enhancing industry adoption through optimizing cost of service composition. We propose the SLAKY composer that solves assignment of appropriate service during composition as an assignment minimization problem to reduce the cost of composition. We also extend OWL-S profile sub ontology to augment cost as a service parameter.

  2. Agreement Workflow Tool (AWT)

    Data.gov (United States)

    Social Security Administration — The Agreement Workflow Tool (AWT) is a role-based Intranet application used for processing SSA's Reimbursable Agreements according to SSA's standards. AWT provides...

  3. Scientific workflows for bibliometrics

    NARCIS (Netherlands)

    Guler, A.T.; Waaijer, C.J.; Palmblad, M.

    2016-01-01

    Scientific workflows organize the assembly of specialized software into an overall data flow and are particularly well suited for multi-step analyses using different types of software tools. They are also favorable in terms of reusability, as previously designed workflows could be made publicly avai

  4. From Workflow to Interworkflow

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    Workflow management systems are being introduced in manyorganizations to automa te the business process. The initial emphasis of introducing a workflow manageme nt system is on its application to the workflow in a given organization. The nex t step is to interconnect the workflow across organizations. We call it interwor kflow, and the total support technologies, which are necessary for its realizati on, interworkflow management mechanism. Interworkflow is being expected as a su pporting mechanism for Business-to-Business Electronic Commerce. We had propos ed this management mechanism and confirmed its realization with the prototype. At the same time, the interface and the protocol for interconnecting heterogeneous workflow management systems has been standardized by the WfMC. So, we advance t he project of the implementation of interworkflow management system for the prac tical use and its experimental proof.

  5. Benchmarking ETL Workflows

    Science.gov (United States)

    Simitsis, Alkis; Vassiliadis, Panos; Dayal, Umeshwar; Karagiannis, Anastasios; Tziovara, Vasiliki

    Extraction-Transform-Load (ETL) processes comprise complex data workflows, which are responsible for the maintenance of a Data Warehouse. A plethora of ETL tools is currently available constituting a multi-million dollar market. Each ETL tool uses its own technique for the design and implementation of an ETL workflow, making the task of assessing ETL tools extremely difficult. In this paper, we identify common characteristics of ETL workflows in an effort of proposing a unified evaluation method for ETL. We also identify the main points of interest in designing, implementing, and maintaining ETL workflows. Finally, we propose a principled organization of test suites based on the TPC-H schema for the problem of experimenting with ETL workflows.

  6. AN AI PLANNING APPROACH FOR GENERATING BIG DATA WORKFLOWS

    Directory of Open Access Journals (Sweden)

    Wesley Deneke

    2015-09-01

    Full Text Available The scale of big data causes the compositions of extract-transform-load (ETL workflows to grow increasingly complex. With the turnaround time for delivering solutions becoming a greater emphasis, stakeholders cannot continue to afford to wait the hundreds of hours it takes for domain experts to manually compose a workflow solution. This paper describes a novel AI planning approach that facilitates rapid composition and maintenance of ETL workflows. The workflow engine is evaluated on real-world scenarios from an industrial partner and results gathered from a prototype are reported to demonstrate the validity of the approach.

  7. 柔性工作流中的服务组合可协调性研究%Coordination Research for Service Composition Based on Flexible Workflow

    Institute of Scientific and Technical Information of China (English)

    张静乐; 杨扬; 卡利勒; 王元卓; 赵晓永

    2011-01-01

    In this paper, we propose a research way about coordination of service composition. First of all, the definition of services and service composition of coordination was proposed. Then, the decision algorithm of coordination is given based on the definition of service composition. At last, take e-commerce systems in the logistics system as an example, based on the Stochastic Petri Net of model, the method of automatic service composition based on service coordination was highlighted.%提出柔性工作流中的服务组合可协调性分析方法.给出服务以及服务组合可协调性的定义;在可协调性定义的基础上给出组合服务间可协调性判定算法;最后,以电子商务系统中的物流系统为例,在随机Petri网模型建模的基础上,着重介绍了柔性工作系统中基于服务可协调性判定的服务自动组合方法.

  8. Integrating configuration workflows with project management system

    Science.gov (United States)

    Nilsen, Dimitri; Weber, Pavel

    2014-06-01

    The complexity of the heterogeneous computing resources, services and recurring infrastructure changes at the GridKa WLCG Tier-1 computing center require a structured approach to configuration management and optimization of interplay between functional components of the whole system. A set of tools deployed at GridKa, including Puppet, Redmine, Foreman, SVN and Icinga, provides the administrative environment giving the possibility to define and develop configuration workflows, reduce the administrative effort and improve sustainable operation of the whole computing center. In this presentation we discuss the developed configuration scenarios implemented at GridKa, which we use for host installation, service deployment, change management procedures, service retirement etc. The integration of Puppet with a project management tool like Redmine provides us with the opportunity to track problem issues, organize tasks and automate these workflows. The interaction between Puppet and Redmine results in automatic updates of the issues related to the executed workflow performed by different system components. The extensive configuration workflows require collaboration and interaction between different departments like network, security, production etc. at GridKa. Redmine plugins developed at GridKa and integrated in its administrative environment provide an effective way of collaboration within the GridKa team. We present the structural overview of the software components, their connections, communication protocols and show a few working examples of the workflows and their automation.

  9. Integrating configuration workflows with project management system

    International Nuclear Information System (INIS)

    The complexity of the heterogeneous computing resources, services and recurring infrastructure changes at the GridKa WLCG Tier-1 computing center require a structured approach to configuration management and optimization of interplay between functional components of the whole system. A set of tools deployed at GridKa, including Puppet, Redmine, Foreman, SVN and Icinga, provides the administrative environment giving the possibility to define and develop configuration workflows, reduce the administrative effort and improve sustainable operation of the whole computing center. In this presentation we discuss the developed configuration scenarios implemented at GridKa, which we use for host installation, service deployment, change management procedures, service retirement etc. The integration of Puppet with a project management tool like Redmine provides us with the opportunity to track problem issues, organize tasks and automate these workflows. The interaction between Puppet and Redmine results in automatic updates of the issues related to the executed workflow performed by different system components. The extensive configuration workflows require collaboration and interaction between different departments like network, security, production etc. at GridKa. Redmine plugins developed at GridKa and integrated in its administrative environment provide an effective way of collaboration within the GridKa team. We present the structural overview of the software components, their connections, communication protocols and show a few working examples of the workflows and their automation.

  10. Deductive Synthesis of Workflows for E-Science

    OpenAIRE

    Yang, B.; Bundy, Alan; Smaill, A.; Dixon, L

    2005-01-01

    In this paper we show that the automated reasoning technique of deductive synthesis can be applied to address the problem of machine-assisted composition of e-Science workflows according to users' specifications. We encode formal specifications of e-Science data, services and workflows, constructed from their descriptions, in the generic theorem prover Isabelle. Workflows meeting this specification are then synthesised as a side-effect of proving that these specifications can be met.

  11. A framework for interoperability of BPEL-based workflows

    Institute of Scientific and Technical Information of China (English)

    Li Xitong; Fan Yushun; Huang Shuangxi

    2008-01-01

    With the prevalence of service-oriented architecture (SOA), web services have become the dominating technology to construct workflow systems. As a workflow is the composition of a series of interrelated web services which realize its activities, the interoperability of workflows can be treated as the composition of web services. To address it, a framework for interoperability of business process execution language (BPEL)-based workflows is presented, which can perform three phases, that is, transformation, conformance test and execution. The core components of the framework are proposed, especially how these components promote interoperability. In particular, dynamic binding and re-composition of workflows in terms of web service testing are presented. Besides, an example of business-to-business (B2B) collaboration is provided to illustrate how to perform composition and conformance test.

  12. Quantitative analysis of probabilistic BPMN workflows

    DEFF Research Database (Denmark)

    Herbert, Luke Thomas; Sharp, Robin

    2012-01-01

    . We present an algorithm for the translation of such models into Markov Decision processes expressed in the syntax of the PRISM model checker. This enables analysis of business processes for the following properties: transient and steadystate probabilities, the timing, occurrence and ordering of...... for more complex annotations and ultimately to automatically synthesise workflows by composing predefined sub-processes, in order to achieve a configuration that is optimal for parameters of interest....

  13. A Model for Semi-Automatic Composition of Educational Content from Open Repositories of Learning Objects

    Directory of Open Access Journals (Sweden)

    Paula Andrea Rodríguez Marín

    2014-04-01

    Full Text Available Learning objects (LOs repositories are important in building educational content and should allow search, retrieval and composition processes to be successfully developed to reach educational goals. However, such processes require so much time-consuming and not always provide the desired results. Thus, the aim of this paper is to propose a model for the semiautomatic composition of LOs, which are automatically recovered from open repositories. For the development of model, various text similarity measures are discussed, while for calibration and validation some comparison experiments were performed using the results obtained by teachers. Experimental results show that when using a value of k (number of LOs selected of at least 3, the percentage of similarities between the model and such made by experts exceeds 75%. To conclude, it can be established that the model proposed allows teachers to save time and effort for LOs selection by performing a pre-filter process.

  14. All-automatic swimmer tracking system based on an optimized scaled composite JTC technique

    Science.gov (United States)

    Benarab, D.; Napoléon, T.; Alfalou, A.; Verney, A.; Hellard, P.

    2016-04-01

    In this paper, an all-automatic optimized JTC based swimmer tracking system is proposed and evaluated on real video database outcome from national and international swimming competitions (French National Championship, Limoges 2015, FINA World Championships, Barcelona 2013 and Kazan 2015). First, we proposed to calibrate the swimming pool using the DLT algorithm (Direct Linear Transformation). DLT calculates the homography matrix given a sufficient set of correspondence points between pixels and metric coordinates: i.e. DLT takes into account the dimensions of the swimming pool and the type of the swim. Once the swimming pool is calibrated, we extract the lane. Then we apply a motion detection approach to detect globally the swimmer in this lane. Next, we apply our optimized Scaled Composite JTC which consists of creating an adapted input plane that contains the predicted region and the head reference image. This latter is generated using a composite filter of fin images chosen from the database. The dimension of this reference will be scaled according to the ratio between the head's dimension and the width of the swimming lane. Finally, applying the proposed approach improves the performances of our previous tracking method by adding a detection module in order to achieve an all-automatic swimmer tracking system.

  15. Automatic 1H-NMR Screening of Fatty Acid Composition in Edible Oils

    Directory of Open Access Journals (Sweden)

    David Castejón

    2016-02-01

    Full Text Available In this work, we introduce an NMR-based screening method for the fatty acid composition analysis of edible oils. We describe the evaluation and optimization needed for the automated analysis of vegetable oils by low-field NMR to obtain the fatty acid composition (FAC. To achieve this, two scripts, which automatically analyze and interpret the spectral data, were developed. The objective of this work was to drive forward the automated analysis of the FAC by NMR. Due to the fact that this protocol can be carried out at low field and that the complete process from sample preparation to printing the report only takes about 3 min, this approach is promising to become a fundamental technique for high-throughput screening. To demonstrate the applicability of this method, the fatty acid composition of extra virgin olive oils from various Spanish olive varieties (arbequina, cornicabra, hojiblanca, manzanilla, and picual was determined by 1H-NMR spectroscopy according to this protocol.

  16. Automatic 1H-NMR Screening of Fatty Acid Composition in Edible Oils

    Science.gov (United States)

    Castejón, David; Fricke, Pascal; Cambero, María Isabel; Herrera, Antonio

    2016-01-01

    In this work, we introduce an NMR-based screening method for the fatty acid composition analysis of edible oils. We describe the evaluation and optimization needed for the automated analysis of vegetable oils by low-field NMR to obtain the fatty acid composition (FAC). To achieve this, two scripts, which automatically analyze and interpret the spectral data, were developed. The objective of this work was to drive forward the automated analysis of the FAC by NMR. Due to the fact that this protocol can be carried out at low field and that the complete process from sample preparation to printing the report only takes about 3 min, this approach is promising to become a fundamental technique for high-throughput screening. To demonstrate the applicability of this method, the fatty acid composition of extra virgin olive oils from various Spanish olive varieties (arbequina, cornicabra, hojiblanca, manzanilla, and picual) was determined by 1H-NMR spectroscopy according to this protocol. PMID:26891323

  17. Automatic ¹H-NMR Screening of Fatty Acid Composition in Edible Oils.

    Science.gov (United States)

    Castejón, David; Fricke, Pascal; Cambero, María Isabel; Herrera, Antonio

    2016-02-01

    In this work, we introduce an NMR-based screening method for the fatty acid composition analysis of edible oils. We describe the evaluation and optimization needed for the automated analysis of vegetable oils by low-field NMR to obtain the fatty acid composition (FAC). To achieve this, two scripts, which automatically analyze and interpret the spectral data, were developed. The objective of this work was to drive forward the automated analysis of the FAC by NMR. Due to the fact that this protocol can be carried out at low field and that the complete process from sample preparation to printing the report only takes about 3 min, this approach is promising to become a fundamental technique for high-throughput screening. To demonstrate the applicability of this method, the fatty acid composition of extra virgin olive oils from various Spanish olive varieties (arbequina, cornicabra, hojiblanca, manzanilla, and picual) was determined by ¹H-NMR spectroscopy according to this protocol. PMID:26891323

  18. Feature-point-extracting-based automatically mosaic for composite microscopic images

    Institute of Scientific and Technical Information of China (English)

    YIN YanSheng; ZHAO XiuYang; TIAN XiaoFeng; LI Jia

    2007-01-01

    Image mosaic is a crucial step in the three-dimensional reconstruction of composite materials to align the serial images. A novel method is adopted to mosaic two SiC/Al microscopic images with an amplification coefficient of 1000. The two images are denoised by Gaussian model, and feature points are then extracted by using Harris corner detector. The feature points are filtered through Canny edge detector. A 40x40 feature template is chosen by sowing a seed in an overlapped area of the reference image, and the homologous region in floating image is acquired automatically by the way of correlation analysis. The feature points in matched templates are used as feature point-sets. Using the transformational parameters acquired by SVD-ICP method, the two images are transformed into the universal coordinates and merged to the final mosaic image.

  19. Chang'E-3 data pre-processing system based on scientific workflow

    Science.gov (United States)

    tan, xu; liu, jianjun; wang, yuanyuan; yan, wei; zhang, xiaoxia; li, chunlai

    2016-04-01

    The Chang'E-3(CE3) mission have obtained a huge amount of lunar scientific data. Data pre-processing is an important segment of CE3 ground research and application system. With a dramatic increase in the demand of data research and application, Chang'E-3 data pre-processing system(CEDPS) based on scientific workflow is proposed for the purpose of making scientists more flexible and productive by automating data-driven. The system should allow the planning, conduct and control of the data processing procedure with the following possibilities: • describe a data processing task, include:1)define input data/output data, 2)define the data relationship, 3)define the sequence of tasks,4)define the communication between tasks,5)define mathematical formula, 6)define the relationship between task and data. • automatic processing of tasks. Accordingly, Describing a task is the key point whether the system is flexible. We design a workflow designer which is a visual environment for capturing processes as workflows, the three-level model for the workflow designer is discussed:1) The data relationship is established through product tree.2)The process model is constructed based on directed acyclic graph(DAG). Especially, a set of process workflow constructs, including Sequence, Loop, Merge, Fork are compositional one with another.3)To reduce the modeling complexity of the mathematical formulas using DAG, semantic modeling based on MathML is approached. On top of that, we will present how processed the CE3 data with CEDPS.

  20. Partitioning Uncertain Workflows

    CERN Document Server

    Huberman, Bernardo A

    2015-01-01

    It is common practice to partition complex workflows into separate channels in order to speed up their completion times. When this is done within a distributed environment, unavoidable fluctuations make individual realizations depart from the expected average gains. We present a method for breaking any complex workflow into several workloads in such a way that once their outputs are joined, their full completion takes less time and exhibit smaller variance than when running in only one channel. We demonstrate the effectiveness of this method in two different scenarios; the optimization of a convex function and the transmission of a large computer file over the Internet.

  1. An Interoperable GridWorkflow Management System

    Science.gov (United States)

    Mirto, Maria; Passante, Marco; Epicoco, Italo; Aloisio, Giovanni

    A WorkFlow Management System (WFMS) is a fundamental componentenabling to integrate data, applications and a wide set of project resources. Although a number of scientific WFMSs support this task, many analysis pipelines require large-scale Grid computing infrastructures to cope with their high compute and storage requirements. Such scientific workflows complicate the management of resources, especially in cases where they are offered by several resource providers, managed by different Grid middleware, since resource access must be synchronised in advance to allow reliable workflow execution. Different types of Grid middleware such as gLite, Unicore and Globus are used around the world and may cause interoperability issues if applications involve two or more of them. In this paperwe describe the ProGenGrid Workflow Management System which the main goal is to provide interoperability among these different grid middleware when executing workflows. It allows the composition of batch; parameter sweep and MPI based jobs. The ProGenGrid engine implements the logic to execute such jobs by using a standard language OGF compliant such as JSDL that has been extended for this purpose. Currently, we are testing our system on some bioinformatics case studies in the International Laboratory of Bioinformatics (LIBI) Project (www.libi.it).

  2. A quantitative fitness analysis workflow.

    Science.gov (United States)

    Banks, A P; Lawless, C; Lydall, D A

    2012-01-01

    Quantitative Fitness Analysis (QFA) is an experimental and computational workflow for comparing fitnesses of microbial cultures grown in parallel(1,2,3,4). QFA can be applied to focused observations of single cultures but is most useful for genome-wide genetic interaction or drug screens investigating up to thousands of independent cultures. The central experimental method is the inoculation of independent, dilute liquid microbial cultures onto solid agar plates which are incubated and regularly photographed. Photographs from each time-point are analyzed, producing quantitative cell density estimates, which are used to construct growth curves, allowing quantitative fitness measures to be derived. Culture fitnesses can be compared to quantify and rank genetic interaction strengths or drug sensitivities. The effect on culture fitness of any treatments added into substrate agar (e.g. small molecules, antibiotics or nutrients) or applied to plates externally (e.g. UV irradiation, temperature) can be quantified by QFA. The QFA workflow produces growth rate estimates analogous to those obtained by spectrophotometric measurement of parallel liquid cultures in 96-well or 200-well plate readers. Importantly, QFA has significantly higher throughput compared with such methods. QFA cultures grow on a solid agar surface and are therefore well aerated during growth without the need for stirring or shaking. QFA throughput is not as high as that of some Synthetic Genetic Array (SGA) screening methods(5,6). However, since QFA cultures are heavily diluted before being inoculated onto agar, QFA can capture more complete growth curves, including exponential and saturation phases(3). For example, growth curve observations allow culture doubling times to be estimated directly with high precision, as discussed previously(1). Here we present a specific QFA protocol applied to thousands of S. cerevisiae cultures which are automatically handled by robots during inoculation, incubation and

  3. Insightful Workflow For Grid Computing

    Energy Technology Data Exchange (ETDEWEB)

    Dr. Charles Earl

    2008-10-09

    We developed a workflow adaptation and scheduling system for Grid workflow. The system currently interfaces with and uses the Karajan workflow system. We developed machine learning agents that provide the planner/scheduler with information needed to make decisions about when and how to replan. The Kubrick restructures workflow at runtime, making it unique among workflow scheduling systems. The existing Kubrick system provides a platform on which to integrate additional quality of service constraints and in which to explore the use of an ensemble of scheduling and planning algorithms. This will be the principle thrust of our Phase II work.

  4. PRODUCT-ORIENTED WORKFLOW MANAGEMENT IN CAPP

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    A product-oriented process workflow management model is proposed based on the multi-agent technology.The autonomy, inter-operability, scalability and flexibility of agent are used to cooperate the whole process planning andachieve the full share of resource and information. Thus, unnecessary waste of human labor, time and work is reducedand the computer-aided process planning (CAPP) system's adaptability and stability are improved. In the detailed im-plementation, according to the products' BOM (Bill of materials) in structural design, the task assignment, managementcontrol, automatic process making, process examination and process sanction are combined into a unified management tomake it convenient for the adjustment, control and management.

  5. CSP for Executable Scientific Workflows

    OpenAIRE

    Friborg, Rune Møllegaard

    2011-01-01

    This thesis presents CSP as a means of orchestrating the execution of tasks in a scientific workflow. Scientific workflow systems are popular in a wide range of scientific areas, where tasks are organised in directed graphs. Execution of such graphs is handled by the scientific workflow systems and can usually benefit performance-wise from both multiprocessing, cluster and grid environments.PyCSP is an implementation of Communicating Sequential Processes (CSP) for the Python programming langu...

  6. Monitoring of Grid scientific workflows

    NARCIS (Netherlands)

    B. Balis; M. Bubak; B. Łabno

    2008-01-01

    Scientific workflows are a means of conducting in silico experiments in modern computing infrastructures for e-Science, often built on top of Grids. Monitoring of Grid scientific workflows is essential not only for performance analysis but also to collect provenance data and gather feedback useful i

  7. New Interactions with Workflow Systems

    OpenAIRE

    Wassink, I.; Vet, de, H.C.W.; Veer, van der, P.T.; Roos, M.; Dijk, van, G.; Norros, L.; Koskinen, H; Salo, L; Savioja, P.

    2009-01-01

    This paper describes the evaluation of our early design ideas of an ad-hoc of workflow system. Using the teach-back technique, we have performed a hermeneutic analysis of the mockup implementation named NIWS to get corrective and creative feedback at the functional, dialogue and representation level of the new workflow system.

  8. Workflow Management in Electronic Commerce

    NARCIS (Netherlands)

    Grefen, P.W.P.J.; Spaccapietra, S.; March, S.T.; Kambayashi, Y.

    2002-01-01

    This tutorial addresses the application of workflow management (WFM) for process support in both these cases. The tutorial is organized into three parts. In the first part, we pay attention to (classical) workflow management in the context of a single organization. In the second part, we extend this

  9. Constructing Workflows from Script Applications

    Directory of Open Access Journals (Sweden)

    Mikołaj Baranowski

    2012-01-01

    Full Text Available For programming and executing complex applications on grid infrastructures, scientific workflows have been proposed as convenient high-level alternative to solutions based on general-purpose programming languages, APIs and scripts. GridSpace is a collaborative programming and execution environment, which is based on a scripting approach and it extends Ruby language with a high-level API for invoking operations on remote resources. In this paper we describe a tool which enables to convert the GridSpace application source code into a workflow representation which, in turn, may be used for scheduling, provenance, or visualization. We describe how we addressed the issues of analyzing Ruby source code, resolving variable and method dependencies, as well as building workflow representation. The solutions to these problems have been developed and they were evaluated by testing them on complex grid application workflows such as CyberShake, Epigenomics and Montage. Evaluation is enriched by representing typical workflow control flow patterns.

  10. Summer Student Report - AV Workflow

    CERN Document Server

    Abramson, Jessie

    2014-01-01

    The AV Workflow is web application which allows cern users to publish, update and delete videos from cds. During my summer internship I implemented the backend of the new version of the AV Worklow in python using the django framework.

  11. Agile parallel bioinformatics workflow management using Pwrake

    Directory of Open Access Journals (Sweden)

    Tanaka Masahiro

    2011-09-01

    Full Text Available Abstract Background In bioinformatics projects, scientific workflow systems are widely used to manage computational procedures. Full-featured workflow systems have been proposed to fulfil the demand for workflow management. However, such systems tend to be over-weighted for actual bioinformatics practices. We realize that quick deployment of cutting-edge software implementing advanced algorithms and data formats, and continuous adaptation to changes in computational resources and the environment are often prioritized in scientific workflow management. These features have a greater affinity with the agile software development method through iterative development phases after trial and error. Here, we show the application of a scientific workflow system Pwrake to bioinformatics workflows. Pwrake is a parallel workflow extension of Ruby's standard build tool Rake, the flexibility of which has been demonstrated in the astronomy domain. Therefore, we hypothesize that Pwrake also has advantages in actual bioinformatics workflows. Findings We implemented the Pwrake workflows to process next generation sequencing data using the Genomic Analysis Toolkit (GATK and Dindel. GATK and Dindel workflows are typical examples of sequential and parallel workflows, respectively. We found that in practice, actual scientific workflow development iterates over two phases, the workflow definition phase and the parameter adjustment phase. We introduced separate workflow definitions to help focus on each of the two developmental phases, as well as helper methods to simplify the descriptions. This approach increased iterative development efficiency. Moreover, we implemented combined workflows to demonstrate modularity of the GATK and Dindel workflows. Conclusions Pwrake enables agile management of scientific workflows in the bioinformatics domain. The internal domain specific language design built on Ruby gives the flexibility of rakefiles for writing scientific workflows

  12. Intelligent Business Transaction Agents for Cross-Organizational Workflow Definition and Execution

    OpenAIRE

    Saleem, Mohammad; Chung, Paul W. H.; Fatima, Shaheen; Dai, Wei

    2010-01-01

    International audience; Business organizations seldom work in isolation; effective interaction and cooperation between different organizations is essential for the success of any organization. In order to work together, organizations must have compatible workflows. This paper proposes a framework for automatically creating compatible workflows from high level requirements given by organizations that intend to work together. The framework uses intelligent agents [1] for the creation and execut...

  13. Observing health professionals' workflow patterns for diabetes care - First steps towards an ontology for EHR services.

    Science.gov (United States)

    Schweitzer, M; Lasierra, N; Hoerbst, A

    2015-01-01

    Increasing the flexibility from a user-perspective and enabling a workflow based interaction, facilitates an easy user-friendly utilization of EHRs for healthcare professionals' daily work. To offer such versatile EHR-functionality, our approach is based on the execution of clinical workflows by means of a composition of semantic web-services. The backbone of such architecture is an ontology which enables to represent clinical workflows and facilitates the selection of suitable services. In this paper we present the methods and results after running observations of diabetes routine consultations which were conducted in order to identify those workflows and the relation among the included tasks. Mentioned workflows were first modeled by BPMN and then generalized. As a following step in our study, interviews will be conducted with clinical personnel to validate modeled workflows.

  14. Within day variation in fatty acid composition of milk from cows in an automatic milking system

    DEFF Research Database (Denmark)

    Larsen, Mette Krogh; Weisbjerg, Martin Riis; Kristensen, Camilla Bjerg;

    2012-01-01

    Milk fatty acid composition is influenced by a range of conditions such as breed, feeding, and stage of lactation. Knowledge of milk fatty acid composition of individual cows would make it possible to sort milk at farm level according to certain fatty acid specifications. In the present study, 22...

  15. Automatic Determination of Fiber-Length Distribution in Composite Material Using 3D CT Data

    Directory of Open Access Journals (Sweden)

    Günther Greiner

    2010-01-01

    Full Text Available Determining fiber length distribution in fiber reinforced polymer components is a crucial step in quality assurance, since fiber length has a strong influence on overall strength, stiffness, and stability of the material. The approximate fiber length distribution is usually determined early in the development process, as conventional methods require a destruction of the sample component. In this paper, a novel, automatic, and nondestructive approach for the determination of fiber length distribution in fiber reinforced polymers is presented. For this purpose, high-resolution computed tomography is used as imaging method together with subsequent image analysis for evaluation. The image analysis consists of an iterative process where single fibers are detected automatically in each iteration step after having applied image enhancement algorithms. Subsequently, a model-based approach is used together with a priori information in order to guide a fiber tracing and segmentation process. Thereby, the length of the segmented fibers can be calculated and a length distribution can be deduced. The performance and the robustness of the segmentation method is demonstrated by applying it to artificially generated test data and selected real components.

  16. A Novel Verification Approach of Workflow Schema

    Institute of Scientific and Technical Information of China (English)

    WANG Guangqi; WANG Juying; WANG Yan; SONG Baoyan; YU Ge

    2006-01-01

    A workflow schema is an abstract description of the business processed by workflow model, and plays a critical role in analyzing, executing and reorganizing business processes. The verification issue on the correctness of complicated workflow schemas is difficult in the field of workflow. We make an intensive study of it in this paper. We present here local errors and schema logic errors (global errors) in workflow schemas in detail, and offer some constraint rules trying to avoid schema errors during modeling. In addition, we propose a verification approach based on graph reduction and graph spread, and give the algorithm. The algorithm is implemented in a workflow prototype system e-ScopeWork.

  17. Office 2010 Workflow Developing Collaborative Solutions

    CERN Document Server

    Mann, David; Enterprises, Creative

    2010-01-01

    Workflow is the glue that binds information worker processes, users, and artifacts. Without workflow, information workers are just islands of data and potential. Office 2010 Workflow details how to implement workflow in SharePoint 2010 and the client Microsoft Office 2010 suite to help information workers share data, enforce processes and business rules, and work more efficiently together or solo. This book covers everything you need to know-from what workflow is all about to creating new activities; from the SharePoint Designer to Visual Studio 2010; from out-of-the-box workflows to state mac

  18. Flexible Early Warning Systems with Workflows and Decision Tables

    Science.gov (United States)

    Riedel, F.; Chaves, F.; Zeiner, H.

    2012-04-01

    are usually only suited for rigid processes. We show how improvements can be achieved by using decision tables and rule-based adaptive workflows. Decision tables have been shown to be an intuitive tool that can be used by domain experts to express rule sets that can be interpreted automatically at runtime. Adaptive workflows use a rule-based approach to increase the flexibility of workflows by providing mechanisms to adapt workflows based on context changes, human intervention and availability of services. The combination of workflows, decision tables and rule-based adaption creates a framework that opens up new possibilities for flexible and adaptable workflows, especially, for use in early warning and crisis management systems.

  19. WARP (workflow for automated and rapid production): a framework for end-to-end automated digital print workflows

    Science.gov (United States)

    Joshi, Parag

    2006-02-01

    Publishing industry is experiencing a major paradigm shift with the advent of digital publishing technologies. A large number of components in the publishing and print production workflow are transformed in this shift. However, the process as a whole requires a great deal of human intervention for decision making and for resolving exceptions during job execution. Furthermore, a majority of the best-of-breed applications for publishing and print production are intrinsically designed and developed to be driven by humans. Thus, the human-intensive nature of the current prepress process accounts for a very significant amount of the overhead costs in fulfillment of jobs on press. It is a challenge to automate the functionality of applications built with the model of human driven exectution. Another challenge is to orchestrate various components in the publishing and print production pipeline such that they work in a seamless manner to enable the system to perform automatic detection of potential failures and take corrective actions in a proactive manner. Thus, there is a great need for a coherent and unifying workflow architecture that streamlines the process and automates it as a whole in order to create an end-to-end digital automated print production workflow that does not involve any human intervention. This paper describes an architecture and building blocks that lay the foundation for a plurality of automated print production workflows.

  20. Toward automatic evaluation of defect detectability in infrared images of composites and honeycomb structures

    Science.gov (United States)

    Florez-Ospina, Juan F.; Benitez-Restrepo, H. D.

    2015-07-01

    Non-destructive testing (NDT) refers to inspection methods employed to assess a material specimen without impairing its future usefulness. An important type of these methods is infrared (IR) for NDT (IRNDT), which employs the heat emitted by bodies/objects to rapidly and noninvasively inspect wide surfaces and to find specific defects such as delaminations, cracks, voids, and discontinuities in materials. Current advancements in sensor technology for IRNDT generate great amounts of image sequences. These data require further processing to determine the integrity of objects. Processing techniques for IRNDT data implicitly looks for defect visibility enhancement. Commonly, IRNDT community employs signal to noise ratio (SNR) to measure defect visibility. Nonetheless, current applications of SNR are local, thereby overseeing spatial information, and depend on a-priori knowledge of defect's location. In this paper, we present a general framework to assess defect detectability based on SNR maps derived from processed IR images. The joint use of image segmentation procedures along with algorithms for filling regions of interest (ROI) estimates a reference background to compute SNR maps. Our main contributions are: (i) a method to compute SNR maps that takes into account spatial variation and are independent of a-priori knowledge of defect location in the sample, (ii) spatial background analysis in processed images, and (iii) semi-automatic calculation of segmentation algorithm parameters. We test our approach in carbon fiber and honeycomb samples with complex geometries and defects with different sizes and depths.

  1. Concurrency & Asynchrony in Declarative Workflows

    DEFF Research Database (Denmark)

    Debois, Søren; Hildebrandt, Thomas; Slaats, Tijs

    2015-01-01

    Declarative or constraint-based business process and workflow notations have received increasing interest in the last decade as possible means of addressing the challenge of supporting at the same time flexibility in execution, adaptability and compliance. However, the definition of concurrent...

  2. Constructing workflows from script applications

    NARCIS (Netherlands)

    M. Baranowski; A. Belloum; M. Bubak; M. Malawski

    2013-01-01

    For programming and executing complex applications on grid infrastructures, scientific workflows have been proposed as convenient high-level alternative to solutions based on general-purpose programming languages, APIs and scripts. GridSpace is a collaborative programming and execution environment,

  3. Delegation Protocols in Human-Centric Workflows

    OpenAIRE

    Gaaloul, Khaled; Proper, Erik; Charoy, François

    2011-01-01

    International audience Organisations are facilitated and conducted using workflow management systems. Currently, we observe a tendency moving away from strict workflow modelling towards dynamic approaches supporting human interactions when deploying a workflow. One specific approach ensuring human-centric workflows is task delegation. Delegating a task may require an access to specific and potentially sensitive data that have to be secured and specified into authorisation policies. In this...

  4. Execution Time Estimation for Workflow Scheduling

    NARCIS (Netherlands)

    Chirkin, A.M.; Belloum, A..S.Z.; Kovalchuk, S.V.; Makkes, M.X.

    2014-01-01

    Estimation of the execution time is an important part of the workflow scheduling problem. The aim of this paper is to highlight common problems in estimating the workflow execution time and propose a solution that takes into account the complexity and the randomness of the workflow components and th

  5. The equivalency between logic Petri workflow nets and workflow nets.

    Science.gov (United States)

    Wang, Jing; Yu, ShuXia; Du, YuYue

    2015-01-01

    Logic Petri nets (LPNs) can describe and analyze batch processing functions and passing value indeterminacy in cooperative systems. Logic Petri workflow nets (LPWNs) are proposed based on LPNs in this paper. Process mining is regarded as an important bridge between modeling and analysis of data mining and business process. Workflow nets (WF-nets) are the extension to Petri nets (PNs), and have successfully been used to process mining. Some shortcomings cannot be avoided in process mining, such as duplicate tasks, invisible tasks, and the noise of logs. The online shop in electronic commerce in this paper is modeled to prove the equivalence between LPWNs and WF-nets, and advantages of LPWNs are presented. PMID:25821845

  6. Modeling Workflow Using UML Activity Diagram

    Institute of Scientific and Technical Information of China (English)

    Wei Yinxing(韦银星); Zhang Shensheng

    2004-01-01

    An enterprise can improve its adaptability in the changing market by means of workflow technologies. In the build time, the main function of Workflow Management System (WFMS) is to model business process. Workflow model is an abstract representation of the real-world business process. The Unified Modeling Language (UML) activity diagram is an important visual process modeling language proposed by the Object Management Group (OMG). The novelty of this paper is representing workflow model by means of UML activity diagram. A translation from UML activity diagram to π-calculus is established. Using π-calculus, the deadlock property of workflow is analyzed.

  7. THE SYSTEM OF WORKFLOW OF THE DEPARTMENT AT THE INSTITUTE

    Directory of Open Access Journals (Sweden)

    Nesterova N. S.

    2015-06-01

    Full Text Available The article describes the subsystem of workflow of the department at the institute “The calculation of teaching load”. As the process of calculation of teaching load is very complicated it has become necessary to make this process automatic. The mental card was developed where we can see the structure of the program for calculating teaching load. The subsystem has simple and understandable interface. The results of its work are represented in the form of filled blanks adopted by the academy in EXCEL. The created subsystem makes easier the teaching process of the department at the academy very much

  8. Towards Automated Design, Analysis and Optimization of Declarative Curation Workflows

    Directory of Open Access Journals (Sweden)

    Tianhong Song

    2014-10-01

    Full Text Available Data curation is increasingly important. Our previous work on a Kepler curation package has demonstrated advantages that come from automating data curation pipelines by using workflow systems. However, manually designed curation workflows can be error-prone and inefficient due to a lack of user understanding of the workflow system, misuse of actors, or human error. Correcting problematic workflows is often very time-consuming. A more proactive workflow system can help users avoid such pitfalls. For example, static analysis before execution can be used to detect the potential problems in a workflow and help the user to improve workflow design. In this paper, we propose a declarative workflow approach that supports semi-automated workflow design, analysis and optimization. We show how the workflow design engine helps users to construct data curation workflows, how the workflow analysis engine detects different design problems of workflows and how workflows can be optimized by exploiting parallelism.

  9. Automatic composition of semantic Web services based on planning graph%基于图规划的语义Web服务自动组合方法

    Institute of Scientific and Technical Information of China (English)

    付鹏斌; 李利波; 杨惠荣

    2011-01-01

    由于单个的Web服务功能有限,难以满足日益增长和不断变化的用户需求.如何根据服务请求者的特定需求进行服务的自动组合来满足用户的需要,就成为了一个迫切需要解决的问题.提出了一种基于图规划的语义Web服务自动组合方法,该方法在建立前驱与后继执行关系知识库的基础上,利用图规划的前向扩张思想和图规划解搜索思想,可实现从服务库中自动地找到满足用户需求的服务组合方案.该方法综合考虑了服务语义和服务组合的效率等因素,在保证Web服务组合质量的前提下,可根据服务请求实现服务的自动组合.最后用仿真实验从服务组合的成功率、效率和组合解质量三方面验证了该方法的有效性和可行性.%Nowadays, the limited function of single Web service can not satisfy the growing and varying custom' s require-ment. Therefore, how to compose Web services automatically according to service request becomes a problem urgent to be solved. This paper proposed an automatic Web service composition method based on planning graph technique, and by estab-lishing precursor-subsequence execution relationship knowledge base to support automatic Web service composition. The meth-od built on automated planning theory and used planning-graph' s expand and search techniques, and could find the service composition solution quickly and automatically. Compared with existing methods, the method took the semantics of Web serv-ices into consideration together with efficiency of the service composition. So the method can ensure quality and efficiency while composing services automatically according to user's service request. Finally using simulation experiment from services composition succeed rate,services composition efficiency and the quality of services composition solution three aspects to vali-date the effectiveness and feasibility of the method.

  10. Layered Workflow Process Model Based on Extended Synchronizer

    Directory of Open Access Journals (Sweden)

    Gang Ni

    2014-07-01

    Full Text Available The layered workflow process model provide a modeling approach and analysis for the key process with Petri Net. It not only describes the relation between the process of business flow and transition nodes clearly, but also limits the rapid increase in the scale of libraries, transition and directed arcs. This paper studies the process like reservation and complaint handling information management system, especially for the multi-mergence and discriminator patterns which can not be directly modeled with existing synchronizers. Petri Net is adopted to provide formalization description for the workflow patterns and the relation between Arcs and weight class are also analyzed. We use the number of in and out arcs to generalize the workflow into three synchronous modes: fully synchronous mode, competition synchronous mode and asynchronous mode. The types and parameters for synchronization are added to extend the modeling ability of the synchronizers and the synchronous distance is also expanded. The extended synchronizers have the ability to terminate branches automatically or activate the next link many times, besides the ability of original synchronizers. By the analyses on cases of the key business, it is verified that the original synchronizers can not model directly, while the extended synchronizers based on Petri Net can provide modeling for multi-mergence and discriminator modes.

  11. Operational Semantic of Workflow Engine and the Realizing Technique

    Institute of Scientific and Technical Information of China (English)

    FU Yan-ning; LIU Lei; ZHAO Dong-fan; JIN Long-fei

    2005-01-01

    At present, there is no formalized description of the executing procedure of workflow models. The procedure of workflow models executing in workflow engine is described using operational semantic. The formalized description of process instances and activity instances leads to very clear structure of the workflow engine, has easy cooperation of the heterogeneous workflow engines and guides the realization of the workflow engine function. Meanwhile, the software of workflow engine has been completed by means of the formalized description.

  12. Automatic generation of 2D micromechanical finite element model of silicon–carbide/aluminum metal matrix composites: Effects of the boundary conditions

    DEFF Research Database (Denmark)

    Qing, Hai

    2013-01-01

    for the automatic generation of 2D micromechanical FE-models with randomly distributed SiC particles. In order to simulate the damage process in aluminum alloy matrix and SiC particles, a damage parameter based on the stress triaxial indicator and the maximum principal stress criterion based elastic brittle damage...... are performed to study the influence of boundary condition, particle number and volume fraction of the representative volume element (RVE) on composite stiffness and strength properties....

  13. Quality of Data Driven Simulation Workflows

    Directory of Open Access Journals (Sweden)

    Michael Reiter

    2014-01-01

    Full Text Available Simulations are long-running computations driven by non-trivial data dependencies. Workflow technology helps to automate these simulations and enable using Quality of Data (QoD frameworks to determine the goodness of simulation data. However, existing frameworks are specific to scientific domains, individual applications, or proprietary workflow engine extensions. In this paper, we propose a generic approach to use QoD as a uniform means to steer complex interdisciplinary simulations implemented as workflows. The approach enables scientists to specify abstract QoD requirements that are considered to steer the workflow for ensuring a precise final result. To realize these Quality of Data-driven workflows, we present a middleware architecture and a WS-Policy-based language to describe QoD requirements and capabilities. To prove technical feasibility, we present a prototype for controlling and steering simulation workflows and a real world simulation scenario.

  14. Enabling adaptive scientific workflows via trigger detection

    OpenAIRE

    Salloum, Maher; Bennett, Janine C.; PINAR, Ali; Bhagatwala, Ankit; Chen, Jacqueline H.

    2015-01-01

    Next generation architectures necessitate a shift away from traditional workflows in which the simulation state is saved at prescribed frequencies for post-processing analysis. While the need to shift to in~situ workflows has been acknowledged for some time, much of the current research is focused on static workflows, where the analysis that would have been done as a post-process is performed concurrently with the simulation at user-prescribed frequencies. Recently, research efforts are striv...

  15. Integration of services into workflow applications

    CERN Document Server

    Czarnul, Pawel

    2015-01-01

    Describing state-of-the-art solutions in distributed system architectures, Integration of Services into Workflow Applications presents a concise approach to the integration of loosely coupled services into workflow applications. It discusses key challenges related to the integration of distributed systems and proposes solutions, both in terms of theoretical aspects such as models and workflow scheduling algorithms, and technical solutions such as software tools and APIs.The book provides an in-depth look at workflow scheduling and proposes a way to integrate several different types of services

  16. VO-compliant workflows and science gateways

    Science.gov (United States)

    Castelli, G.; Taffoni, G.; Sciacca, E.; Becciani, U.; Costa, A.; Krokos, M.; Pasian, F.; Vuerli, C.

    2015-06-01

    Workflow and science gateway technologies have been adopted by scientific communities as a valuable tool to carry out complex experiments. They offer the possibility to perform computations for data analysis and simulations, whereas hiding details of the complex infrastructures underneath. There are many workflow management systems covering a large variety of generic services coordinating execution of workflows. In this paper we describe our experiences in creating workflows oriented science gateways based on gUSE/WS-PGRADE technology and in particular we discuss the efforts devoted to develop a VO-compliant web environment.

  17. Pro WF Windows Workflow in NET 40

    CERN Document Server

    Bukovics, Bruce

    2010-01-01

    Windows Workflow Foundation (WF) is a revolutionary part of the .NET 4 Framework that allows you to orchestrate human and system interactions as a series of workflows that can be easily mapped, analyzed, adjusted, and implemented. As business problems become more complex, the need for workflow-based solutions has never been more evident. WF provides a simple and consistent way to model and implement complex problems. As a developer, you focus on developing the business logic for individual workflow tasks. The runtime handles the execution of those tasks after they have been composed into a wor

  18. The standard-based open workflow system in GeoBrain (Invited)

    Science.gov (United States)

    Di, L.; Yu, G.; Zhao, P.; Deng, M.

    2013-12-01

    GeoBrain is an Earth science Web-service system developed and operated by the Center for Spatial Information Science and Systems, George Mason University. In GeoBrain, a standard-based open workflow system has been implemented to accommodate the automated processing of geospatial data through a set of complex geo-processing functions for advanced production generation. The GeoBrain models the complex geoprocessing at two levels, the conceptual and concrete. At the conceptual level, the workflows exist in the form of data and service types defined by ontologies. The workflows at conceptual level are called geo-processing models and cataloged in GeoBrain as virtual product types. A conceptual workflow is instantiated into a concrete, executable workflow when a user requests a product that matches a virtual product type. Both conceptual and concrete workflows are encoded in Business Process Execution Language (BPEL). A BPEL workflow engine, called BPELPower, has been implemented to execute the workflow for the product generation. A provenance capturing service has been implemented to generate the ISO 19115-compliant complete product provenance metadata before and after the workflow execution. The generation of provenance metadata before the workflow execution allows users to examine the usability of the final product before the lengthy and expensive execution takes place. The three modes of workflow executions defined in the ISO 19119, transparent, translucent, and opaque, are available in GeoBrain. A geoprocessing modeling portal has been developed to allow domain experts to develop geoprocessing models at the type level with the support of both data and service/processing ontologies. The geoprocessing models capture the knowledge of the domain experts and are become the operational offering of the products after a proper peer review of models is conducted. An automated workflow composition has been experimented successfully based on ontologies and artificial

  19. Workflow Patterns for Business Process Modeling

    NARCIS (Netherlands)

    Thom, Lucineia Heloisa; Lochpe, Cirano; Reichert, Manfred

    2007-01-01

    For its reuse advantages, workflow patterns (e.g., control flow patterns, data patterns, resource patterns) are increasingly attracting the interest of both researchers and vendors. Frequently, business process or workflow models can be assembeled out of a set of recurrent process fragments (or recu

  20. Workflow Planning and Execution - Final Results

    Directory of Open Access Journals (Sweden)

    Ravikant Dewangan

    2016-01-01

    Full Text Available An abstract workflow generation is choosing and configuring with application components to form an abstract workflow. The application components are chosen by examining the specification of their capabilities and checking to see if they can generate the desired data products. They are configured by assigning input files that exist or that may be generated by other application components. The abstract workflow specifies the order in which the components must be executed. A concrete workflow generation is selecting specific resources, files, and additional jobs required to form a concrete workflow that can be executed in the Grid environment. In order to generate a concrete workflow, each component in the abstract workflow is turned into an executable job by specifying the locations of the physical files of the component and data, as well as the resources assigned to the component in the execution environment. Additional jobs may be included in the concrete workflow, for example, jobs that transfer files to the appropriate locations where resources are available to execute the application components.

  1. Contracts for Cross-Organizational Workflow Management

    NARCIS (Netherlands)

    Koetsier, M.; Grefen, P.; Vonk, J.

    1999-01-01

    Nowadays, many organizations form dynamic partnerships to deal effectively with market requirements. As companies use automated workflow systems to control their processes, a way of linking workflow processes in different organizations is useful in turning the co-operating companies into a seamless

  2. Implementing bioinformatic workflows within the bioextract server

    Science.gov (United States)

    Computational workflows in bioinformatics are becoming increasingly important in the achievement of scientific advances. These workflows typically require the integrated use of multiple, distributed data sources and analytic tools. The BioExtract Server (http://bioextract.org) is a distributed servi...

  3. Metaworkflows and Workflow Interoperability for Heliophysics

    Science.gov (United States)

    Pierantoni, Gabriele; Carley, Eoin P.

    2014-06-01

    Heliophysics is a relatively new branch of physics that investigates the relationship between the Sun and the other bodies of the solar system. To investigate such relationships, heliophysicists can rely on various tools developed by the community. Some of these tools are on-line catalogues that list events (such as Coronal Mass Ejections, CMEs) and their characteristics as they were observed on the surface of the Sun or on the other bodies of the Solar System. Other tools offer on-line data analysis and access to images and data catalogues. During their research, heliophysicists often perform investigations that need to coordinate several of these services and to repeat these complex operations until the phenomena under investigation are fully analyzed. Heliophysicists combine the results of these services; this service orchestration is best suited for workflows. This approach has been investigated in the HELIO project. The HELIO project developed an infrastructure for a Virtual Observatory for Heliophysics and implemented service orchestration using TAVERNA workflows. HELIO developed a set of workflows that proved to be useful but lacked flexibility and re-usability. The TAVERNA workflows also needed to be executed directly in TAVERNA workbench, and this forced all users to learn how to use the workbench. Within the SCI-BUS and ER-FLOW projects, we have started an effort to re-think and re-design the heliophysics workflows with the aim of fostering re-usability and ease of use. We base our approach on two key concepts, that of meta-workflows and that of workflow interoperability. We have divided the produced workflows in three different layers. The first layer is Basic Workflows, developed both in the TAVERNA and WS-PGRADE languages. They are building blocks that users compose to address their scientific challenges. They implement well-defined Use Cases that usually involve only one service. The second layer is Science Workflows usually developed in TAVERNA. They

  4. Using Mobile Agents to Implement Workflow System

    Institute of Scientific and Technical Information of China (English)

    LI Jie; LIU Xian-xing; GUO Zheng-wei

    2004-01-01

    Current workflow management systems usually adopt the existing technologies such as TCP/IP-based Web technologies and CORBA as well to fulfill the bottom communications.Very often it has been considered only from a theoretical point of view, mainly for the lack of concrete possibilities to execute with elasticity.MAT (Mobile Agent Technology) represents a very attractive approach to the distributed control of computer networks and a valid alternative to the implementation of strategies for workflow system.This paper mainly focuses on improving the performance of workflow system by using MAT.Firstly, the performances of workflow systems based on both CORBA and mobile agent are summarized and analyzed; Secondly, the performance contrast is presented by introducing the mathematic model of each kind of data interaction process respectively.Last, a mobile agent-based workflow system named MAWMS is presented and described in detail.

  5. Workflow Management in CLARIN-DK

    DEFF Research Database (Denmark)

    Jongejan, Bart

    2013-01-01

    output, given the input resource at hand. Still, in such cases it may be possible to reach the set goal by chaining a number of tools. The approach presented here frees the user of having to meddle with tools and the construction of workflows. Instead, the user only needs to supply the workflow manager......The CLARIN-DK infrastructure is not only a repository of resources, but also a place where users can analyse, annotate, reformat and potentially even translate resources, using tools that are integrated in the infrastructure as web services. In many cases a single tool does not produce the desired...... with the features that describe her goal, because the workflow manager not only executes chains of tools in a workflow, but also takes care of autonomously devising workflows that serve the user’s intention, given the tools that currently are integrated in the infrastructure as web services. To do this...

  6. Implementation of WPDL Conforming Workflow Model

    Institute of Scientific and Technical Information of China (English)

    张志君; 范玉顺

    2003-01-01

    Workflow process definition language (WPDL) facilitates the transfer of workflow process definitions between separate workflow products. However, much work is still needed to transfer the specific workflow model to a WPDL conforming model. CIMFlow is a workflow management system developed by the National CIMS Engineering Research Center. This paper discusses the methods by which the CIMFlow model conforms to the WPDL meta-model and the differences between the WPDL meta-model and the CIMFlow model. Some improvements are proposed for the WPDL specification. Finally, the mapping and translating methods between the entities and attributes are given for the two models. The proposed methods and improvements are valuable as a reference for other mapping applications and the WPDL specification.

  7. CSP for Executable Scientific Workflows

    DEFF Research Database (Denmark)

    Friborg, Rune Møllegaard

    and can usually benefit performance-wise from both multiprocessing, cluster and grid environments. PyCSP is an implementation of Communicating Sequential Processes (CSP) for the Python programming language and takes advantage of CSP's formal and verifiable approach to controlling concurrency...... and the readability of Python source code. Python is a popular programming language in the scientific community, with many scientific libraries (modules) and simple integration to external languages. This thesis presents a PyCSP extended with many new features and a more robust implementation to allow scientific...... is demonstrated through examples. By providing a robust library for organising scientific workflows in a Python application I hope to inspire scientific users to adopt PyCSP. As a proof-of-concept this thesis demonstrates three scientific applications: kNN, stochastic minimum search and McStas to scale well...

  8. Workflow Tools for Digital Curation

    Directory of Open Access Journals (Sweden)

    Andrew James Weidner

    2013-04-01

    Full Text Available Maintaining usable and sustainable digital collections requires a complex set of actions that address the many challenges at various stages of the digital object lifecycle. Digital curation activities enhance access and retrieval, maintain quality, add value, and facilitate use and re-use over time. Digital resource lifecycle management is becoming an increasingly important topic as digital curators actively explore software tools that perform metadata curation and file management tasks. Accordingly, the University of North Texas (UNT Libraries develop tools and workflows that streamline production and quality assurance activities. This article demonstrates two open source software tools, AutoHotkey and Selenium IDE, which the UNT Digital Libraries Division has adopted for use during the pre-ingest and post-ingest stages of the digital resource lifecycle.

  9. Dynamic reusable workflows for ocean science

    Science.gov (United States)

    Signell, Richard; Fernandez, Filipe; Wilcox, Kyle

    2016-01-01

    Digital catalogs of ocean data have been available for decades, but advances in standardized services and software for catalog search and data access make it now possible to create catalog-driven workflows that automate — end-to-end — data search, analysis and visualization of data from multiple distributed sources. Further, these workflows may be shared, reused and adapted with ease. Here we describe a workflow developed within the US Integrated Ocean Observing System (IOOS) which automates the skill-assessment of water temperature forecasts from multiple ocean forecast models, allowing improved forecast products to be delivered for an open water swim event. A series of Jupyter Notebooks are used to capture and document the end-to-end workflow using a collection of Python tools that facilitate working with standardized catalog and data services. The workflow first searches a catalog of metadata using the Open Geospatial Consortium (OGC) Catalog Service for the Web (CSW), then accesses data service endpoints found in the metadata records using the OGC Sensor Observation Service (SOS) for in situ sensor data and OPeNDAP services for remotely-sensed and model data. Skill metrics are computed and time series comparisons of forecast model and observed data are displayed interactively, leveraging the capabilities of modern web browsers. The resulting workflow not only solves a challenging specific problem, but highlights the benefits of dynamic, reusable workflows in general. These workflows adapt as new data enters the data system, facilitate reproducible science, provide templates from which new scientific workflows can be developed, and encourage data providers to use standardized services. As applied to the ocean swim event, the workflow exposed problems with two of the ocean forecast products which led to improved regional forecasts once errors were corrected. While the example is specific, the approach is general, and we hope to see increased use of dynamic

  10. Provenance-Based Debugging and Drill-Down in Data-Oriented Workflows

    KAUST Repository

    Ikeda, Robert

    2012-04-01

    Panda (for Provenance and Data) is a system that supports the creation and execution of data-oriented workflows, with automatic provenance generation and built-in provenance tracing operations. Workflows in Panda are arbitrary a cyclic graphs containing both relational (SQL) processing nodes and opaque processing nodes programmed in Python. For both types of nodes, Panda generates logical provenance - provenance information stored at the processing-node level - and uses the generated provenance to support record-level backward tracing and forward tracing operations. In our demonstration we use Panda to integrate, process, and analyze actual education data from multiple sources. We specifically demonstrate how Panda\\'s provenance generation and tracing capabilities can be very useful for workflow debugging, and for drilling down on specific results of interest. © 2012 IEEE.

  11. Taverna Workflows in the Virtual Observatory

    Science.gov (United States)

    Benson, K.; Cecconi, B.

    2015-12-01

    Taverna workflows used in the Virtual ObservatoryPlanetary and Solar applications developed over the last decade generate dataat a previously unimaginable scale. One of these programmes which builds on the strengths of IDIS of Europlanet FP7, is the Virtual European Solar and Planetary Access (VESPA). With VESPA more data will be distributed and the connectivity of tools and infrastructure willimprove. VESPA enables growth of the user and provider community. However the challenge of connectivity persist throughout applications data services. VESPA calls are formed in part by tools and interactions services. One such tool and interaction service is the Taverna workflow management system. Workflows allow to address the challenges of data interconnectivity by establishing pipeline to services offered by other data streaming services. Workflows offer the capability to cross domains and overome interoperability issues. Furthermore, Taverna offers sharing of workflows; academic community 'myExperiment', a social site for scientists, supports search and opens access to pre existing workflows. This presentation focuses on cross domain workflows including use of the infrastructure setup with Helio, EUROPLANET and VAMDC projects. Hands on demonstration and an opportunity to join the community discussion will make the presentation more interactive

  12. Cloud-based bioinformatics workflow platform for large-scale next-generation sequencing analyses.

    Science.gov (United States)

    Liu, Bo; Madduri, Ravi K; Sotomayor, Borja; Chard, Kyle; Lacinski, Lukasz; Dave, Utpal J; Li, Jianqiang; Liu, Chunchen; Foster, Ian T

    2014-06-01

    Due to the upcoming data deluge of genome data, the need for storing and processing large-scale genome data, easy access to biomedical analyses tools, efficient data sharing and retrieval has presented significant challenges. The variability in data volume results in variable computing and storage requirements, therefore biomedical researchers are pursuing more reliable, dynamic and convenient methods for conducting sequencing analyses. This paper proposes a Cloud-based bioinformatics workflow platform for large-scale next-generation sequencing analyses, which enables reliable and highly scalable execution of sequencing analyses workflows in a fully automated manner. Our platform extends the existing Galaxy workflow system by adding data management capabilities for transferring large quantities of data efficiently and reliably (via Globus Transfer), domain-specific analyses tools preconfigured for immediate use by researchers (via user-specific tools integration), automatic deployment on Cloud for on-demand resource allocation and pay-as-you-go pricing (via Globus Provision), a Cloud provisioning tool for auto-scaling (via HTCondor scheduler), and the support for validating the correctness of workflows (via semantic verification tools). Two bioinformatics workflow use cases as well as performance evaluation are presented to validate the feasibility of the proposed approach.

  13. The design of cloud workflow systems

    CERN Document Server

    Liu, Xiao; Zhang, Gaofeng

    2011-01-01

    Cloud computing is the latest market-oriented computing paradigm which brings software design and development into a new era characterized by ""XaaS"", i.e. everything as a service. Cloud workflows, as typical software applications in the cloud, are composed of a set of partially ordered cloud software services to achieve specific goals. However, due to the low QoS (quality of service) nature of the cloud environment, the design of workflow systems in the cloud becomes a challenging issue for the delivery of high quality cloud workflow applications. To address such an issue, this book presents

  14. Application of workflow technology for workshop scheduling

    Institute of Scientific and Technical Information of China (English)

    ZHOU Wan-kun; ZHU Jian-ying

    2005-01-01

    This paper attempts to solve the complexity of scheduling problems and meet the requirement of the ever-changing manufacturing environment. In this paper, a new Workflow-Based Scheduling System (WBSS) is proposed. The integration of Workflow Management System (WfMS) and rule-based scheduler provides us an effective way of generating a task-sheet according to the states of system and the scheduled objects. First, the definition of workflow model for scheduling is proposed, and following are the architecture and mechanism of the proposed WBSS. At last, an application is given to show how the established system works.

  15. Towards a Pattern-based Automatic Generation of Logical Specifications for Software Models

    OpenAIRE

    Klimek, Radoslaw

    2014-01-01

    The work relates to the automatic generation of logical specifications, considered as sets of temporal logic formulas, extracted directly from developed software models. The extraction process is based on the assumption that the whole developed model is structured using only predefined workflow patterns. A method of automatic transformation of workflow patterns to logical specifications is proposed. Applying the presented concepts enables bridging the gap between the benefits of deductive rea...

  16. Reactive workflows for visual analytics

    OpenAIRE

    Manolescu, Ioana; Khemiri, Wael; Benzaken, Veronique; Fekete, Jean-Daniel

    2009-01-01

    The increasing amounts of electronic data of all forms, produced by humans (e.g. Web pages, structured content such as Wikipedia or the blogosphere etc.) and/or automatic tools (loggers, sensors, Web services, scientific tools etc.) leads to a situation of unprecedented potential for extracting new knowledge, finding new correlations etc. Typically, such analysis is performed by using data visualization techniques, and data analysis programs, which perform potentially complex and/or time-cons...

  17. A practical data processing workflow for multi-OMICS projects.

    Science.gov (United States)

    Kohl, Michael; Megger, Dominik A; Trippler, Martin; Meckel, Hagen; Ahrens, Maike; Bracht, Thilo; Weber, Frank; Hoffmann, Andreas-Claudius; Baba, Hideo A; Sitek, Barbara; Schlaak, Jörg F; Meyer, Helmut E; Stephan, Christian; Eisenacher, Martin

    2014-01-01

    Multi-OMICS approaches aim on the integration of quantitative data obtained for different biological molecules in order to understand their interrelation and the functioning of larger systems. This paper deals with several data integration and data processing issues that frequently occur within this context. To this end, the data processing workflow within the PROFILE project is presented, a multi-OMICS project that aims on identification of novel biomarkers and the development of new therapeutic targets for seven important liver diseases. Furthermore, a software called CrossPlatformCommander is sketched, which facilitates several steps of the proposed workflow in a semi-automatic manner. Application of the software is presented for the detection of novel biomarkers, their ranking and annotation with existing knowledge using the example of corresponding Transcriptomics and Proteomics data sets obtained from patients suffering from hepatocellular carcinoma. Additionally, a linear regression analysis of Transcriptomics vs. Proteomics data is presented and its performance assessed. It was shown, that for capturing profound relations between Transcriptomics and Proteomics data, a simple linear regression analysis is not sufficient and implementation and evaluation of alternative statistical approaches are needed. Additionally, the integration of multivariate variable selection and classification approaches is intended for further development of the software. Although this paper focuses only on the combination of data obtained from quantitative Proteomics and Transcriptomics experiments, several approaches and data integration steps are also applicable for other OMICS technologies. Keeping specific restrictions in mind the suggested workflow (or at least parts of it) may be used as a template for similar projects that make use of different high throughput techniques. This article is part of a Special Issue entitled: Computational Proteomics in the Post

  18. Workflow Optimization in Vertebrobasilar Occlusion

    International Nuclear Information System (INIS)

    Objective: In vertebrobasilar occlusion, rapid recanalization is the only substantial means to improve the prognosis. We introduced a standard operating procedure (SOP) for interventional therapy to analyze the effects on interdisciplinary time management. Methods: Intrahospital time periods between hospital admission and neuroradiological intervention were retrospectively analyzed, together with the patients’ outcome, before (n = 18) and after (n = 20) implementation of the SOP. Results: After implementation of the SOP, we observed statistically significant improvement of postinterventional patient neurological status (p = 0.017). In addition, we found a decrease of 5:33 h for the mean time period from hospital admission until neuroradiological intervention. The recanalization rate increased from 72.2% to 80% after implementation of the SOP. Conclusion: Our results underscore the relevance of SOP implementation and analysis of time management for clinical workflow optimization. Both may trigger awareness for the need of efficient interdisciplinary time management. This could be an explanation for the decreased time periods and improved postinterventional patient status after SOP implementation.

  19. Security aspects in teleradiology workflow

    Science.gov (United States)

    Soegner, Peter I.; Helweg, Gernot; Holzer, Heimo; zur Nedden, Dieter

    2000-05-01

    The medicolegal necessity of privacy, security and confidentiality was the aim of the attempt to develop a secure teleradiology workflow between the telepartners -- radiologist and the referring physician. To avoid the lack of dataprotection and datasecurity we introduced biometric fingerprint scanners in combination with smart cards to identify the teleradiology partners and communicated over an encrypted TCP/IP satellite link between Innsbruck and Reutte. We used an asymmetric kryptography method to guarantee authentification, integrity of the data-packages and confidentiality of the medical data. It was necessary to use a biometric feature to avoid a case of mistaken identity of persons, who wanted access to the system. Only an invariable electronical identification allowed a legal liability to the final report and only a secure dataconnection allowed the exchange of sensible medical data between different partners of Health Care Networks. In our study we selected the user friendly combination of a smart card and a biometric fingerprint technique, called SkymedTM Double Guard Secure Keyboard (Agfa-Gevaert) to confirm identities and log into the imaging workstations and the electronic patient record. We examined the interoperability of the used software with the existing platforms. Only the WIN-XX operating systems could be protected at the time of our study.

  20. Workflow Management in Occupational Medicine Using the Simple Workflow Access Protocol (SWAP)

    OpenAIRE

    McClay, James

    2001-01-01

    There are over nine million reported work related injuries a year administered through the workers compensation system. Workers compensation requires extensive communication with employers and payers. Workflow automation tools exist in segments of the industry but there isn't a common communication system. The Internet Engineering Task Force (IETF) Working Group on Simple Workflow Access Protocol (SWAP) is addressing the specifications for workflow across the Internet. We are adapting these p...

  1. Geospatially Constrained Workflow Modeling and Implementation

    Directory of Open Access Journals (Sweden)

    Feng Zhang

    2016-05-01

    Full Text Available With rapid development and application of mobile internet, geographic information in the field of business process is now more widely used. There are more and more researches in the field of the relationships between geographic information and workflow modeling. According to the workflow with geospatial constraints, this paper first discusses the geospatial constraints theory deeply, proposes a new concept of geospatial constraints unit, and then designs a geospatial constraint net model (GCNet. Secondly, this paper designs a new workflow model with geospatial constraints (GCWF-net based on GCNet and workflow net (WF-net, and then analyzes some properties of the model. Finally, this paper discusses how to put GCWF-net into application practice from three aspects: extending PNML (Petri Net Markup Language labels for GCWF-net, converting PNML to BPEL (Business Process Execution Language and implementing BPEL.

  2. Workflow Based Software Development Environment Project

    Data.gov (United States)

    National Aeronautics and Space Administration — The goal of this proposed research is to investigate and develop a workflow based tool, the Software Developers Assistant, to facilitate the collaboration between...

  3. Workflow Patterns for Business Process Modeling

    OpenAIRE

    Thom, Lucineia Heloisa; Lochpe, Cirano; Reichert, Manfred

    2007-01-01

    For its reuse advantages, workflow patterns (e.g., control flow patterns, data patterns, resource patterns) are increasingly attracting the interest of both researchers and vendors. Frequently, business process or workflow models can be assembeled out of a set of recurrent process fragments (or recurrent business functions), each of them having generic semantics that can be described as a pattern. To our best knowledge, so far, there has been no (empirical) work evidencing the existence of su...

  4. Proof-of-concept engineering workflow demonstrator

    OpenAIRE

    Molinari, M; Cox, SJ; Takeda, K.

    2006-01-01

    When Microsoft needed a proof-of-concept implementation of bespoke engineering workflow software for their customer, BAE Systems, it called on the software engineering skills and experience of the Microsoft Institute for High Performance Computing. BAE Systems was looking into converting their in-house SOLAR software suite to run on the MS Compute Cluster Server product with 64-bit MPI support in conjunction with an extended Windows Workflow environment for use by their engineers

  5. Automatic sequences

    CERN Document Server

    Haeseler, Friedrich

    2003-01-01

    Automatic sequences are sequences which are produced by a finite automaton. Although they are not random they may look as being random. They are complicated, in the sense of not being not ultimately periodic, they may look rather complicated, in the sense that it may not be easy to name the rule by which the sequence is generated, however there exists a rule which generates the sequence. The concept automatic sequences has special applications in algebra, number theory, finite automata and formal languages, combinatorics on words. The text deals with different aspects of automatic sequences, in particular:· a general introduction to automatic sequences· the basic (combinatorial) properties of automatic sequences· the algebraic approach to automatic sequences· geometric objects related to automatic sequences.

  6. Multilevel Workflow System in the ATLAS Experiment

    CERN Document Server

    Borodin, M; The ATLAS collaboration; Golubkov, D; Klimentov, A; Maeno, T; Vaniachine, A

    2015-01-01

    The ATLAS experiment is scaling up Big Data processing for the next LHC run using a multilevel workflow system comprised of many layers. In Big Data processing ATLAS deals with datasets, not individual files. Similarly a task (comprised of many jobs) has become a unit of the ATLAS workflow in distributed computing, with about 0.8M tasks processed per year. In order to manage the diversity of LHC physics (exceeding 35K physics samples per year), the individual data processing tasks are organized into workflows. For example, the Monte Carlo workflow is composed of many steps: generate or configure hard-processes, hadronize signal and minimum-bias (pileup) events, simulate energy deposition in the ATLAS detector, digitize electronics response, simulate triggers, reconstruct data, convert the reconstructed data into ROOT ntuples for physics analysis, etc. Outputs are merged and/or filtered as necessary to optimize the chain. The bi-level workflow manager - ProdSys2 - generates actual workflow tasks and their jobs...

  7. Multilevel Workflow System in the ATLAS Experiment

    CERN Document Server

    Borodin, M; The ATLAS collaboration; De, K; Golubkov, D; Klimentov, A; Maeno, T; Vaniachine, A

    2014-01-01

    The ATLAS experiment is scaling up Big Data processing for the next LHC run using a multilevel workflow system comprised of many layers. In Big Data processing ATLAS deals with datasets, not individual files. Similarly a task (comprised of many jobs) has become a unit of the ATLAS workflow in distributed computing, with about 0.8M tasks processed per year. In order to manage the diversity of LHC physics (exceeding 35K physics samples per year), the individual data processing tasks are organized into workflows. For example, the Monte Carlo workflow is composed of many steps: generate or configure hard-processes, hadronize signal and minimum-bias (pileup) events, simulate energy deposition in the ATLAS detector, digitize electronics response, simulate triggers, reconstruct data, convert the reconstructed data into ROOT ntuples for physics analysis, etc. Outputs are merged and/or filtered as necessary to optimize the chain. The bi-level workflow manager - ProdSys2 - generates actual workflow tasks and their jobs...

  8. SHIWA Services for Workflow Creation and Sharing in Hydrometeorolog

    Science.gov (United States)

    Terstyanszky, Gabor; Kiss, Tamas; Kacsuk, Peter; Sipos, Gergely

    2014-05-01

    Researchers want to run scientific experiments on Distributed Computing Infrastructures (DCI) to access large pools of resources and services. To run these experiments requires specific expertise that they may not have. Workflows can hide resources and services as a virtualisation layer providing a user interface that researchers can use. There are many scientific workflow systems but they are not interoperable. To learn a workflow system and create workflows may require significant efforts. Considering these efforts it is not reasonable to expect that researchers will learn new workflow systems if they want to run workflows developed in other workflow systems. To overcome it requires creating workflow interoperability solutions to allow workflow sharing. The FP7 'Sharing Interoperable Workflow for Large-Scale Scientific Simulation on Available DCIs' (SHIWA) project developed the Coarse-Grained Interoperability concept (CGI). It enables recycling and sharing workflows of different workflow systems and executing them on different DCIs. SHIWA developed the SHIWA Simulation Platform (SSP) to implement the CGI concept integrating three major components: the SHIWA Science Gateway, the workflow engines supported by the CGI concept and DCI resources where workflows are executed. The science gateway contains a portal, a submission service, a workflow repository and a proxy server to support the whole workflow life-cycle. The SHIWA Portal allows workflow creation, configuration, execution and monitoring through a Graphical User Interface using the WS-PGRADE workflow system as the host workflow system. The SHIWA Repository stores the formal description of workflows and workflow engines plus executables and data needed to execute them. It offers a wide-range of browse and search operations. To support non-native workflow execution the SHIWA Submission Service imports the workflow and workflow engine from the SHIWA Repository. This service either invokes locally or remotely

  9. YesWorkflow: A User-Oriented, Language-Independent Tool for Recovering Workflow Information from Scripts

    OpenAIRE

    Timothy McPhillips; Tianhong Song; Tyler Kolisnik; Steve Aulenbach; Khalid Belhajjame; R Kyle Bocinsky; Yang Cao; James Cheney; Fernando Chirigati; Saumen Dey; Juliana Freire; Christopher Jones; James Hanken; Kintigh, Keith W.; Kohler, Timothy A.

    2015-01-01

    Scientific workflow management systems offer features for composing complex computational pipelines from modular building blocks, for executing the resulting automated workflows, and for recording the provenance of data products resulting from workflow runs. Despite the advantages such features provide, many automated workflows continue to be implemented and executed outside of scientific workflow systems due to the convenience and familiarity of scripting languages (such as Perl, Python, R, ...

  10. The PBase Scientific Workflow Provenance Repository

    Directory of Open Access Journals (Sweden)

    Víctor Cuevas-Vicenttín

    2014-10-01

    Full Text Available Scientific workflows and their supporting systems are becoming increasingly popular for compute-intensive and data-intensive scientific experiments. The advantages scientific workflows offer include rapid and easy workflow design, software and data reuse, scalable execution, sharing and collaboration, and other advantages that altogether facilitate “reproducible science”. In this context, provenance – information about the origin, context, derivation, ownership, or history of some artifact – plays a key role, since scientists are interested in examining and auditing the results of scientific experiments. However, in order to perform such analyses on scientific results as part of extended research collaborations, an adequate environment and tools are required. Concretely, the need arises for a repository that will facilitate the sharing of scientific workflows and their associated execution traces in an interoperable manner, also enabling querying and visualization. Furthermore, such functionality should be supported while taking performance and scalability into account. With this purpose in mind, we introduce PBase: a scientific workflow provenance repository implementing the ProvONE proposed standard, which extends the emerging W3C PROV standard for provenance data with workflow specific concepts. PBase is built on the Neo4j graph database, thus offering capabilities such as declarative and efficient querying. Our experiences demonstrate the power gained by supporting various types of queries for provenance data. In addition, PBase is equipped with a user friendly interface tailored for the visualization of scientific workflow provenance data, making the specification of queries and the interpretation of their results easier and more effective.

  11. Progress in digital color workflow understanding in the International Color Consortium (ICC) Workflow WG

    Science.gov (United States)

    McCarthy, Ann

    2006-01-01

    The ICC Workflow WG serves as the bridge between ICC color management technologies and use of those technologies in real world color production applications. ICC color management is applicable to and is used in a wide range of color systems, from highly specialized digital cinema color special effects to high volume publications printing to home photography. The ICC Workflow WG works to align ICC technologies so that the color management needs of these diverse use case systems are addressed in an open, platform independent manner. This report provides a high level summary of the ICC Workflow WG objectives and work to date, focusing on the ways in which workflow can impact image quality and color systems performance. The 'ICC Workflow Primitives' and 'ICC Workflow Patterns and Dimensions' workflow models are covered in some detail. Consider the questions, "How much of dissatisfaction with color management today is the result of 'the wrong color transformation at the wrong time' and 'I can't get to the right conversion at the right point in my work process'?" Put another way, consider how image quality through a workflow can be negatively affected when the coordination and control level of the color management system is not sufficient.

  12. YesWorkflow: A User-Oriented, Language-Independent Tool for Recovering Workflow Information from Scripts

    Directory of Open Access Journals (Sweden)

    Timothy McPhillips

    2015-02-01

    Full Text Available Scientific workflow management systems offer features for composing complex computational pipelines from modular building blocks, executing the resulting automated workflows, and recording the provenance of data products resulting from workflow runs. Despite the advantages such features provide, many automated workflows continue to be implemented and executed outside of scientific workflow systems due to the convenience and familiarity of scripting languages (such as Perl, Python, R, and MATLAB, and to the high productivity many scientists experience when using these languages. YesWorkflow is a set of software tools that aim to provide such users of scripting languages with many of the benefits of scientific workflow systems. YesWorkflow requires neither the use of a workflow engine nor the overhead of adapting code to run effectively in such a system. Instead, YesWorkflow enables scientists to annotate existing scripts with special comments that reveal the computational modules and dataflows otherwise implicit in these scripts. YesWorkflow tools extract and analyze these comments, represent the scripts in terms of entities based on the typical scientific workflow model, and provide graphical renderings of this workflow-like view of the scripts. Future version of YesWorkflow will also allow the prospective provenance of the data products of these scripts to be queried in ways similar to those available to users of scientific workflow systems.

  13. Wireless remote control clinical image workflow: utilizing a PDA for offsite distribution

    Science.gov (United States)

    Liu, Brent J.; Documet, Luis; Documet, Jorge; Huang, H. K.; Muldoon, Jean

    2004-04-01

    Last year we presented in RSNA an application to perform wireless remote control of PACS image distribution utilizing a handheld device such as a Personal Digital Assistant (PDA). This paper describes the clinical experiences including workflow scenarios of implementing the PDA application to route exams from the clinical PACS archive server to various locations for offsite distribution of clinical PACS exams. By utilizing this remote control application, radiologists can manage image workflow distribution with a single wireless handheld device without impacting their clinical workflow on diagnostic PACS workstations. A PDA application was designed and developed to perform DICOM Query and C-Move requests by a physician from a clinical PACS Archive to a CD-burning device for automatic burning of PACS data for the distribution to offsite. In addition, it was also used for convenient routing of historical PACS exams to the local web server, local workstations, and teleradiology systems. The application was evaluated by radiologists as well as other clinical staff who need to distribute PACS exams to offsite referring physician"s offices and offsite radiologists. An application for image workflow management utilizing wireless technology was implemented in a clinical environment and evaluated. A PDA application was successfully utilized to perform DICOM Query and C-Move requests from the clinical PACS archive to various offsite exam distribution devices. Clinical staff can utilize the PDA to manage image workflow and PACS exam distribution conveniently for offsite consultations by referring physicians and radiologists. This solution allows the radiologist to expand their effectiveness in health care delivery both within the radiology department as well as offisite by improving their clinical workflow.

  14. 一种基于ODE的服务组合自动化部署方案%An Automatic Deployment Scheme for Service Composition Based on ODE

    Institute of Scientific and Technical Information of China (English)

    金仙力; 杨庚

    2012-01-01

    通过对Apache ODE结构以及部署、执行BPEL流程的原理分析,提出一种Apache ODE引擎环境下服务组合的自动化部署方案.实例测试结果表明了该方案的可行性与有效性.%Based on the analysis of the structure and the deployment of Apache ODE and the principle of BPEL process execution, this paper proposes an automatic deployment scheme for service composition in the environment of Apache ODE engine. The results of example test show that this scheme is feasible and valid.

  15. Development and implementation of an automatic integration system for fibre optic sensors in the braiding process with the objective of online-monitoring of composite structures

    Science.gov (United States)

    Hufenbach, W.; Gude, M.; Czulak, A.; Kretschmann, Martin

    2014-04-01

    Increasing economic, political and ecological pressure leads to steadily rising percentage of modern processing and manufacturing processes for fibre reinforced polymers in industrial batch production. Component weights beneath a level achievable by classic construction materials, which lead to a reduced energy and cost balance during product lifetime, justify the higher fabrication costs. However, complex quality control and failure prediction slow down the substitution by composite materials. High-resolution fibre-optic sensors (FOS), due their low diameter, high measuring point density and simple handling, show a high applicability potential for an automated sensor-integration in manufacturing processes, and therefore the online monitoring of composite products manufactured in industrial scale. Integrated sensors can be used to monitor manufacturing processes, part tests as well as the component structure during product life cycle, which simplifies allows quality control during production and the optimization of single manufacturing processes.[1;2] Furthermore, detailed failure analyses lead to a enhanced understanding of failure processes appearing in composite materials. This leads to a lower wastrel number and products of a higher value and longer product life cycle, whereby costs, material and energy are saved. This work shows an automation approach for FOS-integration in the braiding process. For that purpose a braiding wheel has been supplemented with an appliance for automatic sensor application, which has been used to manufacture preforms of high-pressure composite vessels with FOS-networks integrated between the fibre layers. All following manufacturing processes (vacuum infiltration, curing) and component tests (quasi-static pressure test, programmed delamination) were monitored with the help of the integrated sensor networks. Keywords: SHM, high-pressure composite vessel, braiding, automated sensor integration, pressure test, quality control, optic

  16. Data intensive ATLAS workflows in the Cloud

    CERN Document Server

    Rzehorz, Gerhard Ferdinand; The ATLAS collaboration

    2016-01-01

    This contribution reports on the feasibility of executing data intensive workflows on Cloud infrastructures. In order to assess this, the metric ETC = Events/Time/Cost is formed, which quantifies the different workflow and infrastructure configurations that are tested against each other. In these tests ATLAS reconstruction Jobs are run, examining the effects of overcommitting (more parallel processes running than CPU cores available), scheduling (staggered execution) and scaling (number of cores). The desirability of commissioning storage in the cloud is evaluated, in conjunction with a simple analytical model of the system, and correlated with questions about the network bandwidth, caches and what kind of storage to utilise. In the end a cost/benefit evaluation of different infrastructure configurations and workflows is undertaken, with the goal to find the maximum of the ETC value

  17. Logical provenance in data-oriented workflows?

    KAUST Repository

    Ikeda, R.

    2013-04-01

    We consider the problem of defining, generating, and tracing provenance in data-oriented workflows, in which input data sets are processed by a graph of transformations to produce output results. We first give a new general definition of provenance for general transformations, introducing the notions of correctness, precision, and minimality. We then determine when properties such as correctness and minimality carry over from the individual transformations\\' provenance to the workflow provenance. We describe a simple logical-provenance specification language consisting of attribute mappings and filters. We provide an algorithm for provenance tracing in workflows where logical provenance for each transformation is specified using our language. We consider logical provenance in the relational setting, observing that for a class of Select-Project-Join (SPJ) transformations, logical provenance specifications encode minimal provenance. We have built a prototype system supporting the features and algorithms presented in the paper, and we report a few preliminary experimental results. © 2013 IEEE.

  18. Scientific Workflow Applications on Amazon EC2

    CERN Document Server

    Juve, Gideon; Vahi, Karan; Mehta, Gaurang; Berriman, Bruce; Berman, Benjamin P; Maechling, Phil

    2010-01-01

    The proliferation of commercial cloud computing providers has generated significant interest in the scientific computing community. Much recent research has attempted to determine the benefits and drawbacks of cloud computing for scientific applications. Although clouds have many attractive features, such as virtualization, on-demand provisioning, and "pay as you go" usage-based pricing, it is not clear whether they are able to deliver the performance required for scientific applications at a reasonable price. In this paper we examine the performance and cost of clouds from the perspective of scientific workflow applications. We use three characteristic workflows to compare the performance of a commercial cloud with that of a typical HPC system, and we analyze the various costs associated with running those workflows in the cloud. We find that the performance of clouds is not unreasonable given the hardware resources provided, and that performance comparable to HPC systems can be achieved given similar resour...

  19. Perti Net-Based Workflow Access Control Model

    Institute of Scientific and Technical Information of China (English)

    陈卓; 骆婷; 石磊; 洪帆

    2004-01-01

    Access control is an important protection mechanism for information systems. This paper shows how to make access control in workflow system. We give a workflow access control model (WACM) based on several current access control models. The model supports roles assignment and dynamic authorization. The paper defines the workflow using Petri net. It firstly gives the definition and description of the workflow, and then analyzes the architecture of the workflow access control model (WACM). Finally, an example of an e-commerce workflow access control model is discussed in detail.

  20. NeuroManager: A workflow analysis based simulation management engine for computational neuroscience

    Directory of Open Access Journals (Sweden)

    David Bruce Stockton

    2015-10-01

    Full Text Available We developed NeuroManager, an object-oriented simulation management software engine for computational neuroscience. NeuroManager automates the workflow of simulation job submissions when using heterogeneous computational resources, simulators, and simulation tasks. The object-oriented approach 1 provides flexibility to adapt to a variety of neuroscience simulators, 2 simplifies the use of heterogeneous computational resources, from desktops to super computer clusters, and 3 improves tracking of simulator/simulation evolution. We implemented NeuroManager in Matlab, a widely used engineering and scientific language, for its signal and image processing tools, prevalence in electrophysiology analysis, and increasing use in college Biology education. To design and develop NeuroManager we analyzed the workflow of simulation submission for a variety of simulators, operating systems, and computational resources, including the handling of input parameters, data, models, results, and analyses. This resulted in twenty-two stages of simulation submission workflow. The software incorporates progress notification, automatic organization, labeling, and time-stamping of data and results, and integrated access to Matlab's analysis and visualization tools. NeuroManager provides users with the tools to automate daily tasks, and assists principal investigators in tracking and recreating the evolution of research projects performed by multiple people. Overall, NeuroManager provides the infrastructure needed to improve workflow, manage multiple simultaneous simulations, and maintain provenance of the potentially large amounts of data produced during the course of a research project.

  1. A system for deduction-based formal verification of workflow-oriented software models

    Directory of Open Access Journals (Sweden)

    Klimek Radosław

    2014-12-01

    Full Text Available The work concerns formal verification of workflow-oriented software models using the deductive approach. The formal correctness of a model’s behaviour is considered. Manually building logical specifications, which are regarded as a set of temporal logic formulas, seems to be a significant obstacle for an inexperienced user when applying the deductive approach. A system, along with its architecture, for deduction-based verification of workflow-oriented models is proposed. The process inference is based on the semantic tableaux method, which has some advantages when compared with traditional deduction strategies. The algorithm for automatic generation of logical specifications is proposed. The generation procedure is based on predefined workflow patterns for BPMN, which is a standard and dominant notation for the modeling of business processes. The main idea behind the approach is to consider patterns, defined in terms of temporal logic, as a kind of (logical primitives which enable the transformation of models to temporal logic formulas constituting a logical specification. Automation of the generation process is crucial for bridging the gap between the intuitiveness of deductive reasoning and the difficulty of its practical application when logical specifications are built manually. This approach has gone some way towards supporting, hopefully enhancing, our understanding of deduction-based formal verification of workflow-oriented models.

  2. Designing Flexible E-Business Workflow Systems

    Directory of Open Access Journals (Sweden)

    Cătălin Silvestru

    2010-01-01

    Full Text Available In today’s business environment organizations must cope with complex interactions between actors adapt fast to frequent market changes and be innovative. In this context, integrating knowledge with processes and Business Intelligenceis a major step towards improving organization agility. Therefore, traditional environments for workflow design have been adapted to answer the new business models and current requirements in the field of collaborative processes. This paper approaches the design of flexible and dynamic workflow management systems for electronic businesses that can lead to agility.

  3. Workflow-Based Dynamic Enterprise Modeling

    Institute of Scientific and Technical Information of China (English)

    黄双喜; 范玉顺; 罗海滨; 林慧萍

    2002-01-01

    Traditional systems for enterprise modeling and business process control are often static and cannot adapt to the changing environment. This paper presents a workflow-based method to dynamically execute the enterprise model. This method gives an explicit representation of the business process logic and the relationships between the elements involved in the process. An execution-oriented integrated enterprise modeling system is proposed in combination with other enterprise views. The enterprise model can be established and executed dynamically in the actual environment due to the dynamic properties of the workflow model.

  4. RESTFul based heterogeneous Geoprocessing workflow interoperation for Sensor Web Service

    Science.gov (United States)

    Yang, Chao; Chen, Nengcheng; Di, Liping

    2012-10-01

    Advanced sensors on board satellites offer detailed Earth observations. A workflow is one approach for designing, implementing and constructing a flexible and live link between these sensors' resources and users. It can coordinate, organize and aggregate the distributed sensor Web services to meet the requirement of a complex Earth observation scenario. A RESTFul based workflow interoperation method is proposed to integrate heterogeneous workflows into an interoperable unit. The Atom protocols are applied to describe and manage workflow resources. The XML Process Definition Language (XPDL) and Business Process Execution Language (BPEL) workflow standards are applied to structure a workflow that accesses sensor information and one that processes it separately. Then, a scenario for nitrogen dioxide (NO2) from a volcanic eruption is used to investigate the feasibility of the proposed method. The RESTFul based workflows interoperation system can describe, publish, discover, access and coordinate heterogeneous Geoprocessing workflows.

  5. Creating Bioinformatic Workflows within the BioExtract Server

    Science.gov (United States)

    Computational workflows in bioinformatics are becoming increasingly important in the achievement of scientific advances. These workflows generally require access to multiple, distributed data sources and analytic tools. The requisite data sources may include large public data repositories, community...

  6. Adaptive workflow simulation of emergency response

    NARCIS (Netherlands)

    Bruinsma, Guido Wybe Jan

    2010-01-01

    Recent incidents and major training exercises in and outside the Netherlands have persistently shown that not having or not sharing information during emergency response are major sources of emergency response inefficiency and error, and affect incident mitigation outcomes through workflow planning

  7. Distributed interoperable workflow support for electronic commerce

    NARCIS (Netherlands)

    Papazoglou, M.; Jeusfeld, M.A.; Weigand, H.; Jarke, M.

    1998-01-01

    Abstract. This paper describes a flexible distributed transactional workflow environment based on an extensible object-oriented framework built around class libraries, application programming interfaces, and shared services. The purpose of this environment is to support a range of EC-like business a

  8. Soundness of Timed-Arc Workflow Nets

    DEFF Research Database (Denmark)

    Mateo, Jose Antonio; Srba, Jiri; Sørensen, Mathias Grund

    2014-01-01

    , we demonstrate the usability of our theory on the case studies of a Brake System Control Unit used in aircraft certification, the MPEG2 encoding algorithm, and a blood transfusion workflow. The implementation of the algorithms is freely available as a part of the model checker TAPAAL....

  9. Evolutionary optimization of production materials workflow processes

    DEFF Research Database (Denmark)

    Herbert, Luke Thomas; Hansen, Zaza Nadja Lee; Jacobsen, Peter;

    2014-01-01

    We present an evolutionary optimisation technique for stochastic production processes, which is able to find improved production materials workflow processes with respect to arbitrary combinations of numerical quantities associated with the production process. Working from a core fragment of the ...... where a baked goods company seeks to improve production time while simultaneously minimising the cost and use of resources....

  10. On Secure Workflow Decentralisation on the Internet

    Directory of Open Access Journals (Sweden)

    Petteri Kaskenpalo

    2010-06-01

    Full Text Available Decentralised workflow management systems are a new research area, where most work to-date has focused on the system's overall architecture. As little attention has been given to the security aspects in such systems, we follow a security driven approach, and consider, from the perspective of available security building blocks, how security can be implemented and what new opportunities are presented when empowering the decentralised environment with modern distributed security protocols. Our research is motivated by a more general question of how to combine the positive enablers that email exchange enjoys, with the general benefits of workflow systems, and more specifically with the benefits that can be introduced in a decentralised environment. This aims to equip email users with a set of tools to manage the semantics of a message exchange, contents, participants and their roles in the exchange in an environment that provides inherent assurances of security and privacy. This work is based on a survey of contemporary distributed security protocols, and considers how these protocols could be used in implementing a distributed workflow management system with decentralised control . We review a set of these protocols, focusing on the required message sequences in reviewing the protocols, and discuss how these security protocols provide the foundations for implementing core control-flow, data, and resource patterns in a distributed workflow environment.

  11. Workflow Automation: A Collective Case Study

    Science.gov (United States)

    Harlan, Jennifer

    2013-01-01

    Knowledge management has proven to be a sustainable competitive advantage for many organizations. Knowledge management systems are abundant, with multiple functionalities. The literature reinforces the use of workflow automation with knowledge management systems to benefit organizations; however, it was not known if process automation yielded…

  12. Evaluation of Workflow Management Systems - A Meta Model Approach

    OpenAIRE

    Michael Rosemann; Michael zur Muehlen

    1998-01-01

    The automated enactment of processes through the use of workflow management systems enables the outsourcing of the control flow from application systems. By now a large number of systems, that follow different workflow paradigms, are available. This leads to the problem of selecting the appropriate workflow management system for a given situation. In this paper we outline the benefits of a meta model approach for the evaluation and comparison of different workflow management systems. Af...

  13. From Requirements via Colored Workflow Nets to an Implementation in Several Workflow Systems

    DEFF Research Database (Denmark)

    Mans, Ronnie S:; van der Aalst, Wil M.P.; Bakker, Piet J.M.;

    2007-01-01

    Care organizations, such as hospitals, need to support complex and dynamic workflows. More- over, many disciplines are involved. This makes it important to avoid the typical disconnect between requirements and the actual implementation of the system. This paper proposes an approach where an Execu......Care organizations, such as hospitals, need to support complex and dynamic workflows. More- over, many disciplines are involved. This makes it important to avoid the typical disconnect between requirements and the actual implementation of the system. This paper proposes an approach where...... an Executable Use Case (EUC) and Colored Workflow Net (CWN) are used to close the gap between the given requirements specification and the realization of these requirements with the help of a workflow system. This paper describes a large case study where the diagnostic tra jectory of the gynaecological oncology...

  14. From Requirements via Colored Workflow Nets to an Implementation in Several Workflow Systems

    DEFF Research Database (Denmark)

    Mans, Ronny S.; van der Aalst, Willibrordus Martinus Pancratius; Molemann, A.J.;

    2007-01-01

    an Executable Use Case (EUC) and Colored Care organizations, such as hospitals, need to support complex and dynamic workflows. Moreover, many disciplines are involved. This makes it important to avoid the typical disconnect between requirements and the actual implementation of the system. This paper proposes......Care organizations, such as hospitals, need to support complex and dynamic workflows. More- over, many disciplines are involved. This makes it important to avoid the typical disconnect between requirements and the actual implementation of the system. This paper proposes an approach where...... an approach where an Executable Use Case (EUC) and Colored Workflow Net (CWN) are used to close the gap between the given requirements specification and the realization of these requirements with the help of a workflow system. This paper describes a large case study where the diagnostic trajectory...

  15. Understanding dental CAD/CAM for restorations--the digital workflow from a mechanical engineering viewpoint.

    Science.gov (United States)

    Tapie, L; Lebon, N; Mawussi, B; Fron Chabouis, H; Duret, F; Attal, J-P

    2015-01-01

    As digital technology infiltrates every area of daily life, including the field of medicine, so it is increasingly being introduced into dental practice. Apart from chairside practice, computer-aided design/computer-aided manufacturing (CAD/CAM) solutions are available for creating inlays, crowns, fixed partial dentures (FPDs), implant abutments, and other dental prostheses. CAD/CAM dental solutions can be considered a chain of digital devices and software for the almost automatic design and creation of dental restorations. However, dentists who want to use the technology often do not have the time or knowledge to understand it. A basic knowledge of the CAD/CAM digital workflow for dental restorations can help dentists to grasp the technology and purchase a CAM/CAM system that meets the needs of their office. This article provides a computer-science and mechanical-engineering approach to the CAD/CAM digital workflow to help dentists understand the technology. PMID:25911827

  16. From Data to Knowledge to Discoveries: Artificial Intelligence and Scientific Workflows

    Directory of Open Access Journals (Sweden)

    Yolanda Gil

    2009-01-01

    Full Text Available Scientific computing has entered a new era of scale and sharing with the arrival of cyberinfrastructure facilities for computational experimentation. A key emerging concept is scientific workflows, which provide a declarative representation of complex scientific applications that can be automatically managed and executed in distributed shared resources. In the coming decades, computational experimentation will push the boundaries of current cyberinfrastructure in terms of inter-disciplinary scope and integrative models of scientific phenomena under study. This paper argues that knowledge-rich workflow environments will provide necessary capabilities for that vision by assisting scientists to validate and vet complex analysis processes and by automating important aspects of scientific exploration and discovery.

  17. Workflows in bioinformatics: meta-analysis and prototype implementation of a workflow generator

    Directory of Open Access Journals (Sweden)

    Thoraval Samuel

    2005-04-01

    Full Text Available Abstract Background Computational methods for problem solving need to interleave information access and algorithm execution in a problem-specific workflow. The structures of these workflows are defined by a scaffold of syntactic, semantic and algebraic objects capable of representing them. Despite the proliferation of GUIs (Graphic User Interfaces in bioinformatics, only some of them provide workflow capabilities; surprisingly, no meta-analysis of workflow operators and components in bioinformatics has been reported. Results We present a set of syntactic components and algebraic operators capable of representing analytical workflows in bioinformatics. Iteration, recursion, the use of conditional statements, and management of suspend/resume tasks have traditionally been implemented on an ad hoc basis and hard-coded; by having these operators properly defined it is possible to use and parameterize them as generic re-usable components. To illustrate how these operations can be orchestrated, we present GPIPE, a prototype graphic pipeline generator for PISE that allows the definition of a pipeline, parameterization of its component methods, and storage of metadata in XML formats. This implementation goes beyond the macro capacities currently in PISE. As the entire analysis protocol is defined in XML, a complete bioinformatic experiment (linked sets of methods, parameters and results can be reproduced or shared among users. Availability: http://if-web1.imb.uq.edu.au/Pise/5.a/gpipe.html (interactive, ftp://ftp.pasteur.fr/pub/GenSoft/unix/misc/Pise/ (download. Conclusion From our meta-analysis we have identified syntactic structures and algebraic operators common to many workflows in bioinformatics. The workflow components and algebraic operators can be assimilated into re-usable software components. GPIPE, a prototype implementation of this framework, provides a GUI builder to facilitate the generation of workflows and integration of heterogeneous

  18. 基于流演算的Web服务自动组合方法%An Approach for Automatic Web Services Composition Based on Fluent Calculus

    Institute of Scientific and Technical Information of China (English)

    陈志勇; 李庆忠; 王文明; 崔立真; 丛国进

    2013-01-01

    近年来,基于语义的Web服务组合,尤其是Web服务的自动组合方法已成为服务计算领域的一个研究热点.实现了从一个OWL-S过程模型到流演算概念的映射,并给出了相应的转换算法.在此基础上,提出了一个新颖的、基于流演算形式化体系的Web服务自动组合方法.该方法采用前推推理机制对状态和动作进行推理,有效地克服了以传统的情景演算为代表的人工智能规划算法执行效率较低的问题.设计实现了一个实验性的原型系统,结合一个旅游行程规划的实例说明了本文提出的方法的有效性.对提出的BCABFC(Backward-Chaining Algorithm Based On Fluent Calculus)算法与基于情景演算的同类算法进行性能比较,实验结果表明该算法具有较好的性能.%In recent years, semantics-based Web Services composition, especially automated composition method has become popularity in the research area of Service Computing. This paper has identified a mapping between an OWL-S process ontology and the fluent calculus concepts. We present an algorithm to translate OWL-S service descriptions into an equivalent fluent calculus service specification. This paper presents a novel approach for automatic Web service composition method based on the formalism of fluent calculus. In our approach, the Web service composition process is viewed as an AI planning problem in the fluent calculus formalism. We show how the planning capabilities of the fluent calculus can be used to automatically generate an abstract composition model in terms of user personalized requests. This method applies the principle of progression for reasoning the status and action of the object. As a result, it brings a higher efficiency than traditional AI planning algorithms characterized by Situation Calculus. For testing our composition method, we have designed and implemented an experimental prototype and demonstrate its effectiveness with the help of an application

  19. Automatically varying the composition of a mixed refrigerant solution for single mixed refrigerant LNG (liquefied natural gas) process at changing working conditions

    International Nuclear Information System (INIS)

    The SMR (single mixed refrigerant) process is widely used in the small- and medium-scale liquefaction of NG (natural gas). Operating the MR (mixed-refrigerant) process outside of the design specifications is difficult but essential to save energy. Nevertheless, it is difficult to realize because the process needs to alter the working refrigerant composition. To address this challenge, this study investigated the performance diagnosis mechanism for SMR process. A control strategy was then proposed to control the changes in working refrigerant composition under different working conditions. This strategy separates the working refrigerant flow in the SMR process into three flows through two phase separators before it flows into the cold box. The first liquid flow is rich in the high-temperature component (isopentane). The second liquid flow is rich in the middle-temperature components (ethylene and propane), and the gas flow is rich in the low-temperature components (nitrogen and methane). By adjusting the flow rates, it is easy to decouple the control variables and automate the system. Finally, this approach was validated by process simulation and shown to be highly adaptive and exergy efficient in response to changing working conditions. - Highlights: • The performance diagnosis mechanism of SMR LNG process is studied. • A measure to automatically change the operation composition as per the working conditions is proposed for SMR process. • SMR process simulation is performed to verify the validity of the control solution. • The control solution notably improves the energy efficiency of SMR process at changing working condition

  20. 基于有向层次图的Web服务自动组合方法%Directed level graph-based approach to automatic Web services composition

    Institute of Scientific and Technical Information of China (English)

    冯兴杰; 王辉; 许亚娟

    2011-01-01

    To solve the problem of automatic Web services composition with multiple inputs/outputs, an approach based on directed level graph was proposed. It provided an optimal composition sequence through these steps as follows: 1) Built a directed level graph by inputs/outputs of user request; 2) Built a complete reduction graph of the directed level graph;3) Searched all reachable paths for every node of complete reduction graph; 4) Converted the optimal path for user request into services composition sequence. This approach can generate all composition sequences with least steps and an optimal composition sequence according to the quality of services. Compared with traditional graph-based approach, it reduces search space and avoids cycle searching and can be applied in a large scale of Web services repository.%为解决多输入/输出的Web服务自动组合问题,提出了基于有向层次图的Web服务自动组合方法,主要步骤如下:1)根据用户请求的输入/输出参数集生成有向层次图;2)在有向层次图中构造完全规约图;3)在完全规约图中计算每一顶点的所有可达路径;4)为用户请求选择最优路径,并转化为Web服务组合序列.该方法能够求得最短步数内的所有Web服务组合序列,根据Web服务的服务质量(QoS)获得最优的组合序列,从而满足多输入/输出的用户请求.与基于图的Web服务组合方法相比,减少了搜索空间,适用于大规模的Web服务库.

  1. Flexible workflow sharing and execution services for e-scientists

    Science.gov (United States)

    Kacsuk, Péter; Terstyanszky, Gábor; Kiss, Tamas; Sipos, Gergely

    2013-04-01

    The sequence of computational and data manipulation steps required to perform a specific scientific analysis is called a workflow. Workflows that orchestrate data and/or compute intensive applications on Distributed Computing Infrastructures (DCIs) recently became standard tools in e-science. At the same time the broad and fragmented landscape of workflows and DCIs slows down the uptake of workflow-based work. The development, sharing, integration and execution of workflows is still a challenge for many scientists. The FP7 "Sharing Interoperable Workflow for Large-Scale Scientific Simulation on Available DCIs" (SHIWA) project significantly improved the situation, with a simulation platform that connects different workflow systems, different workflow languages, different DCIs and workflows into a single, interoperable unit. The SHIWA Simulation Platform is a service package, already used by various scientific communities, and used as a tool by the recently started ER-flow FP7 project to expand the use of workflows among European scientists. The presentation will introduce the SHIWA Simulation Platform and the services that ER-flow provides based on the platform to space and earth science researchers. The SHIWA Simulation Platform includes: 1. SHIWA Repository: A database where workflows and meta-data about workflows can be stored. The database is a central repository to discover and share workflows within and among communities . 2. SHIWA Portal: A web portal that is integrated with the SHIWA Repository and includes a workflow executor engine that can orchestrate various types of workflows on various grid and cloud platforms. 3. SHIWA Desktop: A desktop environment that provides similar access capabilities than the SHIWA Portal, however it runs on the users' desktops/laptops instead of a portal server. 4. Workflow engines: the ASKALON, Galaxy, GWES, Kepler, LONI Pipeline, MOTEUR, Pegasus, P-GRADE, ProActive, Triana, Taverna and WS-PGRADE workflow engines are already

  2. Solutions for complex, multi data type and multi tool analysis: principles and applications of using workflow and pipelining methods.

    Science.gov (United States)

    Munro, Robin E J; Guo, Yike

    2009-01-01

    Analytical workflow technology, sometimes also called data pipelining, is the fundamental component that provides the scalable analytical middleware that can be used to enable the rapid building and deployment of an analytical application. Analytical workflows enable researchers, analysts and informaticians to integrate and access data and tools from structured and non-structured data sources so that analytics can bridge different silos of information; compose multiple analytical methods and data transformations without coding; rapidly develop applications and solutions by visually constructing analytical workflows that are easy to revise should the requirements change; access domain-specific extensions for specific projects or areas, for example, text extraction, visualisation, reporting, genetics, cheminformatics, bioinformatics and patient-based analytics; automatically deploy workflows directly into web portals and as web services to be part of a service-oriented architecture (SOA). By performing workflow building, using a middleware layer for data integration, it is a relatively simple exercise to visually design an analytical process for data analysis and then publish this as a service to a web browser. All this is encapsulated into what can be referred to as an 'Embedded Analytics' methodology which will be described here with examples covering different scientifically focused data analysis problems. PMID:19597790

  3. geoKepler Workflow Module for Computationally Scalable and Reproducible Geoprocessing and Modeling

    Science.gov (United States)

    Cowart, C.; Block, J.; Crawl, D.; Graham, J.; Gupta, A.; Nguyen, M.; de Callafon, R.; Smarr, L.; Altintas, I.

    2015-12-01

    The NSF-funded WIFIRE project has developed an open-source, online geospatial workflow platform for unifying geoprocessing tools and models for for fire and other geospatially dependent modeling applications. It is a product of WIFIRE's objective to build an end-to-end cyberinfrastructure for real-time and data-driven simulation, prediction and visualization of wildfire behavior. geoKepler includes a set of reusable GIS components, or actors, for the Kepler Scientific Workflow System (https://kepler-project.org). Actors exist for reading and writing GIS data in formats such as Shapefile, GeoJSON, KML, and using OGC web services such as WFS. The actors also allow for calling geoprocessing tools in other packages such as GDAL and GRASS. Kepler integrates functions from multiple platforms and file formats into one framework, thus enabling optimal GIS interoperability, model coupling, and scalability. Products of the GIS actors can be fed directly to models such as FARSITE and WRF. Kepler's ability to schedule and scale processes using Hadoop and Spark also makes geoprocessing ultimately extensible and computationally scalable. The reusable workflows in geoKepler can be made to run automatically when alerted by real-time environmental conditions. Here, we show breakthroughs in the speed of creating complex data for hazard assessments with this platform. We also demonstrate geoKepler workflows that use Data Assimilation to ingest real-time weather data into wildfire simulations, and for data mining techniques to gain insight into environmental conditions affecting fire behavior. Existing machine learning tools and libraries such as R and MLlib are being leveraged for this purpose in Kepler, as well as Kepler's Distributed Data Parallel (DDP) capability to provide a framework for scalable processing. geoKepler workflows can be executed via an iPython notebook as a part of a Jupyter hub at UC San Diego for sharing and reporting of the scientific analysis and results from

  4. Optimizing CyberShake Seismic Hazard Workflows for Large HPC Resources

    Science.gov (United States)

    Callaghan, S.; Maechling, P. J.; Juve, G.; Vahi, K.; Deelman, E.; Jordan, T. H.

    2014-12-01

    The CyberShake computational platform is a well-integrated collection of scientific software and middleware that calculates 3D simulation-based probabilistic seismic hazard curves and hazard maps for the Los Angeles region. Currently each CyberShake model comprises about 235 million synthetic seismograms from about 415,000 rupture variations computed at 286 sites. CyberShake integrates large-scale parallel and high-throughput serial seismological research codes into a processing framework in which early stages produce files used as inputs by later stages. Scientific workflow tools are used to manage the jobs, data, and metadata. The Southern California Earthquake Center (SCEC) developed the CyberShake platform using USC High Performance Computing and Communications systems and open-science NSF resources.CyberShake calculations were migrated to the NSF Track 1 system NCSA Blue Waters when it became operational in 2013, via an interdisciplinary team approach including domain scientists, computer scientists, and middleware developers. Due to the excellent performance of Blue Waters and CyberShake software optimizations, we reduced the makespan (a measure of wallclock time-to-solution) of a CyberShake study from 1467 to 342 hours. We will describe the technical enhancements behind this improvement, including judicious introduction of new GPU software, improved scientific software components, increased workflow-based automation, and Blue Waters-specific workflow optimizations.Our CyberShake performance improvements highlight the benefits of scientific workflow tools. The CyberShake workflow software stack includes the Pegasus Workflow Management System (Pegasus-WMS, which includes Condor DAGMan), HTCondor, and Globus GRAM, with Pegasus-mpi-cluster managing the high-throughput tasks on the HPC resources. The workflow tools handle data management, automatically transferring about 13 TB back to SCEC storage.We will present performance metrics from the most recent Cyber

  5. Applying direct observation to model workflow and assess adoption.

    Science.gov (United States)

    Unertl, Kim M; Weinger, Matthew B; Johnson, Kevin B

    2006-01-01

    Lack of understanding about workflow can impair health IT system adoption. Observational techniques can provide valuable information about clinical workflow. A pilot study using direct observation was conducted in an outpatient chronic disease clinic. The goals of the study were to assess workflow and information flow and to develop a general model of workflow and information behavior. Over 55 hours of direct observation showed that the pilot site utilized many of the features of the informatics systems available to them, but also employed multiple non-electronic artifacts and workarounds. Gaps existed between clinic workflow and informatics tool workflow, as well as between institutional expectations of informatics tool use and actual use. Concurrent use of both paper-based and electronic systems resulted in duplication of effort and inefficiencies. A relatively short period of direct observation revealed important information about workflow and informatics tool adoption.

  6. An ever-changing systemic environment for migrating workflows

    Science.gov (United States)

    Assimakopoulos, Nikitas A.

    2000-05-01

    In this paper we present the concept of the systemic and dynamic environment for migrating workflows, and the considerations related to the implementation of this concept. Migrating workflows are a computational metaphor for the way most people conduct their daily business: they visit a place, use a service (perhaps after some negotiation), and move on to the next place. A migrating workflow behaves similarly: it transfers its code (specification) and its execution state to a site, negotiates a service to be executed on its behalf, receives the results, and moves on. Dialog between the workflow and individual sites may influence the workflow's migration. Thus the actual workflow instance is defined during run-time, as an effect of merging the static workflow specification and the local site rules and policies.

  7. Evaluation of Workflow Management Systems - A Meta Model Approach

    Directory of Open Access Journals (Sweden)

    Michael Rosemann

    1998-11-01

    Full Text Available The automated enactment of processes through the use of workflow management systems enables the outsourcing of the control flow from application systems. By now a large number of systems, that follow different workflow paradigms, are available. This leads to the problem of selecting the appropriate workflow management system for a given situation. In this paper we outline the benefits of a meta model approach for the evaluation and comparison of different workflow management systems. After a general introduction on the topic of meta modeling the meta models of the workflow management systems WorkParty (Siemens Nixdorf and FlowMark (IBM are compared as an example. These product specific meta models can be generalized to meta reference models, which helps to specify a workflow methodology. Exemplary, an organisational reference meta model is presented, which helps users in specifying their requirements for a workflow management system.

  8. SegMine workflows for semantic microarray data analysis in Orange4WS

    Directory of Open Access Journals (Sweden)

    Kulovesi Kimmo

    2011-10-01

    Full Text Available Abstract Background In experimental data analysis, bioinformatics researchers increasingly rely on tools that enable the composition and reuse of scientific workflows. The utility of current bioinformatics workflow environments can be significantly increased by offering advanced data mining services as workflow components. Such services can support, for instance, knowledge discovery from diverse distributed data and knowledge sources (such as GO, KEGG, PubMed, and experimental databases. Specifically, cutting-edge data analysis approaches, such as semantic data mining, link discovery, and visualization, have not yet been made available to researchers investigating complex biological datasets. Results We present a new methodology, SegMine, for semantic analysis of microarray data by exploiting general biological knowledge, and a new workflow environment, Orange4WS, with integrated support for web services in which the SegMine methodology is implemented. The SegMine methodology consists of two main steps. First, the semantic subgroup discovery algorithm is used to construct elaborate rules that identify enriched gene sets. Then, a link discovery service is used for the creation and visualization of new biological hypotheses. The utility of SegMine, implemented as a set of workflows in Orange4WS, is demonstrated in two microarray data analysis applications. In the analysis of senescence in human stem cells, the use of SegMine resulted in three novel research hypotheses that could improve understanding of the underlying mechanisms of senescence and identification of candidate marker genes. Conclusions Compared to the available data analysis systems, SegMine offers improved hypothesis generation and data interpretation for bioinformatics in an easy-to-use integrated workflow environment.

  9. Workflow Fault Tree Generation Through Model Checking

    DEFF Research Database (Denmark)

    Herbert, Luke Thomas; Sharp, Robin

    2014-01-01

    We present a framework for the automated generation of fault trees from models of realworld process workflows, expressed in a formalised subset of the popular Business Process Modelling and Notation (BPMN) language. To capture uncertainty and unreliability in workflows, we extend this formalism...... with probabilistic non-deterministic branching. We present an algorithm that allows for exhaustive generation of possible error states that could arise in execution of the model, where the generated error states allow for both fail-stop behaviour and continued system execution. We employ stochastic model checking...... to calculate the probabilities of reaching each non-error system state. Each generated error state is assigned a variable indicating its individual probability of occurrence. Our method can determine the probability of combined faults occurring, while accounting for the basic probabilistic structure...

  10. Case Study: Using Perl and CGI Scripts to Automate a Quality Control Workflow for Scanned Congressional Documents

    OpenAIRE

    Doreva Belfiore

    2012-01-01

    The Law Library Digitization Project of the Rutgers University School of Law in Camden, New Jersey, developed a series of scripts in Perl and CGI that take advantage of the open-source module PerlMagick to automatically review the image quality of scanned government documents. By implementing these procedures, Rutgers was able to save staff working hours for document quality control by an estimated 25% percent from the previous manual-only workflow. These scripts can be adapted by novice Perl...

  11. Computing Workflows for Biologists: A Roadmap

    OpenAIRE

    Shade, Ashley; Teal, Tracy K.

    2015-01-01

    Extremely large datasets have become routine in biology. However, performing a computational analysis of a large dataset can be overwhelming, especially for novices. Here, we present a step-by-step guide to computing workflows with the biologist end-user in mind. Starting from a foundation of sound data management practices, we make specific recommendations on how to approach and perform computational analyses of large datasets, with a view to enabling sound, reproducible biological research.

  12. Quantifying nursing workflow in medication administration.

    Science.gov (United States)

    Keohane, Carol A; Bane, Anne D; Featherstone, Erica; Hayes, Judy; Woolf, Seth; Hurley, Ann; Bates, David W; Gandhi, Tejal K; Poon, Eric G

    2008-01-01

    New medication administration systems are showing promise in improving patient safety at the point of care, but adoption of these systems requires significant changes in nursing workflow. To prepare for these changes, the authors report on a time-motion study that measured the proportion of time that nurses spend on various patient care activities, focusing on medication administration-related activities. Implications of their findings are discussed.

  13. IDD Archival Hardware Architecture and Workflow

    Energy Technology Data Exchange (ETDEWEB)

    Mendonsa, D; Nekoogar, F; Martz, H

    2008-10-09

    This document describes the functionality of every component in the DHS/IDD archival and storage hardware system shown in Fig. 1. The document describes steps by step process of image data being received at LLNL then being processed and made available to authorized personnel and collaborators. Throughout this document references will be made to one of two figures, Fig. 1 describing the elements of the architecture and the Fig. 2 describing the workflow and how the project utilizes the available hardware.

  14. Tailored business solutions by workflow technologies

    Directory of Open Access Journals (Sweden)

    Alexandra Fortiş

    2006-01-01

    Full Text Available VISP (Virtual Internet Service Provider is an IST-STREP project, which is conducting research in the field of these new technologies, targeted to telecom/ISP companies. One of the first tasks of the VISP project is to identify the most appropriate technologies in order to construct the VISP platform. This paper presents the most significant results in the field of choreography and orchestration, two key domains that must accompany process modeling in the construction of a workflow environment.

  15. ASP, Amalgamation and the Conceptual Blending Workflow

    OpenAIRE

    Eppe, Manfred; Maclean, Ewen; Confalonieri, Roberto; Kutz, Oliver; Schorlemmer, Marco; Plaza, Enric

    2015-01-01

    We present an amalgamation technique used for conceptual blending – a concept invention method that is advocated in cognitive science as a fundamental, and uniquely human engine for creative thinking. Herein, we employ the search capabilities of ASP to find commonalities among input concepts as part of the blending process, and we show how our approach fits within a generalised conceptual blending workflow. Specifically, we orchestrate ASP with imperative programming languages like Python, to...

  16. Research on an Intelligent Automatic Turning System

    Directory of Open Access Journals (Sweden)

    Lichong Huang

    2012-12-01

    Full Text Available Equipment manufacturing industry is the strategic industries of a country. And its core part is the CNC machine tool. Therefore, enhancing the independent research of relevant technology of CNC machine, especially the open CNC system, is of great significance. This paper presented some key techniques of an Intelligent Automatic Turning System and gave a viable solution for system integration. First of all, the integrated system architecture and the flexible and efficient workflow for perfoming the intelligent automatic turning process is illustrated. Secondly, the innovated methods of the workpiece feature recognition and expression and process planning of the NC machining are put forward. Thirdly, the cutting tool auto-selection and the cutting parameter optimization solution are generated with a integrated inference of rule-based reasoning and case-based reasoning. Finally, the actual machining case based on the developed intelligent automatic turning system proved the presented solutions are valid, practical and efficient.

  17. Text-mining-assisted biocuration workflows in Argo.

    Science.gov (United States)

    Rak, Rafal; Batista-Navarro, Riza Theresa; Rowley, Andrew; Carter, Jacob; Ananiadou, Sophia

    2014-01-01

    Biocuration activities have been broadly categorized into the selection of relevant documents, the annotation of biological concepts of interest and identification of interactions between the concepts. Text mining has been shown to have a potential to significantly reduce the effort of biocurators in all the three activities, and various semi-automatic methodologies have been integrated into curation pipelines to support them. We investigate the suitability of Argo, a workbench for building text-mining solutions with the use of a rich graphical user interface, for the process of biocuration. Central to Argo are customizable workflows that users compose by arranging available elementary analytics to form task-specific processing units. A built-in manual annotation editor is the single most used biocuration tool of the workbench, as it allows users to create annotations directly in text, as well as modify or delete annotations created by automatic processing components. Apart from syntactic and semantic analytics, the ever-growing library of components includes several data readers and consumers that support well-established as well as emerging data interchange formats such as XMI, RDF and BioC, which facilitate the interoperability of Argo with other platforms or resources. To validate the suitability of Argo for curation activities, we participated in the BioCreative IV challenge whose purpose was to evaluate Web-based systems addressing user-defined biocuration tasks. Argo proved to have the edge over other systems in terms of flexibility of defining biocuration tasks. As expected, the versatility of the workbench inevitably lengthened the time the curators spent on learning the system before taking on the task, which may have affected the usability of Argo. The participation in the challenge gave us an opportunity to gather valuable feedback and identify areas of improvement, some of which have already been introduced. Database URL: http://argo.nactem.ac.uk.

  18. Tavaxy: Integrating Taverna and Galaxy workflows with cloud computing support

    Directory of Open Access Journals (Sweden)

    Abouelhoda Mohamed

    2012-05-01

    Full Text Available Abstract Background Over the past decade the workflow system paradigm has evolved as an efficient and user-friendly approach for developing complex bioinformatics applications. Two popular workflow systems that have gained acceptance by the bioinformatics community are Taverna and Galaxy. Each system has a large user-base and supports an ever-growing repository of application workflows. However, workflows developed for one system cannot be imported and executed easily on the other. The lack of interoperability is due to differences in the models of computation, workflow languages, and architectures of both systems. This lack of interoperability limits sharing of workflows between the user communities and leads to duplication of development efforts. Results In this paper, we present Tavaxy, a stand-alone system for creating and executing workflows based on using an extensible set of re-usable workflow patterns. Tavaxy offers a set of new features that simplify and enhance the development of sequence analysis applications: It allows the integration of existing Taverna and Galaxy workflows in a single environment, and supports the use of cloud computing capabilities. The integration of existing Taverna and Galaxy workflows is supported seamlessly at both run-time and design-time levels, based on the concepts of hierarchical workflows and workflow patterns. The use of cloud computing in Tavaxy is flexible, where the users can either instantiate the whole system on the cloud, or delegate the execution of certain sub-workflows to the cloud infrastructure. Conclusions Tavaxy reduces the workflow development cycle by introducing the use of workflow patterns to simplify workflow creation. It enables the re-use and integration of existing (sub- workflows from Taverna and Galaxy, and allows the creation of hybrid workflows. Its additional features exploit recent advances in high performance cloud computing to cope with the increasing data size and

  19. A Web-Based Rapid Prototyping Workflow Management Information System for Computer Repair and Maintenance

    Directory of Open Access Journals (Sweden)

    A. H. El-Mousa

    2008-01-01

    Full Text Available Problem statement: Response to paper-based requests for computer and peripheral repair and maintenance has become very troublesome and slow due to the large demand and expansion at the University of Jordan. The objectives of this study were to: (i investigate the current system processes associated with the paper-based workflow system. (ii design and implement, using a suitable workflow management approach, a totally electronic alterative to improve performance. Approach: The methodology followed in the transform of the business processes from the paper to the electronic-based was using the rapid prototyping workflow management approach. This approach is seen to be especially effective in such cases where there is direct continuous interaction and involvement between the different stakeholders during the lifecycle of the project. Results: The system had been implemented and tested with the result that efficiency, accountability and response time have greatly improved in handling repair and maintenance orders. The transform from paper to electronic resulted in greatly enhanced user satisfaction especially since the developed system provided automatic feedback regarding order status. Conclusion: The design process and results provide a working blueprint for easy and quick various similar university-based business processes to be transformed to electronic. This should highly motivate internal in-house restructuring of business process to utilize technology and IT to enhance performance and accountability.

  20. Automatic Reading

    Institute of Scientific and Technical Information of China (English)

    胡迪

    2007-01-01

    <正>Reading is the key to school success and,like any skill,it takes practice.A child learns to walk by practising until he no longer has to think about how to put one foot in front of the other.The great athlete practises until he can play quickly,accurately and without thinking.Ed- ucators call it automaticity.

  1. Wildfire: distributed, Grid-enabled workflow construction and execution

    Directory of Open Access Journals (Sweden)

    Issac Praveen

    2005-03-01

    Full Text Available Abstract Background We observe two trends in bioinformatics: (i analyses are increasing in complexity, often requiring several applications to be run as a workflow; and (ii multiple CPU clusters and Grids are available to more scientists. The traditional solution to the problem of running workflows across multiple CPUs required programming, often in a scripting language such as perl. Programming places such solutions beyond the reach of many bioinformatics consumers. Results We present Wildfire, a graphical user interface for constructing and running workflows. Wildfire borrows user interface features from Jemboss and adds a drag-and-drop interface allowing the user to compose EMBOSS (and other programs into workflows. For execution, Wildfire uses GEL, the underlying workflow execution engine, which can exploit available parallelism on multiple CPU machines including Beowulf-class clusters and Grids. Conclusion Wildfire simplifies the tasks of constructing and executing bioinformatics workflows.

  2. BioMoby extensions to the Taverna workflow management and enactment software

    Directory of Open Access Journals (Sweden)

    Senger Martin

    2006-11-01

    Full Text Available Abstract Background As biology becomes an increasingly computational science, it is critical that we develop software tools that support not only bioinformaticians, but also bench biologists in their exploration of the vast and complex data-sets that continue to build from international genomic, proteomic, and systems-biology projects. The BioMoby interoperability system was created with the goal of facilitating the movement of data from one Web-based resource to another to fulfill the requirements of non-expert bioinformaticians. In parallel with the development of BioMoby, the European myGrid project was designing Taverna, a bioinformatics workflow design and enactment tool. Here we describe the marriage of these two projects in the form of a Taverna plug-in that provides access to many of BioMoby's features through the Taverna interface. Results The exposed BioMoby functionality aids in the design of "sensible" BioMoby workflows, aids in pipelining BioMoby and non-BioMoby-based resources, and ensures that end-users need only a minimal understanding of both BioMoby, and the Taverna interface itself. Users are guided through the construction of syntactically and semantically correct workflows through plug-in calls to the Moby Central registry. Moby Central provides a menu of only those BioMoby services capable of operating on the data-type(s that exist at any given position in the workflow. Moreover, the plug-in automatically and correctly connects a selected service into the workflow such that users are not required to understand the nature of the inputs or outputs for any service, leaving them to focus on the biological meaning of the workflow they are constructing, rather than the technical details of how the services will interoperate. Conclusion With the availability of the BioMoby plug-in to Taverna, we believe that BioMoby-based Web Services are now significantly more useful and accessible to bench scientists than are more traditional

  3. CPOE/EHR-Driven Healthcare Workflow Generation and Scheduling

    OpenAIRE

    Han, Minmin; Song, Xiping; DeHaan, Jan; Cao, Hui; Kennedy, Rosemary; Gugerty, Brian

    2006-01-01

    Automated healthcare workflow generation and scheduling is an approach to ensure the use of the evidence-based protocols. Generating efficient and practical workflows is challenging due to the dynamic nature of healthcare practice and operations. We propose to use Computerized Physician Order Entry (CPOE) and Electronic Health Record (EHR) components to generate workflows (consisting of scheduled work items) to aid healthcare (nursing) operations. Currently, we are prototyping and developing ...

  4. CamBAfx: workflow design, implementation and application for neuroimaging

    OpenAIRE

    Cinly Ooi; Bullmore, Edward T; Alle-Meije Wink; Levent Sendur; Anna Barnes; Sophie Achard; John Aspden; Sanja Abbott; Shigang Yue; Manfred Kitzbichler; David Meunier; Voichita Maxim; Raymond Salvador; Julian Henty; Roger Tait

    2009-01-01

    CamBAfx is a workflow application designed for both researchers who use workflows to process data (consumers) and those who design them (designers). It provides a front-end (user interface) optimized for data processing designed in a way familiar to consumers. The back-end uses a pipeline model to represent workflows since this is a common and useful metaphor used by designers and is easy to manipulate compared to other representations like programming scripts. As an Eclipse Rich Client Platf...

  5. CamBAfx: Workflow Design, Implementation and Application for Neuroimaging

    OpenAIRE

    Ooi, Cinly; Bullmore, Edward T; Wink, Alle-Meije; Sendur, Levent; Barnes, Anna; Achard, Sophie; Aspden, John; Abbott, Sanja; Yue, Shigang; Kitzbichler, Manfred; Meunier, David; Maxim, Voichita; Salvador, Raymond; Henty, Julian; Tait, Roger

    2009-01-01

    CamBAfx is a workflow application designed for both researchers who use workflows to process data (consumers) and those who design them (designers). It provides a front-end (user interface) optimized for data processing designed in a way familiar to consumers. The back-end uses a pipeline model to represent workflows since this is a common and useful metaphor used by designers and is easy to manipulate compared to other representations like programming scripts. As an Eclipse Rich Client Platf...

  6. Text mining meets workflow: linking U-Compare with Taverna

    OpenAIRE

    Kano, Yoshinobu; Dobson, Paul; Nakanishi, Mio; Tsujii, Jun'ichi; Ananiadou, Sophia

    2010-01-01

    Summary: Text mining from the biomedical literature is of increasing importance, yet it is not easy for the bioinformatics community to create and run text mining workflows due to the lack of accessibility and interoperability of the text mining resources. The U-Compare system provides a wide range of bio text mining resources in a highly interoperable workflow environment where workflows can very easily be created, executed, evaluated and visualized without coding. We have linked U-Compare t...

  7. Effective and Efficient Similarity Search in Scientific Workflow Repositories

    OpenAIRE

    Starlinger, Johannes; Cohen-Boulakia, Sarah; Khanna, Sanjeev; Davidson, Susan; Leser, Ulf

    2015-01-01

    Scientific workflows have become a valuable tool for large-scale data processing and analysis. This has led to the creation of specialized online repositories to facilitate worflkow sharing and reuse. Over time, these repositories have grown to sizes that call for advanced methods to support workflow discovery, in particular for similarity search. Effective similarity search requires both high quality algorithms for the comparison of scientific workflows and efficient strategies for indexing,...

  8. Electronic resource management systems a workflow approach

    CERN Document Server

    Anderson, Elsa K

    2014-01-01

    To get to the bottom of a successful approach to Electronic Resource Management (ERM), Anderson interviewed staff at 11 institutions about their ERM implementations. Among her conclusions, presented in this issue of Library Technology Reports, is that grasping the intricacies of your workflow-analyzing each step to reveal the gaps and problems-at the beginning is crucial to selecting and implementing an ERM. Whether the system will be used to fill a gap, aggregate critical data, or replace a tedious manual process, the best solution for your library depends on factors such as your current soft

  9. Research on an Integrated Enterprise Workflow Model

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    An integrated enterprise workflow model called PPROCE is presented firstly. Then, an enterprise's ontology established by TOVE and Process Specification Language (PSL) is studied. Combined with TOVE's partition idea, PSL is extended and new PSL Extensions is created to define the ontology of process, organization, resource and product in the PPROCE model. As a result, PPROCE model can be defined by a set of corresponding formal language. It facilitates the future work not only in the model verification, model optimization and model simulation, but also in the model translation.

  10. SPATIAL DATA QUALITY AND A WORKFLOW TOOL

    OpenAIRE

    Meijer, M; Vullings, L.A.E.; J. D. Bulens; F. I. Rip; M. Boss; Hazeu, G.; Storm, M.

    2015-01-01

    Although by many perceived as important, spatial data quality has hardly ever been taken centre stage unless something went wrong due to bad quality. However, we think this is going to change soon. We are more and more relying on data driven processes and due to the increased availability of data, there is a choice in what data to use. How to make that choice? We think spatial data quality has potential as a selection criterion. In this paper we focus on how a workflow tool can help th...

  11. CMS data and workflow management system

    CERN Document Server

    Fanfani, A; Bacchi, W; Codispoti, G; De Filippis, N; Pompili, A; My, S; Abbrescia, M; Maggi, G; Donvito, G; Silvestris, L; Calzolari, F; Sarkar, S; Spiga, D; Cinquili, M; Lacaprara, S; Biasotto, M; Farina, F; Merlo, M; Belforte, S; Kavka, C; Sala, L; Harvey, J; Hufnagel, D; Fanzago, F; Corvo, M; Magini, N; Rehn, J; Toteva, Z; Feichtinger, D; Tuura, L; Eulisse, G; Bockelman, B; Lundstedt, C; Egeland, R; Evans, D; Mason, D; Gutsche, O; Sexton-Kennedy, L; Dagenhart, D W; Afaq, A; Guo, Y; Kosyakov, S; Lueking, L; Sekhri, V; Fisk, I; McBride, P; Bauerdick, L; Bakken, J; Rossman, P; Wicklund, E; Wu, Y; Jones, C; Kuznetsov, V; Riley, D; Dolgert, A; van Lingen, F; Narsky, I; Paus, C; Klute, M; Gomez-Ceballos, G; Piedra-Gomez, J; Miller, M; Mohapatra, A; Lazaridis, C; Bradley, D; Elmer, P; Wildish, T; Wuerthwein, F; Letts, J; Bourilkov, D; Kim, B; Smith, P; Hernandez, J M; Caballero, J; Delgado, A; Flix, J; Cabrillo-Bartolome, I; Kasemann, M; Flossdorf, A; Stadie, H; Kreuzer, P; Khomitch, A; Hof, C; Zeidler, C; Kalini, S; Trunov, A; Saout, C; Felzmann, U; Metson, S; Newbold, D; Geddes, N; Brew, C; Jackson, J; Wakefield, S; De Weirdt, S; Adler, V; Maes, J; Van Mulders, P; Villella, I; Hammad, G; Pukhaeva, N; Kurca, T; Semneniouk, I; Guan, W; Lajas, J A; Teodoro, D; Gregores, E; Baquero, M; Shehzad, A; Kadastik, M; Kodolova, O; Chao, Y; Ming Kuo, C; Filippidis, C; Walzel, G; Han, D; Kalinowski, A; Giro de Almeida, N M; Panyam, N

    CMS expects to manage many tens of peta bytes of data to be distributed over several computing centers around the world. The CMS distributed computing and analysis model is designed to serve, process and archive the large number of events that will be generated when the CMS detector starts taking data. The underlying concepts and the overall architecture of the CMS data and workflow management system will be presented. In addition the experience in using the system for MC production, initial detector commissioning activities and data analysis will be summarized.

  12. Business and scientific workflows a web service-oriented approach

    CERN Document Server

    Tan, Wei

    2013-01-01

    Focuses on how to use web service computing and service-based workflow technologies to develop timely, effective workflows for both business and scientific fields Utilizing web computing and Service-Oriented Architecture (SOA), Business and Scientific Workflows: A Web Service-Oriented Approach focuses on how to design, analyze, and deploy web service-based workflows for both business and scientific applications in many areas of healthcare and biomedicine. It also discusses and presents the recent research and development results. This informative reference features app

  13. Building asynchronous geospatial processing workflows with web services

    Science.gov (United States)

    Zhao, Peisheng; Di, Liping; Yu, Genong

    2012-02-01

    Geoscience research and applications often involve a geospatial processing workflow. This workflow includes a sequence of operations that use a variety of tools to collect, translate, and analyze distributed heterogeneous geospatial data. Asynchronous mechanisms, by which clients initiate a request and then resume their processing without waiting for a response, are very useful for complicated workflows that take a long time to run. Geospatial contents and capabilities are increasingly becoming available online as interoperable Web services. This online availability significantly enhances the ability to use Web service chains to build distributed geospatial processing workflows. This paper focuses on how to orchestrate Web services for implementing asynchronous geospatial processing workflows. The theoretical bases for asynchronous Web services and workflows, including asynchrony patterns and message transmission, are examined to explore different asynchronous approaches to and architecture of workflow code for the support of asynchronous behavior. A sample geospatial processing workflow, issued by the Open Geospatial Consortium (OGC) Web Service, Phase 6 (OWS-6), is provided to illustrate the implementation of asynchronous geospatial processing workflows and the challenges in using Web Services Business Process Execution Language (WS-BPEL) to develop them.

  14. A Safety Analysis Approach to Clinical Workflows: Application and Evaluation

    Directory of Open Access Journals (Sweden)

    Lamis Al-Qora’n

    2014-11-01

    Full Text Available Clinical workflows are safety critical workflows as they have the potential to cause harm or death to patients. Their safety needs to be considered as early as possible in the development process. Effective safety analysis methods are required to ensure the safety of these high-risk workflows, because errors that may happen through routine workflow could propagate within the workflow to result in harmful failures of the system’s output. This paper shows how to apply an approach for safety analysis of clinical workflows to analyse the safety of the workflow within a radiology department and evaluates the approach in terms of usability and benefits. The outcomes of using this approach include identification of the root causes of hazardous workflow failures that may put patients’ lives at risk. We show that the approach is applicable to this area of healthcare and is able to present added value through the detailed information on possible failures, of both their causes and effects; therefore, it has the potential to improve the safety of radiology and other clinical workflows.

  15. Comparison of Resource Platform Selection Approaches for Scientific Workflows

    Energy Technology Data Exchange (ETDEWEB)

    Simmhan, Yogesh; Ramakrishnan, Lavanya

    2010-03-05

    Cloud computing is increasingly considered as an additional computational resource platform for scientific workflows. The cloud offers opportunity to scale-out applications from desktops and local cluster resources. At the same time, it can eliminate the challenges of restricted software environments and queue delays in shared high performance computing environments. Choosing from these diverse resource platforms for a workflow execution poses a challenge for many scientists. Scientists are often faced with deciding resource platform selection trade-offs with limited information on the actual workflows. While many workflow planning methods have explored task scheduling onto different resources, these methods often require fine-scale characterization of the workflow that is onerous for a scientist. In this position paper, we describe our early exploratory work into using blackbox characteristics to do a cost-benefit analysis across of using cloud platforms. We use only very limited high-level information on the workflow length, width, and data sizes. The length and width are indicative of the workflow duration and parallelism. The data size characterizes the IO requirements. We compare the effectiveness of this approach to other resource selection models using two exemplar scientific workflows scheduled on desktops, local clusters, HPC centers, and clouds. Early results suggest that the blackbox model often makes the same resource selections as a more fine-grained whitebox model. We believe the simplicity of the blackbox model can help inform a scientist on the applicability of cloud computing resources even before porting an existing workflow.

  16. Process Makna - A Semantic Wiki for Scientific Workflows

    CERN Document Server

    Paschke, Adrian

    2010-01-01

    Virtual e-Science infrastructures supporting Web-based scientific workflows are an example for knowledge-intensive collaborative and weakly-structured processes where the interaction with the human scientists during process execution plays a central role. In this paper we propose the lightweight dynamic user-friendly interaction with humans during execution of scientific workflows via the low-barrier approach of Semantic Wikis as an intuitive interface for non-technical scientists. Our Process Makna Semantic Wiki system is a novel combination of an business process management system adapted for scientific workflows with a Corporate Semantic Web Wiki user interface supporting knowledge intensive human interaction tasks during scientific workflow execution.

  17. Facilitating Stewardship of scientific data through standards based workflows

    Science.gov (United States)

    Bastrakova, I.; Kemp, C.; Potter, A. K.

    2013-12-01

    scientific data acquisition and analysis requirements and effective interoperable data management and delivery. This includes participating in national and international dialogue on development of standards, embedding data management activities in business processes, and developing scientific staff as effective data stewards. Similar approach is applied to the geophysical data. By ensuring the geophysical datasets at GA strictly follow metadata and industry standards we are able to implement a provenance based workflow where the data is easily discoverable, geophysical processing can be applied to it and results can be stored. The provenance based workflow enables metadata records for the results to be produced automatically from the input dataset metadata.

  18. Advanced Architectures for Transactional Workflows or Advanced Transactions in Workflow Architectures

    NARCIS (Netherlands)

    Grefen, Paul

    1999-01-01

    In this short paper, we outline the workflow management systems research in the Information Systems division at the University of Twente. We discuss the two main themes in this research: architecture design and advanced transaction management. Attention is paid to the coverage of these themes in the

  19. Lowering the Barriers to Integrative Aquatic Ecosystem Science: Semantic Provenance, Open Linked Data, and Workflows

    Science.gov (United States)

    Harmon, T.; Hofmann, A. F.; Utz, R.; Deelman, E.; Hanson, P. C.; Szekely, P.; Villamizar, S. R.; Knoblock, C.; Guo, Q.; Crichton, D. J.; McCann, M. P.; Gil, Y.

    2011-12-01

    Environmental cyber-observatory (ECO) planning and implementation has been ongoing for more than a decade now, and several major efforts have recently come online or will soon. Some investigators in the relevant research communities will use ECO data, traditionally by developing their own client-side services to acquire data and then manually create custom tools to integrate and analyze it. However, a significant portion of the aquatic ecosystem science community will need more custom services to manage locally collected data. The latter group represents enormous intellectual capacity when one envisions thousands of ecosystems scientists supplementing ECO baseline data by sharing their own locally intensive observational efforts. This poster summarizes the outcomes of the June 2011 Workshop for Aquatic Ecosystem Sustainability (WAES) which focused on the needs of aquatic ecosystem research on inland waters and oceans. Here we advocate new approaches to support scientists to model, integrate, and analyze data based on: 1) a new breed of software tools in which semantic provenance is automatically created and used by the system, 2) the use of open standards based on RDF and Linked Data Principles to facilitate sharing of data and provenance annotations, 3) the use of workflows to represent explicitly all data preparation, integration, and processing steps in a way that is automatically repeatable. Aquatic ecosystems workflow exemplars are provided and discussed in terms of their potential broaden data sharing, analysis and synthesis thereby increasing the impact of aquatic ecosystem research.

  20. Workflow Management for a Cosmology Collaboratory

    Institute of Scientific and Technical Information of China (English)

    StewartC.Loken; CharlesMcParland

    2001-01-01

    The Nearby Supernova Factory Project will provide a unique opportunity to bring together simulation and observation to address crucial problms in particle and nuclear physics.Itsd goal is to significantly enhance our understanding of the nuclear processes in supernovae and to improve our ability to use both Type Ia and Type II supernovae as reference light sources (standard candles)in precision measurements of cosmological parameters.Over the past several years,astronomers and astrophysicists have been conducting in-depth sky searches with the goal of identifying supernovae in their earliest evolutionary stages and,during the 4 to 8 weeks of their most"explosive~ activity,measure their changing magnitude and spectra.The search program currently under development at LBNL is an earth-based observation program utilizing observational instruments at Haleakala and MaunaKea,Hawaii and Mt.Palomar,California,This new program provides a demanding testbed for the integration of computational,data management and collaboratory technologies.A citical element of this effort is the use of emerging workflow management tools to permit collaborating scientists to manage data processing and storage and to integrate advanced supernova simulation into the real-time control of the experiments .This paper describes the workflow management framework for the project,discusses security and resource allocation requirements and reviews emerging tools to support this important aspect of collaborative work.

  1. Delta: Data Reduction for Integrated Application Workflows.

    Energy Technology Data Exchange (ETDEWEB)

    Lofstead, Gerald Fredrick [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Jean-Baptiste, Gregory [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Oldfield, Ron A. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)

    2015-06-01

    Integrated Application Workflows (IAWs) run multiple simulation workflow components con- currently on an HPC resource connecting these components using compute area resources and compensating for any performance or data processing rate mismatches. These IAWs require high frequency and high volume data transfers between compute nodes and staging area nodes during the lifetime of a large parallel computation. The available network band- width between the two areas may not be enough to efficiently support the data movement. As the processing power available to compute resources increases, the requirements for this data transfer will become more difficult to satisfy and perhaps will not be satisfiable at all since network capabilities are not expanding at a comparable rate. Furthermore, energy consumption in HPC environments is expected to grow by an order of magnitude as exas- cale systems become a reality. The energy cost of moving large amounts of data frequently will contribute to this issue. It is necessary to reduce the volume of data without reducing the quality of data when it is being processed and analyzed. Delta resolves the issue by addressing the lifetime data transfer operations. Delta removes subsequent identical copies of already transmitted data during transfers and restores those copies once the data has reached the destination. Delta is able to identify duplicated information and determine the most space efficient way to represent it. Initial tests show about 50% reduction in data movement while maintaining the same data quality and transmission frequency.

  2. Workflow-Based Software Development Environment

    Science.gov (United States)

    Izygon, Michel E.

    2013-01-01

    The Software Developer's Assistant (SDA) helps software teams more efficiently and accurately conduct or execute software processes associated with NASA mission-critical software. SDA is a process enactment platform that guides software teams through project-specific standards, processes, and procedures. Software projects are decomposed into all of their required process steps or tasks, and each task is assigned to project personnel. SDA orchestrates the performance of work required to complete all process tasks in the correct sequence. The software then notifies team members when they may begin work on their assigned tasks and provides the tools, instructions, reference materials, and supportive artifacts that allow users to compliantly perform the work. A combination of technology components captures and enacts any software process use to support the software lifecycle. It creates an adaptive workflow environment that can be modified as needed. SDA achieves software process automation through a Business Process Management (BPM) approach to managing the software lifecycle for mission-critical projects. It contains five main parts: TieFlow (workflow engine), Business Rules (rules to alter process flow), Common Repository (storage for project artifacts, versions, history, schedules, etc.), SOA (interface to allow internal, GFE, or COTS tools integration), and the Web Portal Interface (collaborative web environment

  3. Accelerating the scientific exploration process with scientific workflows

    Science.gov (United States)

    Altintas, Ilkay; Barney, Oscar; Cheng, Zhengang; Critchlow, Terence; Ludaescher, Bertram; Parker, Steve; Shoshani, Arie; Vouk, Mladen

    2006-09-01

    Although an increasing amount of middleware has emerged in the last few years to achieve remote data access, distributed job execution, and data management, orchestrating these technologies with minimal overhead still remains a difficult task for scientists. Scientific workflow systems improve this situation by creating interfaces to a variety of technologies and automating the execution and monitoring of the workflows. Workflow systems provide domain-independent customizable interfaces and tools that combine different tools and technologies along with efficient methods for using them. As simulations and experiments move into the petascale regime, the orchestration of long running data and compute intensive tasks is becoming a major requirement for the successful steering and completion of scientific investigations. A scientific workflow is the process of combining data and processes into a configurable, structured set of steps that implement semi-automated computational solutions of a scientific problem. Kepler is a cross-project collaboration, co-founded by the SciDAC Scientific Data Management (SDM) Center, whose purpose is to develop a domain-independent scientific workflow system. It provides a workflow environment in which scientists design and execute scientific workflows by specifying the desired sequence of computational actions and the appropriate data flow, including required data transformations, between these steps. Currently deployed workflows range from local analytical pipelines to distributed, high-performance and high-throughput applications, which can be both data- and compute-intensive. The scientific workflow approach offers a number of advantages over traditional scripting-based approaches, including ease of configuration, improved reusability and maintenance of workflows and components (called actors), automated provenance management, ''smart'' re-running of different versions of workflow instances, on-the-fly updateable parameters

  4. Clothes Dryer Automatic Termination Evaluation

    Energy Technology Data Exchange (ETDEWEB)

    TeGrotenhuis, Ward E.

    2014-10-01

    Volume 2: Improved Sensor and Control Designs Many residential clothes dryers on the market today provide automatic cycles that are intended to stop when the clothes are dry, as determined by the final remaining moisture content (RMC). However, testing of automatic termination cycles has shown that many dryers are susceptible to over-drying of loads, leading to excess energy consumption. In particular, tests performed using the DOE Test Procedure in Appendix D2 of 10 CFR 430 subpart B have shown that as much as 62% of the energy used in a cycle may be from over-drying. Volume 1 of this report shows an average of 20% excess energy from over-drying when running automatic cycles with various load compositions and dryer settings. Consequently, improving automatic termination sensors and algorithms has the potential for substantial energy savings in the U.S.

  5. Argo: enabling the development of bespoke workflows and services for disease annotation.

    Science.gov (United States)

    Batista-Navarro, Riza; Carter, Jacob; Ananiadou, Sophia

    2016-01-01

    Argo (http://argo.nactem.ac.uk) is a generic text mining workbench that can cater to a variety of use cases, including the semi-automatic annotation of literature. It enables its technical users to build their own customised text mining solutions by providing a wide array of interoperable and configurable elementary components that can be seamlessly integrated into processing workflows. With Argo's graphical annotation interface, domain experts can then make use of the workflows' automatically generated output to curate information of interest.With the continuously rising need to understand the aetiology of diseases as well as the demand for their informed diagnosis and personalised treatment, the curation of disease-relevant information from medical and clinical documents has become an indispensable scientific activity. In the Fifth BioCreative Challenge Evaluation Workshop (BioCreative V), there was substantial interest in the mining of literature for disease-relevant information. Apart from a panel discussion focussed on disease annotations, the chemical-disease relations (CDR) track was also organised to foster the sharing and advancement of disease annotation tools and resources.This article presents the application of Argo's capabilities to the literature-based annotation of diseases. As part of our participation in BioCreative V's User Interactive Track (IAT), we demonstrated and evaluated Argo's suitability to the semi-automatic curation of chronic obstructive pulmonary disease (COPD) phenotypes. Furthermore, the workbench facilitated the development of some of the CDR track's top-performing web services for normalising disease mentions against the Medical Subject Headings (MeSH) database. In this work, we highlight Argo's support for developing various types of bespoke workflows ranging from ones which enabled us to easily incorporate information from various databases, to those which train and apply machine learning-based concept recognition models

  6. Grid-enabled Workflows for Industrial Product Design

    OpenAIRE

    Boniface, M.J.; Ferris, J.; Ghanem, M; Azam, N

    2006-01-01

    This paper presents a generic approach for developing and using Grid-based workflow technology for enabling cross-organizational engineering applications. Using industrial product design examples from the automotive and aerospace industries we highlight the main requirements and challenges addressed by our approach and describe how it can be used for enabling interoperability between heterogeneous workflow engines.

  7. DOCFLOW: AN INTEGRATED DOCUMENT WORKFLOW FOR BUSINESS PROCESS MANAGEMENT

    Directory of Open Access Journals (Sweden)

    Boonsit Yimwadsana

    2011-01-01

    Full Text Available Document management and workflow management systems have been widely used in large business enterprises to improve productivity. However, they still do not gain large acceptance in small and mediumsized businesses due to their cost and complexity. In addition, document management and workflow management systems are often used separately because they solve different problems. Only some part of document management systems should be tied together with workflow management systems. However, in most business environment, documents actually flow according to workflow definitions. Our work, thus, combines the two concepts together and simplifies the management of both document and workflow to fit business users. Our application, DocFlow, is designed with simplicity in mind while still maintaining necessary workflow and document management standard features with security. Approval mechanism is naturally included in the workflow, and the approval can be performed by a group of actors such that only one of the team members is sufficient to make the group's decision. A case study of news publishing process is shown to demonstrate how DocFlow can be used to create a workflow that fits the news publishing process.

  8. Research of Web-based Workflow Management System

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    The state of the art of workflow management techniques in research is introduced. The research and development trends of Workflow Manag ement System (WFMS) are presented. On basis of analysis and comparison of kinds of WFMSs, a WFMS based on Web technology and distributed object management is pr oposed. Finally, the application of the WFMS in supply chain management is descr ibed in detail.

  9. Conceptual Framework and Architecture for Service Mediating Workflow Management

    NARCIS (Netherlands)

    Hu, Jinmin; Grefen, Paul

    2003-01-01

    This paper proposes a three-layer workflow concept framework to realize workflow enactment flexibility by dynamically binding activities to their implementations at run time. A service mediating layer is added to bridge business process definition and its implementation. Based on this framework, we

  10. The influence of workflow systems on team learning

    NARCIS (Netherlands)

    Offenbeek, Marjolein A.G. van

    1999-01-01

    The question is raised what influence a team’s use of a workflow system will have on teamlearning. In office environments where the work is organised in semi-autonomous teams thatare responsible for whole processes, workflow systems are being implemented to effectivelyand efficiently realise the con

  11. Towards an actor-driven workflow management system for Grids

    NARCIS (Netherlands)

    F. Berretz; S. Skorupa; V. Sander; A. Belloum

    2010-01-01

    Currently, most workflow management systems in Grid environments provide push-oriented job distribution strategies, where jobs are explicitly delegated to resources. In those scenarios the dedicated resources execute submitted jobs according to the request of a workflow engine or Grid wide scheduler

  12. From Paper Based Clinical Practice Guidelines to Declarative Workflow Management

    DEFF Research Database (Denmark)

    Lyng, Karen Marie; Hildebrandt, Thomas; Mukkamala, Raghava Rao

    2009-01-01

    a sub workflow can be described in a declarative workflow management system: the Resultmaker Online Consultant (ROC). The example demonstrates that declarative primitives allow to naturally extend the paper based flowchart to an executable model without introducing a complex cyclic control flow graph....

  13. Modelling and analysis of workflow for lean supply chains

    Science.gov (United States)

    Ma, Jinping; Wang, Kanliang; Xu, Lida

    2011-11-01

    Cross-organisational workflow systems are a component of enterprise information systems which support collaborative business process among organisations in supply chain. Currently, the majority of workflow systems is developed in perspectives of information modelling without considering actual requirements of supply chain management. In this article, we focus on the modelling and analysis of the cross-organisational workflow systems in the context of lean supply chain (LSC) using Petri nets. First, the article describes the assumed conditions of cross-organisation workflow net according to the idea of LSC and then discusses the standardisation of collaborating business process between organisations in the context of LSC. Second, the concept of labelled time Petri nets (LTPNs) is defined through combining labelled Petri nets with time Petri nets, and the concept of labelled time workflow nets (LTWNs) is also defined based on LTPNs. Cross-organisational labelled time workflow nets (CLTWNs) is then defined based on LTWNs. Third, the article proposes the notion of OR-silent CLTWNS and a verifying approach to the soundness of LTWNs and CLTWNs. Finally, this article illustrates how to use the proposed method by a simple example. The purpose of this research is to establish a formal method of modelling and analysis of workflow systems for LSC. This study initiates a new perspective of research on cross-organisational workflow management and promotes operation management of LSC in real world settings.

  14. Web service automatic composition based on semantic relationship graph%基于语义关系图的Web服务自动组合方法

    Institute of Scientific and Technical Information of China (English)

    冯建周; 孔令富; 王晓寰

    2012-01-01

    针对基于图搜索实现Web服务自动组合存在搜索空间太大以及难以表达各种组合结构的问题,提出一种基于语义匹配关系确定组合结构的方法。该方法首先对Web服务进行形式化的语义描述,然后基于语义匹配关系,将服务库中只与用户请求的输入输出关联的服务构成语义关系图。在此基础上,基于语义匹配关系定义各种组合结构模型,以综合语义匹配度为寻优目标改进广度优先搜索算法,定义不同结构的语义匹配度计算方法,生成一条综合语义匹配度最优的Web服务组合路径。通过实例验证了该算法的可行性。%The method based on graph search was a simple and direct way to realize the Web service automatic composition, hut the search space was too large and it was difficult to express various combination structures among serv ices. To solve this problem, a method based on semantic matching relationship to determine combination structure was presented. Formal description of the Web services semantics were presented, and then based on semantic matehing relationship, the semantic relationship graph was established by services which were only related to user provided input and expected output. On this basis, various combination structure models were defined based on semantic matching relationship, and taking integrated semantic matching degree as optimal goal, the breadth-first search algorithm was improved, the calculation method of semantic matching degree in various combination structure was defined, and the service combination path which owned the optimal integrated semantic matching degree was generated. The feasibility of proposed algorithm was verified though an example.

  15. Distributed execution of aggregated multi domain workflows using an agent framework

    NARCIS (Netherlands)

    Z. Zhao; A. Belloum; C. de Laat; P. Adriaans; B. Hertzberger

    2007-01-01

    In e-Science, meaningful experiment processes and workflow engines emerge as important scientific resources. A complex experiment often involves services and processes developed in different scientific domains. Aggregating different workflows into one meta workflow avoids unnecessary rewriting of ex

  16. Phonon Gas Model (PGM) workflow in the VLab Science Gateway

    Science.gov (United States)

    da Silveira, P.; Zhang, D.; Wentzcovitch, R. M.

    2013-12-01

    This contribution describes a scientific workflow for first principles computations of free energy of crystalline solids using the phonon gas model (PGM). This model was recently implemented as a hybrid method combining molecular dynamics and phonon normal mode analysis to extract temperature dependent phonon frequencies and life times beyond perturbation theory. This is a demanding high throughout workflow and is currently being implemented in VLab Cyberinfrastructure [da Silveira et al., 2008], which has recently been integrated to the XSEDE. First we review the underlying PGM, its practical implementation, and calculation requirements. We then describe the workflow management and its general method for handling actions. We illustrate the PGM application with a calculation of MgSiO3-perovskite's anharmonic phonons. We conclude with an outlook of workflows to compute other material's properties that will use the PGM workflow. Research supported by NSF award EAR-1019853.

  17. Federated Database Services for Wind Tunnel Experiment Workflows

    Directory of Open Access Journals (Sweden)

    A. Paventhan

    2006-01-01

    Full Text Available Enabling the full life cycle of scientific and engineering workflows requires robust middleware and services that support effective data management, near-realtime data movement and custom data processing. Many existing solutions exploit the database as a passive metadata catalog. In this paper, we present an approach that makes use of federation of databases to host data-centric wind tunnel application workflows. The user is able to compose customized application workflows based on database services. We provide a reference implementation that leverages typical business tools and technologies: Microsoft SQL Server for database services and Windows Workflow Foundation for workflow services. The application data and user's code are both hosted in federated databases. With the growing interest in XML Web Services in scientific Grids, and with databases beginning to support native XML types and XML Web services, we can expect the role of databases in scientific computation to grow in importance.

  18. A Multi-Dimensional Classification Model for Scientific Workflow Characteristics

    Energy Technology Data Exchange (ETDEWEB)

    Ramakrishnan, Lavanya; Plale, Beth

    2010-04-05

    Workflows have been used to model repeatable tasks or operations in manufacturing, business process, and software. In recent years, workflows are increasingly used for orchestration of science discovery tasks that use distributed resources and web services environments through resource models such as grid and cloud computing. Workflows have disparate re uirements and constraints that affects how they might be managed in distributed environments. In this paper, we present a multi-dimensional classification model illustrated by workflow examples obtained through a survey of scientists from different domains including bioinformatics and biomedical, weather and ocean modeling, astronomy detailing their data and computational requirements. The survey results and classification model contribute to the high level understandingof scientific workflows.

  19. A systematic workflow process for heavy oil characterization : experimental techniques and challenges

    Energy Technology Data Exchange (ETDEWEB)

    Memon, A.I.; Gao, J.; Taylor, S.D.; Davies, T.L.; Jia, N. [Schlumberger, Edmonton, AB (Canada)

    2010-07-01

    Fluid characterization of heavy oil and bitumen is necessary when choosing the best extraction, production, and processing methods. High viscosity, low API, low saturation pressure, and low gas to oil ratios impose challenges in measuring fluid properties of heavy oil. This paper summarized the heavy oil fluid characterization technique that includes fluid sample handling, PVT analysis, fluid viscosity, emulsion and rheology, slow kinetics of gas evolution during constant composition expansion (CCE) experiments, solvent solubility, steam stripping, and high temperature vapor-liquid equilibrium of oil-solvent-steam systems. The paper also proposed a heavy oil characterization workflow to address a broad range of heavy oil production scenarios, including cold depletion, steam flow and heavy oil flow assurance. The workflow was based on various experimental techniques and challenges facing heavy oil sample preparation. Fluid property measurement requirements for each production technique were also compiled. 16 refs., 13 figs.

  20. An Integrated Workflow for DNA Methylation Analysis

    Institute of Scientific and Technical Information of China (English)

    Pingchuan Li; Feray Demirci; Gayathri Mahalingam; Caghan Demirci; Mayumi Nakano; Blake C.Meyers

    2013-01-01

    The analysis of cytosine methylation provides a new way to assess and describe epigenetic regulation at a whole-genome level in many eukaryotes.DNA methylation has a demonstrated role in the genome stability and protection,regulation of gene expression and many other aspects of genome function and maintenance.BS-seq is a relatively unbiased method for profiling the DNA methylation,with a resolution capable of measuring methylation at individual cytosines.Here we describe,as an example,a workflow to handle DNA methylation analysis,from BS-seq library preparation to the data visualization.We describe some applications for the analysis and interpretation of these data.Our laboratory provides public access to plant DNA methylation data via visualization tools available at our "Next-Gen Sequence" websites (http://mpss.udel.edu),along with small RNA,RNA-seq and other data types.

  1. A Framework for Distributed Preservation Workflows

    Directory of Open Access Journals (Sweden)

    Rainer Schmidt

    2010-07-01

    Full Text Available The Planets Project is developing a service-oriented environment for the definition and evaluation of preservation strategies for human-centric data. It focuses on the question of logically preserving digital materials, as opposed to the physical preservation of content bit-streams. This includes the development of preservation tools for the automated characterisation, migration, and comparison of different types of Digital Objects as well as the emulation of their original runtime environment in order to ensure long-time access and interpretability. The Planets integrated environment provides a number of end-user applications that allow data curators to execute and scientifically evaluate preservation experiments based on composable preservation services. In this paper, we focus on the middleware and programming model and show how it can be utilised in order to create complex preservation workflows.

  2. Managing Library IT Workflow with Bugzilla

    Directory of Open Access Journals (Sweden)

    Nina McHale

    2010-09-01

    Full Text Available Prior to September 2008, all technology issues at the University of Colorado Denver's Auraria Library were reported to a dedicated departmental phone line. A variety of staff changes necessitated a more formal means of tracking, delegating, and resolving reported issues, and the department turned to Bugzilla, an open source bug tracking application designed by Mozilla.org developers. While designed with software development bug tracking in mind, Bugzilla can be easily customized and modified to serve as an IT ticketing system. Twenty-three months and over 2300 trouble tickets later, Auraria's IT department workflow is much smoother and more efficient. This article includes two Perl Template Toolkit code samples for customized Bugzilla screens for its use in a library environment; readers will be able to easily replicate the project in their own environments.

  3. Radiology information system: a workflow-based approach

    International Nuclear Information System (INIS)

    Introducing workflow management technology in healthcare seems to be prospective in dealing with the problem that the current healthcare Information Systems cannot provide sufficient support for the process management, although several challenges still exist. The purpose of this paper is to study the method of developing workflow-based information system in radiology department as a use case. First, a workflow model of typical radiology process was established. Second, based on the model, the system could be designed and implemented as a group of loosely coupled components. Each component corresponded to one task in the process and could be assembled by the workflow management system. The legacy systems could be taken as special components, which also corresponded to the tasks and were integrated through transferring non-work- flow-aware interfaces to the standard ones. Finally, a workflow dashboard was designed and implemented to provide an integral view of radiology processes. The workflow-based Radiology Information System was deployed in the radiology department of Zhejiang Chinese Medicine Hospital in China. The results showed that it could be adjusted flexibly in response to the needs of changing process, and enhance the process management in the department. It can also provide a more workflow-aware integration method, comparing with other methods such as IHE-based ones. The workflow-based approach is a new method of developing radiology information system with more flexibility, more functionalities of process management and more workflow-aware integration. The work of this paper is an initial endeavor for introducing workflow management technology in healthcare. (orig.)

  4. Implementing Workflow Reconfiguration in WS-BPEL

    DEFF Research Database (Denmark)

    Mazzara, Manuel; Dragoni, Nicola; Zhou, Mu

    2012-01-01

    not naturally support dynamic change, is used as a target for implementation. The WS-BPEL recovery framework is here exploited to implement the reconfiguration using principles derived from previous research in process algebra and two mappings from BPMN to WS-BPEL are presented, one automatic and only mostly...

  5. Research into automatic scoring method of English composition and its feasibility%英语自动作文评分方法及其可行性研究

    Institute of Scientific and Technical Information of China (English)

    杨有统

    2011-01-01

    in order to test the feasibility of automatic scoring model of English compositions written the Chinese students,this paper adopts 35 positions written by senior English majors as sample and explores the relation between automatic extraction language use characteristics and man-scoring.The result shows that the use number of chunk of composition,type,the fourth root of composition length and writing score are markedly correlated.%为了检验中国学生英语作文自动评分模型的可行性,采用某高校英语专业高年级学生35篇作文为样本,探讨计算机提取语言使用特征和人工评分之间的关系。研究表明作文中语块的使用数量、类符数、作文长度四次方根和写作得分显著相关。

  6. CA-PLAN, a Service-Oriented Workflow

    Institute of Scientific and Technical Information of China (English)

    Shung-Bin Yan; Feng-Jian Wang

    2005-01-01

    Workflow management systems (WfMSs) are accepted worldwide due to their ability to model and control business processes. Previously, we defined an intra-organizational workflow specification model, Process LANguage (PLAN).PLAN, with associated tools, allowed a user to describe a graph specification for processes, artifacts, and participants in an organization. PLAN has been successfully implemented in Agentflow to support workflow (Agentflow) applications. PLAN,and most current WfMSs are designed to adopt a centralized architecture so that they can be applied to a single organization.However, in such a structure, participants in Agentflow applications in different organizations cannot serve each other with workflows.In this paper, a service-oriented cooperative workflow model, Cooperative Agentflow Process LANguage (CA-PLAN) is presented. CA-PLAN proposes a workflow component model to model inter-organizational processes. In CA-PLAN, an interorganizational process is partitioned into several intra-organizational processes. Each workflow system inside an organization is modeled as an Integrated Workflow Component (IWC). Each IWC contains a process service interface, specifying process services provided by an organization, in conjunction with a remote process interface specifying what remote processes are used to refer to remote process services provided by other organizations, and intra-organizational processes. An IWC is a workflow node and participant. An inter-organizational process is made up of connections among these process services and remote processes with respect to different IWCs. In this paper, the related service techniques and supporting tools provided in Agentflow systems are presented.

  7. CMS Alignement and Calibration workflows lesson learned and future plans

    CERN Document Server

    De Guio, Federico

    2014-01-01

    We review the online and offline workflows designed to align and calibrate the CMS detector. Starting from the gained experience during the first LHC run, we discuss the expected developments for Run II. In particular, we describe the envisioned different stages, from the alignment using cosmic rays data to the detector alignment and calibration using the first proton-proton collisions data ( O(100 pb-1) ) and a larger dataset ( O(1 fb-1) ) to reach the target precision. The automatisation of the workflow and the integration in the online and offline activity (dedicated triggers and datasets, data skims, workflows to compute the calibration and alignment constants) are discussed.

  8. A Workflow Process Mining Algorithm Based on Synchro-Net

    Institute of Scientific and Technical Information of China (English)

    Xing-Qi Huang; Li-Fu Wang; Wen Zhao; Shi-Kun Zhang; Chong-Yi Yuan

    2006-01-01

    Sometimes historic information about workflow execution is needed to analyze business processes. Process mining aims at extracting information from event logs for capturing a business process in execution. In this paper a process mining algorithm is proposed based on Synchro-Net which is a synchronization-based model of workflow logic and workflow semantics. With this mining algorithm based on the model, problems such as invisible tasks and short-loops can be dealt with at ease. A process mining example is presented to illustrate the algorithm, and the evaluation is also given.

  9. Workflow logs analysis system for enterprise performance measurement

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    Workflow logs that record the execution of business processes offer very valuable data resource for real-time enterprise performance measurement. In this paper, a novel scheme that uses the technology of data warehouse and OLAP to explore workflow logs and create complex analysis reports for enterprise performance measurement is proposed. Three key points of this scheme are studied: 1) the measure set; 2) the open and flexible architecture for workflow logs analysis system; 3) the data models in WFMS and data warehouse. A case study that shows the validity of the scheme is also provided.

  10. Investigation on Efficient Management of workflows in cloud computing Environment

    Directory of Open Access Journals (Sweden)

    M.Sudha,

    2010-08-01

    Full Text Available Cloud computing is an on-demand service model often based on virtualization technique and this paper explores the use of cloud computing for scientific workflows, focusing on a widely used application. The approach is to evaluate from the point of view of a scientific workflow the tradeoffs between running in a local environment, if such is available, and running in a virtual environment via remote, wide-area network resource access. Our results show that a workflow with short job runtimes, the virtualenvironment can provide good compute time performance but it can suffer from resource scheduling delays and wide area communications.

  11. Service-based flexible workflow system for virtual enterprise

    Institute of Scientific and Technical Information of China (English)

    WU Shao-fei

    2008-01-01

    Using the services provided by virtual enterprises, we presented a solution to implement flexible inter-enterprise workflow management. Services were the responses of events that can be accessed programmatically on the Internet by HTTP protocol. Services were obtained according to some standardized service templates. The workflow engine's flexible control to a request was bound to appropriate services and their providers by using a constraint-based, dynamic binding mechanism. Hence, a flexible and collaborative business was achieved. The workflow management system supports virtual enterprise, and the styles of virtual enterprises can be adjusted readily to adapt various situations.

  12. Reduction techniques of workflow verification and its implementation

    Institute of Scientific and Technical Information of China (English)

    李沛武; 卢正鼎; 付湘林

    2004-01-01

    Many workflow management systems have emerged in recent years, but few of them provide any form of support for verification. This frequently results in runtime errors that need to be corrected at prohibitive costs. In Ref. [ 1 ], a few reduction rules of verifying workflow graph are given. After analyzing the reduction rules, the overlapped reduction rule is found to be inaccurate. In this paper, the improved reduction rules are presented and the matrix-based implementing algorithm is given, so that the scope of the verification of workflow is expanded and the efficiency of the algorithm is enhanced. The method is simple and natural, and its implementation is easy too.

  13. Confusion Analysis and Detection for Workflow Nets

    Directory of Open Access Journals (Sweden)

    Xiao-liang Chen

    2014-01-01

    Full Text Available Option processes often occur in a business procedure with respect to resource competition. In a business procedure modeled with a workflow net (WF-net, all decision behavior and option operations for business tasks are modeled and performed by the conflicts in corresponding WF-net. Concurrency in WF-nets is applied to keep a high-performance operation of business procedures. However, the firing of concurrent transitions in a WF-net may lead to the disappearance of conflicts in the WF-net. The phenomenon is usually called confusions that produces difficulties for the resolution of conflicts. This paper investigates confusion detection problems in WF-nets. First, confusions are formalized as a class of marked subnets with special conflicting and concurrent features. Second, a detection approach based on the characteristics of confusion subnets and the integer linear programming (ILP is developed, which is not required to compute the reachability graph of a WF-net. Examples of the confusion detection in WF-nets are presented. Finally, the impact of confusions on the properties of WF-nets is specified.

  14. SPATIAL DATA QUALITY AND A WORKFLOW TOOL

    Directory of Open Access Journals (Sweden)

    M. Meijer

    2015-08-01

    Full Text Available Although by many perceived as important, spatial data quality has hardly ever been taken centre stage unless something went wrong due to bad quality. However, we think this is going to change soon. We are more and more relying on data driven processes and due to the increased availability of data, there is a choice in what data to use. How to make that choice? We think spatial data quality has potential as a selection criterion. In this paper we focus on how a workflow tool can help the consumer as well as the producer to get a better understanding about which product characteristics are important. For this purpose, we have developed a framework in which we define different roles (consumer, producer and intermediary and differentiate between product specifications and quality specifications. A number of requirements is stated that can be translated into quality elements. We used case studies to validate our framework. This framework is designed following the fitness for use principle. Also part of this framework is software that in some cases can help ascertain the quality of datasets.

  15. Workflow to numerically reproduce laboratory ultrasonic datasets

    Institute of Scientific and Technical Information of China (English)

    A. Biryukov; N. Tisato; G. Grasselli

    2014-01-01

    The risks and uncertainties related to the storage of high-level radioactive waste (HLRW) can be reduced thanks to focused studies and investigations. HLRWs are going to be placed in deep geological re-positories, enveloped in an engineered bentonite barrier, whose physical conditions are subjected to change throughout the lifespan of the infrastructure. Seismic tomography can be employed to monitor its physical state and integrity. The design of the seismic monitoring system can be optimized via con-ducting and analyzing numerical simulations of wave propagation in representative repository geometry. However, the quality of the numerical results relies on their initial calibration. The main aim of this paper is to provide a workflow to calibrate numerical tools employing laboratory ultrasonic datasets. The finite difference code SOFI2D was employed to model ultrasonic waves propagating through a laboratory sample. Specifically, the input velocity model was calibrated to achieve a best match between experi-mental and numerical ultrasonic traces. Likely due to the imperfections of the contact surfaces, the resultant velocities of P- and S-wave propagation tend to be noticeably lower than those a priori assigned. Then, the calibrated model was employed to estimate the attenuation in a montmorillonite sample. The obtained low quality factors (Q) suggest that pronounced inelastic behavior of the clay has to be taken into account in geophysical modeling and analysis. Consequently, this contribution should be considered as a first step towards the creation of a numerical tool to evaluate wave propagation in nuclear waste repositories.

  16. Automatic chemical monitoring in the composition of functions performed by the unit level control system in the new projects of nuclear power plant units

    Science.gov (United States)

    Denisova, L. G.; Khrennikov, N. N.

    2014-08-01

    The article presents information on the state of regulatory framework and development of a subsystem for automated chemical monitoring of water chemistries in the primary and secondary coolant circuits used as part of the automatic process control system in new projects of VVER reactor-based nuclear power plant units. For the strategy of developing and putting in use the water chemistry-related part of the automated process control system within the standard AES-2006 nuclear power plant project to be implemented, it is necessary to develop regulatory documents dealing with certain requirements imposed on automatic water chemistry monitoring systems in accordance with the requirements of federal codes and regulations in the field of using atomic energy.

  17. A Community-Driven Workflow Recommendation and Reuse Infrastructure Project

    Data.gov (United States)

    National Aeronautics and Space Administration — Promote and encourage process and workflow reuse  within NASA Earth eXchange (NEX) by developing a proactive recommendation technology based on collective NEX...

  18. Network resource control for grid workflow management systems

    NARCIS (Netherlands)

    Strijkers, R.J.; Cristea, M.; Korkhov, V.; Marchal, D.; Belloum, A.; Laat, C.de; Meijer, R.J.

    2010-01-01

    Grid workflow management systems automate the orchestration of scientific applications with large computational and data processing needs, but lack control over network resources. Consequently, the management system cannot prevent multiple communication intensive applications to compete for network

  19. Approach for workflow modeling using π-calculus

    Institute of Scientific and Technical Information of China (English)

    杨东; 张申生

    2003-01-01

    As a variant of process algebra, π-calculus can describe the interactions between evolving processes. By modeling activity as a process interacting with other processes through ports, this paper presents a new approach: representing workflow models using π-calculus. As a result, the model can characterize the dynamic behaviors of the workflow process in terms of the LTS (Labeled Transition Semantics) semantics of π-calculus. The main advantage of the workflow model's formal semantic is that it allows for verification of the model's properties, such as deadlock-free and normal termination. Moreover, the equivalence of workflow models can be checked through weak bisimulation theorem in the π-calculus, thus facilitating the optimization of business processes.

  20. Workflows for microarray data processing in the Kepler environment

    Directory of Open Access Journals (Sweden)

    Stropp Thomas

    2012-05-01

    Full Text Available Abstract Background Microarray data analysis has been the subject of extensive and ongoing pipeline development due to its complexity, the availability of several options at each analysis step, and the development of new analysis demands, including integration with new data sources. Bioinformatics pipelines are usually custom built for different applications, making them typically difficult to modify, extend and repurpose. Scientific workflow systems are intended to address these issues by providing general-purpose frameworks in which to develop and execute such pipelines. The Kepler workflow environment is a well-established system under continual development that is employed in several areas of scientific research. Kepler provides a flexible graphical interface, featuring clear display of parameter values, for design and modification of workflows. It has capabilities for developing novel computational components in the R, Python, and Java programming languages, all of which are widely used for bioinformatics algorithm development, along with capabilities for invoking external applications and using web services. Results We developed a series of fully functional bioinformatics pipelines addressing common tasks in microarray processing in the Kepler workflow environment. These pipelines consist of a set of tools for GFF file processing of NimbleGen chromatin immunoprecipitation on microarray (ChIP-chip datasets and more comprehensive workflows for Affymetrix gene expression microarray bioinformatics and basic primer design for PCR experiments, which are often used to validate microarray results. Although functional in themselves, these workflows can be easily customized, extended, or repurposed to match the needs of specific projects and are designed to be a toolkit and starting point for specific applications. These workflows illustrate a workflow programming paradigm focusing on local resources (programs and data and therefore are close to

  1. Supporting exploration and collaboration in scientific workflow systems

    Science.gov (United States)

    Marini, L.; Kooper, R.; Bajcsy, P.; Myers, J.

    2007-12-01

    As the amount of observation data captured everyday increases, running scientific workflows will soon become a fundamental step of scientific inquiry. Current scientific workflow systems offer ways to link together data, software and computational resources, but often accomplish this by requiring a deep understanding of the system with a steep learning curve. Thus, there is a need to lower user adoption barriers for workflow systems and improve the plug-and-play functionality of these systems. We created a system that allows the user to easily create and share workflows, data and algorithms. Our goal of lowering user adoption barriers is to support discoveries and to provide means for conducting research more efficiently. Current paradigms for workflow creation focus on the visual programming using a graph based metaphor. This can be a powerful metaphor in the hands of expert users, but can become daunting when graphs become large, the steps in the graph include engineering level steps such as loading and visualizing data, and the users are not very familiar with all the possible tools available. We present a different method of workflow creation that co- exists with the standard graph based editors. The method builds on exploratory interface using a macro- recording style, and focuses on the data being analyzed during the step by step creation of the workflow. Instead of storing data in system specific data structures, the use of more flexible open standards that are platform independent would create systems that are easier to extend and that provide a simple interface for external applications to query and analyze the data and metadata produced. We have explored and implemented a system that stores workflows and related metadata using the Resource Description Framework (RDF) metadata model and that is build on top of the Tupelo data and metadata archiving system. The scientific workflow system connects to shared content repositories, where users can easily share

  2. Implementation and evaluation of a new workflow for registration and segmentation of pulmonary MRI data for regional lung perfusion assessment

    Science.gov (United States)

    Böttger, T.; Grunewald, K.; Schöbinger, M.; Fink, C.; Risse, F.; Kauczor, H. U.; Meinzer, H. P.; Wolf, Ivo

    2007-03-01

    Recently it has been shown that regional lung perfusion can be assessed using time-resolved contrast-enhanced magnetic resonance (MR) imaging. Quantification of the perfusion images has been attempted, based on definition of small regions of interest (ROIs). Use of complete lung segmentations instead of ROIs could possibly increase quantification accuracy. Due to the low signal-to-noise ratio, automatic segmentation algorithms cannot be applied. On the other hand, manual segmentation of the lung tissue is very time consuming and can become inaccurate, as the borders of the lung to adjacent tissues are not always clearly visible. We propose a new workflow for semi-automatic segmentation of the lung from additionally acquired morphological HASTE MR images. First the lung is delineated semi-automatically in the HASTE image. Next the HASTE image is automatically registered with the perfusion images. Finally, the transformation resulting from the registration is used to align the lung segmentation from the morphological dataset with the perfusion images. We evaluated rigid, affine and locally elastic transformations, suitable optimizers and different implementations of mutual information (MI) metrics to determine the best possible registration algorithm. We located the shortcomings of the registration procedure and under which conditions automatic registration will succeed or fail. Segmentation results were evaluated using overlap and distance measures. Integration of the new workflow reduces the time needed for post-processing of the data, simplifies the perfusion quantification and reduces interobserver variability in the segmentation process. In addition, the matched morphological data set can be used to identify morphologic changes as the source for the perfusion abnormalities.

  3. Automated evolutionary restructuring of workflows to minimise errors via stochastic model checking

    DEFF Research Database (Denmark)

    Herbert, Luke Thomas; Hansen, Zaza Nadja Lee; Jacobsen, Peter

    2014-01-01

    This paper presents a framework for the automated restructuring of workflows that allows one to minimise the impact of errors on a production workflow. The framework allows for the modelling of workflows by means of a formalised subset of the Business Process Modelling and Notation (BPMN) languag...... of the production workflows and the expression of the goals require manual input....

  4. Optimierung datenintensiver Workflows: Konzepte und Realisierung eines heuristischen, regelbasierten Optimierers

    OpenAIRE

    Vrhovnik, Marko

    2011-01-01

    Um die Modellierung datenintensiver Workflows, die große relationale Datenmengen verarbeiten, zu vereinfachen, wurden Workflowbeschreibungssprachen, wie BPEL, von führenden Herstellern von Workflow- und Datenbankmanagementsystemen um SQL-Funktionalität erweitert. Dadurch müssen Datenverarbeitungsoperationen, wie SQL-Anweisungen oder Aufrufe benutzerdefinierter Prozeduren, nicht mehr in Web-Services gekapselt werden, sondern können direkt auf der Workflowebene definiert werden. Daraus resultie...

  5. An Architecture for Decentralised Orchestration of Web Service Workflows

    OpenAIRE

    Jaradat, Ward; Dearle, Alan; Barker, Adam

    2013-01-01

    Service-oriented workflows are typically executed using a centralised orchestration approach that presents significant scalability challenges. These challenges include the consumption of network bandwidth, degradation of performance, and single-points of failure. We provide a decentralised orchestration architecture that attempts to address these challenges. Our architecture adopts a design model that permits the computation to be moved "closer" to services in a workflow. This is achieved by ...

  6. Process Makna - A Semantic Wiki for Scientific Workflows

    OpenAIRE

    Paschke, Adrian; Zhao, Zhili

    2010-01-01

    Virtual e-Science infrastructures supporting Web-based scientific workflows are an example for knowledge-intensive collaborative and weakly-structured processes where the interaction with the human scientists during process execution plays a central role. In this paper we propose the lightweight dynamic user-friendly interaction with humans during execution of scientific workflows via the low-barrier approach of Semantic Wikis as an intuitive interface for non-technical scientists. Our Proces...

  7. Workflow-based semantics for peer-to-peer specifications

    Institute of Scientific and Technical Information of China (English)

    Antonio BROGI; Razvan POPESCU

    2008-01-01

    In this paper we introduce SMoL, a simplified BPEL-like language for specifying peer and service beha-viour in P2P systems. We then define a transformational semantics of SMoL in terms of Yet Another Workflow Language (YAWL) workflows, which enables the simu-lation (e.g., testing possible execution scenarios) and ana-lysis (e.g., verifying reachability or lock freedom) of the behaviour of P2P peers and services.

  8. Optimization of tomographic reconstruction workflows on geographically distributed resources.

    Science.gov (United States)

    Bicer, Tekin; Gürsoy, Dogˇa; Kettimuthu, Rajkumar; De Carlo, Francesco; Foster, Ian T

    2016-07-01

    New technological advancements in synchrotron light sources enable data acquisitions at unprecedented levels. This emergent trend affects not only the size of the generated data but also the need for larger computational resources. Although beamline scientists and users have access to local computational resources, these are typically limited and can result in extended execution times. Applications that are based on iterative processing as in tomographic reconstruction methods require high-performance compute clusters for timely analysis of data. Here, time-sensitive analysis and processing of Advanced Photon Source data on geographically distributed resources are focused on. Two main challenges are considered: (i) modeling of the performance of tomographic reconstruction workflows and (ii) transparent execution of these workflows on distributed resources. For the former, three main stages are considered: (i) data transfer between storage and computational resources, (i) wait/queue time of reconstruction jobs at compute resources, and (iii) computation of reconstruction tasks. These performance models allow evaluation and estimation of the execution time of any given iterative tomographic reconstruction workflow that runs on geographically distributed resources. For the latter challenge, a workflow management system is built, which can automate the execution of workflows and minimize the user interaction with the underlying infrastructure. The system utilizes Globus to perform secure and efficient data transfer operations. The proposed models and the workflow management system are evaluated by using three high-performance computing and two storage resources, all of which are geographically distributed. Workflows were created with different computational requirements using two compute-intensive tomographic reconstruction algorithms. Experimental evaluation shows that the proposed models and system can be used for selecting the optimum resources, which in turn can

  9. Optimization of tomographic reconstruction workflows on geographically distributed resources.

    Science.gov (United States)

    Bicer, Tekin; Gürsoy, Dogˇa; Kettimuthu, Rajkumar; De Carlo, Francesco; Foster, Ian T

    2016-07-01

    New technological advancements in synchrotron light sources enable data acquisitions at unprecedented levels. This emergent trend affects not only the size of the generated data but also the need for larger computational resources. Although beamline scientists and users have access to local computational resources, these are typically limited and can result in extended execution times. Applications that are based on iterative processing as in tomographic reconstruction methods require high-performance compute clusters for timely analysis of data. Here, time-sensitive analysis and processing of Advanced Photon Source data on geographically distributed resources are focused on. Two main challenges are considered: (i) modeling of the performance of tomographic reconstruction workflows and (ii) transparent execution of these workflows on distributed resources. For the former, three main stages are considered: (i) data transfer between storage and computational resources, (i) wait/queue time of reconstruction jobs at compute resources, and (iii) computation of reconstruction tasks. These performance models allow evaluation and estimation of the execution time of any given iterative tomographic reconstruction workflow that runs on geographically distributed resources. For the latter challenge, a workflow management system is built, which can automate the execution of workflows and minimize the user interaction with the underlying infrastructure. The system utilizes Globus to perform secure and efficient data transfer operations. The proposed models and the workflow management system are evaluated by using three high-performance computing and two storage resources, all of which are geographically distributed. Workflows were created with different computational requirements using two compute-intensive tomographic reconstruction algorithms. Experimental evaluation shows that the proposed models and system can be used for selecting the optimum resources, which in turn can

  10. INTRODUCTION OF WINDOWS WORKFLOW FOUNDATION INTO EXISTING APPLICATIONS

    OpenAIRE

    Kržič, Jernej

    2008-01-01

    In this dissertation we discuss the process of implementing the Windows Workflow foundation model in existing applications. We present several possible approaches to solving this problem and their advantages, as well as limitations. First, we describe the main concepts behind Business Process Management and the Windows Workflow foundation programming model. Other related technologies are also described, including .NET Framwork, Windows Communication Foundation, ASP.NET etc. The practical p...

  11. How Workflow Systems Facilitate Business Process Reengineering and Improvement

    OpenAIRE

    Mohamed El Khadiri; Abdelaziz El Fazziki

    2012-01-01

    This paper investigates the relationship between workflow systems and business process reengineering and improvement. The study is based on a real case study at the “Centre Rgional dInvestissement” (CRI) of Marrakech, Morocco. The CRI is entrusted to coordinate various investment projects at the regional level. Our previous work has shown that workflow system can be a basis for business process reengineering. However, for continuous process improvement, the system has shown to be insufficient...

  12. BReW: Blackbox Resource Selection for e-Science Workflows

    Energy Technology Data Exchange (ETDEWEB)

    Simmhan, Yogesh [Univ. of Southern California, Los Angeles, CA (United States); Soroush, Emad [Univ. of Washington, Seattle, WA (United States); Van Ingen, Catharine [Microsoft Research, San Francisco, CA (United States); Agarwal, Deb [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Ramakrishnan, Lavanya [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)

    2010-10-04

    Workflows are commonly used to model data intensive scientific analysis. As computational resource needs increase for eScience, emerging platforms like clouds present additional resource choices for scientists and policy makers. We introduce BReW, a tool enables users to make rapid, highlevel platform selection for their workflows using limited workflow knowledge. This helps make informed decisions on whether to port a workflow to a new platform. Our analysis of synthetic and real eScience workflows shows that using just total runtime length, maximum task fanout, and total data used and produced by the workflow, BReW can provide platform predictions comparable to whitebox models with detailed workflow knowledge.

  13. A scientific workflow framework for (13)C metabolic flux analysis.

    Science.gov (United States)

    Dalman, Tolga; Wiechert, Wolfgang; Nöh, Katharina

    2016-08-20

    Metabolic flux analysis (MFA) with (13)C labeling data is a high-precision technique to quantify intracellular reaction rates (fluxes). One of the major challenges of (13)C MFA is the interactivity of the computational workflow according to which the fluxes are determined from the input data (metabolic network model, labeling data, and physiological rates). Here, the workflow assembly is inevitably determined by the scientist who has to consider interacting biological, experimental, and computational aspects. Decision-making is context dependent and requires expertise, rendering an automated evaluation process hardly possible. Here, we present a scientific workflow framework (SWF) for creating, executing, and controlling on demand (13)C MFA workflows. (13)C MFA-specific tools and libraries, such as the high-performance simulation toolbox 13CFLUX2, are wrapped as web services and thereby integrated into a service-oriented architecture. Besides workflow steering, the SWF features transparent provenance collection and enables full flexibility for ad hoc scripting solutions. To handle compute-intensive tasks, cloud computing is supported. We demonstrate how the challenges posed by (13)C MFA workflows can be solved with our approach on the basis of two proof-of-concept use cases.

  14. LQCD workflow execution framework: Models, provenance and fault-tolerance

    Science.gov (United States)

    Piccoli, Luciano; Dubey, Abhishek; Simone, James N.; Kowalkowlski, James B.

    2010-04-01

    Large computing clusters used for scientific processing suffer from systemic failures when operated over long continuous periods for executing workflows. Diagnosing job problems and faults leading to eventual failures in this complex environment is difficult, specifically when the success of an entire workflow might be affected by a single job failure. In this paper, we introduce a model-based, hierarchical, reliable execution framework that encompass workflow specification, data provenance, execution tracking and online monitoring of each workflow task, also referred to as participants. The sequence of participants is described in an abstract parameterized view, which is translated into a concrete data dependency based sequence of participants with defined arguments. As participants belonging to a workflow are mapped onto machines and executed, periodic and on-demand monitoring of vital health parameters on allocated nodes is enabled according to pre-specified rules. These rules specify conditions that must be true pre-execution, during execution and post-execution. Monitoring information for each participant is propagated upwards through the reflex and healing architecture, which consists of a hierarchical network of decentralized fault management entities, called reflex engines. They are instantiated as state machines or timed automatons that change state and initiate reflexive mitigation action(s) upon occurrence of certain faults. We describe how this cluster reliability framework is combined with the workflow execution framework using formal rules and actions specified within a structure of first order predicate logic that enables a dynamic management design that reduces manual administrative workload, and increases cluster-productivity.

  15. CO2 Storage Feasibility: A Workflow for Site Characterisation

    Directory of Open Access Journals (Sweden)

    Nepveu Manuel

    2015-04-01

    Full Text Available In this paper, we present an overview of the SiteChar workflow model for site characterisation and assessment for CO2 storage. Site characterisation and assessment is required when permits are requested from the legal authorities in the process of starting a CO2 storage process at a given site. The goal is to assess whether a proposed CO2 storage site can indeed be used for permanent storage while meeting the safety requirements demanded by the European Commission (EC Storage Directive (9, Storage Directive 2009/31/EC. Many issues have to be scrutinised, and the workflow presented here is put forward to help efficiently organise this complex task. Three issues are highlighted: communication within the working team and with the authorities; interdependencies in the workflow and feedback loops; and the risk-based character of the workflow. A general overview (helicopter view of the workflow is given; the issues involved in communication and the risk assessment process are described in more detail. The workflow as described has been tested within the SiteChar project on five potential storage sites throughout Europe. This resulted in a list of key aspects of site characterisation which can help prepare and focus new site characterisation studies.

  16. A scientific workflow framework for (13)C metabolic flux analysis.

    Science.gov (United States)

    Dalman, Tolga; Wiechert, Wolfgang; Nöh, Katharina

    2016-08-20

    Metabolic flux analysis (MFA) with (13)C labeling data is a high-precision technique to quantify intracellular reaction rates (fluxes). One of the major challenges of (13)C MFA is the interactivity of the computational workflow according to which the fluxes are determined from the input data (metabolic network model, labeling data, and physiological rates). Here, the workflow assembly is inevitably determined by the scientist who has to consider interacting biological, experimental, and computational aspects. Decision-making is context dependent and requires expertise, rendering an automated evaluation process hardly possible. Here, we present a scientific workflow framework (SWF) for creating, executing, and controlling on demand (13)C MFA workflows. (13)C MFA-specific tools and libraries, such as the high-performance simulation toolbox 13CFLUX2, are wrapped as web services and thereby integrated into a service-oriented architecture. Besides workflow steering, the SWF features transparent provenance collection and enables full flexibility for ad hoc scripting solutions. To handle compute-intensive tasks, cloud computing is supported. We demonstrate how the challenges posed by (13)C MFA workflows can be solved with our approach on the basis of two proof-of-concept use cases. PMID:26721184

  17. Applying Business Process Re-engineering Patterns to optimize WS-BPEL Workflows

    Science.gov (United States)

    Buys, Jonas; de Florio, Vincenzo; Blondia, Chris

    With the advent of XML-based SOA, WS-BPEL shortly turned out to become a widely accepted standard for modeling business processes. Though SOA is said to embrace the principle of business agility, BPEL process definitions are still manually crafted into their final executable version. While SOA has proven to be a giant leap forward in building flexible IT systems, this static BPEL workflow model is somewhat paradoxical to the need for real business agility and should be enhanced to better sustain continual process evolution. In this paper, we point out the potential of adding business intelligence with respect to business process re-engineering patterns to the system to allow for automatic business process optimization. Furthermore, we point out that BPR macro-rules could be implemented leveraging micro-techniques from computer science. We present some practical examples that illustrate the benefit of such adaptive process models and our preliminary findings.

  18. 工作流管理规范综述%The Workflow Management Specification Overview

    Institute of Scientific and Technical Information of China (English)

    陈畅; 吴朝晖

    2000-01-01

    Workflow Management is a fast evolving technology,many software vendors have WFM products available today in the market.To enable interoperability between heterogeneous workflow products and improve integration of workflow applications with other IT services,it is necessary to work out common specifications.The purpose of this paper is to provide a framework to specifications for implementation in workflow products developed by the WFM Coalition.It provides a common"Reference Model"for workflow management systems.

  19. The CESM Workflow Re-Engineering Project

    Science.gov (United States)

    Strand, G.

    2015-12-01

    The Community Earth System Model (CESM) Workflow Re-Engineering Project is a collaborative project between the CESM Software Engineering Group (CSEG) and the NCAR Computation and Information Systems Lab (CISL) Application Scalability and Performance (ASAP) Group to revamp how CESM saves its output. The CMIP3 and particularly CMIP5 experiences in submitting CESM data to those intercomparison projects revealed that the output format of the CESM is not well-suited for the data requirements common to model intercomparison projects. CESM, for efficiency reasons, creates output files containing all fields for each model time sampling, but MIPs require individual files for each field comprising all model time samples. This transposition of model output can be very time-consuming; depending on the volume of data written by the specific simulation, the time to re-orient the data can be comparable to the time required for the simulation to complete. Previous strategies including using serial tools to perform this transposition, but they are now far too inefficient to deal with the many terabytes of output a single simulation can generate. A new set of Python tools, using data parallelism, have been written to enable this re-orientation, and have achieved markedly improved I/O performance. The perspective of a data manager/data producer in the use of these new tools is presented, and likely future work on their development and use will be shown. These tools are a critical part of the NCAR CESM submission to the upcoming CMIP6, with the intention that a much more timely and efficient submission of the expected petabytes of data will be accomplished in the given time frame.

  20. Run-time revenue maximization for composite web services with response time commitments

    NARCIS (Netherlands)

    Živković, M.; Bosman, J.W.; Berg, H. van den; Mei, R. van der; Meeuwissen, H.B.; Núñez-Queija, R.

    2012-01-01

    We investigate dynamic decision mechanisms for composite web services maximizing the expected revenue for the providers of composite services. A composite web service is represented by a (sequential) workflow, and for each task within this workflow, a number of service alternatives may be available.

  1. Automatically updating predictive modeling workflows support decision-making in drug design.

    Science.gov (United States)

    Muegge, Ingo; Bentzien, Jörg; Mukherjee, Prasenjit; Hughes, Robert O

    2016-09-01

    Using predictive models for early decision-making in drug discovery has become standard practice. We suggest that model building needs to be automated with minimum input and low technical maintenance requirements. Models perform best when tailored to answering specific compound optimization related questions. If qualitative answers are required, 2-bin classification models are preferred. Integrating predictive modeling results with structural information stimulates better decision making. For in silico models supporting rapid structure-activity relationship cycles the performance deteriorates within weeks. Frequent automated updates of predictive models ensure best predictions. Consensus between multiple modeling approaches increases the prediction confidence. Combining qualified and nonqualified data optimally uses all available information. Dose predictions provide a holistic alternative to multiple individual property predictions for reaching complex decisions.

  2. Visual Workflows for Oil and Gas Exploration

    KAUST Repository

    Hollt, Thomas

    2013-04-14

    The most important resources to fulfill today’s energy demands are fossil fuels, such as oil and natural gas. When exploiting hydrocarbon reservoirs, a detailed and credible model of the subsurface structures to plan the path of the borehole, is crucial in order to minimize economic and ecological risks. Before that, the placement, as well as the operations of oil rigs need to be planned carefully, as off-shore oil exploration is vulnerable to hazards caused by strong currents. The oil and gas industry therefore relies on accurate ocean forecasting systems for planning their operations. This thesis presents visual workflows for creating subsurface models as well as planning the placement and operations of off-shore structures. Creating a credible subsurface model poses two major challenges: First, the structures in highly ambiguous seismic data are interpreted in the time domain. Second, a velocity model has to be built from this interpretation to match the model to depth measurements from wells. If it is not possible to obtain a match at all positions, the interpretation has to be updated, going back to the first step. This results in a lengthy back and forth between the different steps, or in an unphysical velocity model in many cases. We present a novel, integrated approach to interactively creating subsurface models from reflection seismics, by integrating the interpretation of the seismic data using an interactive horizon extraction technique based on piecewise global optimization with velocity modeling. Computing and visualizing the effects of changes to the interpretation and velocity model on the depth-converted model, on the fly enables an integrated feedback loop that enables a completely new connection of the seismic data in time domain, and well data in depth domain. For planning the operations of off-shore structures we present a novel integrated visualization system that enables interactive visual analysis of ensemble simulations used in ocean

  3. Composites

    OpenAIRE

    Zhao, Hanqing; Guo, Yuanzheng

    2014-01-01

    This thesis was a literature study concerning composites. With composites becoming increasingly popular in various areas such as aerospace industry and construction, the research about composites has a significant meaning accordingly. This thesis was aim at introducing some basic information of polymer matrix composites including raw mate-rial, processing, testing, applications and recycling to make a rough understanding of this kind of material for readers. Polymeric matrices, fillers,...

  4. Composition

    DEFF Research Database (Denmark)

    Bergstrøm-Nielsen, Carl

    2010-01-01

    New Year is an open composition to be realised by improvising musicians. It is included in "From the Danish Seasons" (see under this title). See more about my composition practise in the entry "Composition - General Introduction". This work is licensed under a Creative Commons "by-nc" License. You...

  5. Provenance-based refresh in data-oriented workflows

    KAUST Repository

    Ikeda, Robert

    2011-01-01

    We consider a general workflow setting in which input data sets are processed by a graph of transformations to produce output results. Our goal is to perform efficient selective refresh of elements in the output data, i.e., compute the latest values of specific output elements when the input data may have changed. We explore how data provenance can be used to enable efficient refresh. Our approach is based on capturing one-level data provenance at each transformation when the workflow is run initially. Then at refresh time provenance is used to determine (transitively) which input elements are responsible for given output elements, and the workflow is rerun only on that portion of the data needed for refresh. Our contributions are to formalize the problem setting and the problem itself, to specify properties of transformations and provenance that are required for efficient refresh, and to provide algorithms that apply to a wide class of transformations and workflows. We have built a prototype system supporting the features and algorithms presented in the paper. We report preliminary experimental results on the overhead of provenance capture, and on the crossover point between selective refresh and full workflow recomputation. © 2011 ACM.

  6. Experiences with workflows for automating data-intensive bioinformatics.

    Science.gov (United States)

    Spjuth, Ola; Bongcam-Rudloff, Erik; Hernández, Guillermo Carrasco; Forer, Lukas; Giovacchini, Mario; Guimera, Roman Valls; Kallio, Aleksi; Korpelainen, Eija; Kańduła, Maciej M; Krachunov, Milko; Kreil, David P; Kulev, Ognyan; Łabaj, Paweł P; Lampa, Samuel; Pireddu, Luca; Schönherr, Sebastian; Siretskiy, Alexey; Vassilev, Dimitar

    2015-01-01

    High-throughput technologies, such as next-generation sequencing, have turned molecular biology into a data-intensive discipline, requiring bioinformaticians to use high-performance computing resources and carry out data management and analysis tasks on large scale. Workflow systems can be useful to simplify construction of analysis pipelines that automate tasks, support reproducibility and provide measures for fault-tolerance. However, workflow systems can incur significant development and administration overhead so bioinformatics pipelines are often still built without them. We present the experiences with workflows and workflow systems within the bioinformatics community participating in a series of hackathons and workshops of the EU COST action SeqAhead. The organizations are working on similar problems, but we have addressed them with different strategies and solutions. This fragmentation of efforts is inefficient and leads to redundant and incompatible solutions. Based on our experiences we define a set of recommendations for future systems to enable efficient yet simple bioinformatics workflow construction and execution. PMID:26282399

  7. Optimizing high performance computing workflow for protein functional annotation.

    Science.gov (United States)

    Stanberry, Larissa; Rekepalli, Bhanu; Liu, Yuan; Giblock, Paul; Higdon, Roger; Montague, Elizabeth; Broomall, William; Kolker, Natali; Kolker, Eugene

    2014-09-10

    Functional annotation of newly sequenced genomes is one of the major challenges in modern biology. With modern sequencing technologies, the protein sequence universe is rapidly expanding. Newly sequenced bacterial genomes alone contain over 7.5 million proteins. The rate of data generation has far surpassed that of protein annotation. The volume of protein data makes manual curation infeasible, whereas a high compute cost limits the utility of existing automated approaches. In this work, we present an improved and optmized automated workflow to enable large-scale protein annotation. The workflow uses high performance computing architectures and a low complexity classification algorithm to assign proteins into existing clusters of orthologous groups of proteins. On the basis of the Position-Specific Iterative Basic Local Alignment Search Tool the algorithm ensures at least 80% specificity and sensitivity of the resulting classifications. The workflow utilizes highly scalable parallel applications for classification and sequence alignment. Using Extreme Science and Engineering Discovery Environment supercomputers, the workflow processed 1,200,000 newly sequenced bacterial proteins. With the rapid expansion of the protein sequence universe, the proposed workflow will enable scientists to annotate big genome data.

  8. Development of the workflow kine systems for support on KAIZEN.

    Science.gov (United States)

    Mizuno, Yuki; Ito, Toshihiko; Yoshikawa, Toru; Yomogida, Satoshi; Morio, Koji; Sakai, Kazuhiro

    2012-01-01

    In this paper, we introduce the new workflow line system consisted of the location and image recording, which led to the acquisition of workflow information and the analysis display. From the results of workflow line investigation, we considered the anticipated effects and the problems on KAIZEN. Workflow line information included the location information and action contents information. These technologies suggest the viewpoints to help improvement, for example, exclusion of useless movement, the redesign of layout and the review of work procedure. Manufacturing factory, it was clear that there was much movement from the standard operation place and accumulation residence time. The following was shown as a result of this investigation, to be concrete, the efficient layout was suggested by this system. In the case of the hospital, similarly, it is pointed out that the workflow has the problem of layout and setup operations based on the effective movement pattern of the experts. This system could adapt to routine work, including as well as non-routine work. By the development of this system which can fit and adapt to industrial diversification, more effective "visual management" (visualization of work) is expected in the future. PMID:22317594

  9. Distributing Workflows over a Ubiquitous P2P Network

    Directory of Open Access Journals (Sweden)

    Eddie Al-Shakarchi

    2007-01-01

    Full Text Available This paper discusses issues in the distribution of bundled workflows across ubiquitous peer-to-peer networks for the application of music information retrieval. The underlying motivation for this work is provided by the DART project, which aims to develop a novel music recommendation system by gathering statistical data using collaborative filtering techniques and the analysis of the audio itsel, in order to create a reliable and comprehensive database of the music that people own and which they listen to. To achieve this, the DART scientists creating the algorithms need the ability to distribute the Triana workflows they create, representing the analysis to be performed, across the network on a regular basis (perhaps even daily in order to update the network as a whole with new workflows to be executed for the analysis. DART uses a similar approach to BOINC but differs in that the workers receive input data in the form of a bundled Triana workflow, which is executed in order to process any MP3 files that they own on their machine. Once analysed, the results are returned to DART's distributed database that collects and aggregates the resulting information. DART employs the use of package repositories to decentralise the distribution of such workflow bundles and this approach is validated in this paper through simulations that show that suitable scalability is maintained through the system as the number of participants increases. The results clearly illustrate the effectiveness of the approach.

  10. CamBAfx: Workflow Design, Implementation and Application for Neuroimaging.

    Science.gov (United States)

    Ooi, Cinly; Bullmore, Edward T; Wink, Alle-Meije; Sendur, Levent; Barnes, Anna; Achard, Sophie; Aspden, John; Abbott, Sanja; Yue, Shigang; Kitzbichler, Manfred; Meunier, David; Maxim, Voichita; Salvador, Raymond; Henty, Julian; Tait, Roger; Subramaniam, Naresh; Suckling, John

    2009-01-01

    CamBAfx is a workflow application designed for both researchers who use workflows to process data (consumers) and those who design them (designers). It provides a front-end (user interface) optimized for data processing designed in a way familiar to consumers. The back-end uses a pipeline model to represent workflows since this is a common and useful metaphor used by designers and is easy to manipulate compared to other representations like programming scripts. As an Eclipse Rich Client Platform application, CamBAfx's pipelines and functions can be bundled with the software or downloaded post-installation. The user interface contains all the workflow facilities expected by consumers. Using the Eclipse Extension Mechanism designers are encouraged to customize CamBAfx for their own pipelines. CamBAfx wraps a workflow facility around neuroinformatics software without modification. CamBAfx's design, licensing and Eclipse Branding Mechanism allow it to be used as the user interface for other software, facilitating exchange of innovative computational tools between originating labs.

  11. CamBAfx: workflow design, implementation and application for neuroimaging

    Directory of Open Access Journals (Sweden)

    Cinly Ooi

    2009-08-01

    Full Text Available CamBAfx is a workflow application designed for both researchers who use workflows to process data (consumers and those who design them (designers. It provides a front-end (user interface optimized for data processing designed in a way familiar to consumers. The back-end uses a pipeline model to represent workflows since this is a common and useful metaphor used by designers and is easy to manipulate compared to other representations like programming scripts. As an Eclipse Rich Client Platform application, CamBAfx's pipelines and functions can be bundled with the software or downloaded post-installation. The user interface contains all the workflow facilities expected by consumers. Using the Eclipse Extension Mechanism designers are encouraged to customize CamBAfx for their own pipelines. CamBAfx wraps a workflow facility around neuroinformatics software without modification. CamBAfx's design, licensing and Eclipse Branding Mechanism allow it to be used as the user interface for other software, facilitating exchange of innovative computational tools between originating labs.

  12. Development of the workflow kine systems for support on KAIZEN.

    Science.gov (United States)

    Mizuno, Yuki; Ito, Toshihiko; Yoshikawa, Toru; Yomogida, Satoshi; Morio, Koji; Sakai, Kazuhiro

    2012-01-01

    In this paper, we introduce the new workflow line system consisted of the location and image recording, which led to the acquisition of workflow information and the analysis display. From the results of workflow line investigation, we considered the anticipated effects and the problems on KAIZEN. Workflow line information included the location information and action contents information. These technologies suggest the viewpoints to help improvement, for example, exclusion of useless movement, the redesign of layout and the review of work procedure. Manufacturing factory, it was clear that there was much movement from the standard operation place and accumulation residence time. The following was shown as a result of this investigation, to be concrete, the efficient layout was suggested by this system. In the case of the hospital, similarly, it is pointed out that the workflow has the problem of layout and setup operations based on the effective movement pattern of the experts. This system could adapt to routine work, including as well as non-routine work. By the development of this system which can fit and adapt to industrial diversification, more effective "visual management" (visualization of work) is expected in the future.

  13. Brain-Wide Mapping of Axonal Connections: Workflow for Automated Detection and Spatial Analysis of Labeling in Microscopic Sections.

    Science.gov (United States)

    Papp, Eszter A; Leergaard, Trygve B; Csucs, Gergely; Bjaalie, Jan G

    2016-01-01

    Axonal tracing techniques are powerful tools for exploring the structural organization of neuronal connections. Tracers such as biotinylated dextran amine (BDA) and Phaseolus vulgaris leucoagglutinin (Pha-L) allow brain-wide mapping of connections through analysis of large series of histological section images. We present a workflow for efficient collection and analysis of tract-tracing datasets with a focus on newly developed modules for image processing and assignment of anatomical location to tracing data. New functionality includes automatic detection of neuronal labeling in large image series, alignment of images to a volumetric brain atlas, and analytical tools for measuring the position and extent of labeling. To evaluate the workflow, we used high-resolution microscopic images from axonal tracing experiments in which different parts of the rat primary somatosensory cortex had been injected with BDA or Pha-L. Parameters from a set of representative images were used to automate detection of labeling in image series covering the entire brain, resulting in binary maps of the distribution of labeling. For high to medium labeling densities, automatic detection was found to provide reliable results when compared to manual analysis, whereas weak labeling required manual curation for optimal detection. To identify brain regions corresponding to labeled areas, section images were aligned to the Waxholm Space (WHS) atlas of the Sprague Dawley rat brain (v2) by custom-angle slicing of the MRI template to match individual sections. Based on the alignment, WHS coordinates were obtained for labeled elements and transformed to stereotaxic coordinates. The new workflow modules increase the efficiency and reliability of labeling detection in large series of images from histological sections, and enable anchoring to anatomical atlases for further spatial analysis and comparison with other data. PMID:27148038

  14. Hybrid Workflow Policy Management for Heart Disease Identification

    CERN Document Server

    Kim, Dong-Hyun; Youn, Chan-Hyun

    2010-01-01

    As science technology grows, medical application is becoming more complex to solve the physiological problems within expected time. Workflow management systems (WMS) in Grid computing are promising solution to solve the sophisticated problem such as genomic analysis, drug discovery, disease identification, etc. Although existing WMS can provide basic management functionality in Grid environment, consideration of user requirements such as performance, reliability and interaction with user is missing. In this paper, we propose hybrid workflow management system for heart disease identification and discuss how to guarantee different user requirements according to user SLA. The proposed system is applied to Physio-Grid e-health platform to identify human heart disease with ECG analysis and Virtual Heart Simulation (VHS) workflow applications.

  15. Implementation of the electronic DDA workflow for NSSS system design

    International Nuclear Information System (INIS)

    For improving NSSS design quality, and productivity several cases of the nuclear developed nation's integrated management system, such as Mitsubishi's NUWINGS (Japan), AECL's CANDID (Canada) and Duke Powes's (USA) were investigated, and it was studied in this report that the system implementation of NSSS design document computerization and the major workflow process of the DDA (Document Distribution for Agreement). On the basis of the requirements of design document computerization which covered preparation, review, approval and distribution of the engineering documents, KAERI Engineering Information Management System (KEIMS) was implemented. Major effects of this report are to implement GUI panel for input and retrieval of the document index information, to setup electronic document workflow, and to provide quality assurance verification by tracing the workflow history. Major effects of NSSS design document computerization are the improvement of efficiency and reliability and the engineering cost reduction by means of the fast documents verification capability and electronic document transferring system. 2 tabs., 16 figs., 9 refs. (Author)

  16. Talkoot Portals: Discover, Tag, Share, and Reuse Collaborative Science Workflows

    Science.gov (United States)

    Wilson, B. D.; Ramachandran, R.; Lynnes, C.

    2009-05-01

    A small but growing number of scientists are beginning to harness Web 2.0 technologies, such as wikis, blogs, and social tagging, as a transformative way of doing science. These technologies provide researchers easy mechanisms to critique, suggest and share ideas, data and algorithms. At the same time, large suites of algorithms for science analysis are being made available as remotely-invokable Web Services, which can be chained together to create analysis workflows. This provides the research community an unprecedented opportunity to collaborate by sharing their workflows with one another, reproducing and analyzing research results, and leveraging colleagues' expertise to expedite the process of scientific discovery. However, wikis and similar technologies are limited to text, static images and hyperlinks, providing little support for collaborative data analysis. A team of information technology and Earth science researchers from multiple institutions have come together to improve community collaboration in science analysis by developing a customizable "software appliance" to build collaborative portals for Earth Science services and analysis workflows. The critical requirement is that researchers (not just information technologists) be able to build collaborative sites around service workflows within a few hours. We envision online communities coming together, much like Finnish "talkoot" (a barn raising), to build a shared research space. Talkoot extends a freely available, open source content management framework with a series of modules specific to Earth Science for registering, creating, managing, discovering, tagging and sharing Earth Science web services and workflows for science data processing, analysis and visualization. Users will be able to author a "science story" in shareable web notebooks, including plots or animations, backed up by an executable workflow that directly reproduces the science analysis. New services and workflows of interest will be

  17. An Overview of Workflow Management on Mobile Agent Technology

    Directory of Open Access Journals (Sweden)

    Anup Patnaik

    2014-07-01

    Full Text Available Mobile agent workflow management/plugins is quite appropriate to handle control flows in open distributed system; basically it is the emerging technology which can bring the process oriented tasks to run as a single unit from diverse frameworks. This workflow technology offers organizations the opportunity to reshape business processes beyond the boundaries of their own organizations so that instead of static models, modern era incurring dynamic workflows which can respond the changes during its execution, provide necessary security measures, great degree of adaptivity, troubleshoot the running processes and recovery of lost states through fault tolerance. The prototype that we are planning to design makes sure to hold reliability, security, robustness, scalability without being forced to make tradeoffs the performance. This paper is concerned with design, implementation and evaluation of performance on the improved methods of proposed prototype models based on current research in this domain.

  18. A Hybrid Authorization Model For Project-Oriented Workflow

    Institute of Scientific and Technical Information of China (English)

    Zhang Xiaoguang(张晓光); Cao Jian; Zhang Shensheng

    2003-01-01

    In the context of workflow systems, security-relevant aspect is related to the assignment of activities to (human or automated) agents. This paper intends to cast light on the management of project-oriented workflow. A comprehensive authorization model is proposed from the perspective of project management. In this model, the concept of activity decomposition and team is introduced, which improves the security of conventional role-based access control. Furthermore, policy is provided to define the static and dynamic constraints such as Separation of Duty (SoD). Validity of constraints is proposed to provide a fine-grained assignment, which improves the performance of policy management. The model is applicable not only to project-oriented workflow applications but also to other teamwork environments such as virtual enterprise.

  19. Declarative Modelling and Safe Distribution of Healthcare Workflows

    DEFF Research Database (Denmark)

    Hildebrandt, Thomas; Mukkamala, Raghava Rao; Slaats, Tijs

    2012-01-01

    We present a formal technique for safe distribution of workflow processes described declaratively as Nested Condition Response (NCR) Graphs and apply the technique to a distributed healthcare workflow. Concretely, we provide a method to synthesize from a NCR Graph and any distribution of its events......-organizational case management. The contributions of this paper is to adapt the technique to allow for nested processes and milestones and to apply it to a healthcare workflow identified in a previous field study at danish hospitals....... a set of local process graphs communicating by shared events, such that the distributed execution of the local processes is equivalent to executing the original process. The technique is based on our recent similar work on safe distribution of Dynamic Condition Response (DCR) Graphs applied to cross...

  20. Hybrid Workflow Policy Management for Heart Disease Identification

    Directory of Open Access Journals (Sweden)

    Dong-Hyun Kim

    2009-12-01

    Full Text Available As science technology grows, medical application is becoming more complex to solve the physiological problems within expected time. Workflow management systems (WMS in Grid computing are promisingsolution to solve the sophisticated problem such as genomic analysis, drug discovery, disease identification, etc. Although existing WMS can provide basic management functionality in Grid environment, consideration of user requirements such as performance, reliability and interaction with user is missing. In this paper, we proposehybrid workflow management system for heart disease identification and discuss how to guarantee different user requirements according to user SLA. The proposed system is applied to Physio-Grid e-health platform to identify human heart disease with ECG analysis and Virtual Heart Simulation (VHS workflow applications.

  1. Dynamic Service Selection in Workflows Using Performance Data

    Directory of Open Access Journals (Sweden)

    David W. Walker

    2007-01-01

    Full Text Available An approach to dynamic workflow management and optimisation using near-realtime performance data is presented. Strategies are discussed for choosing an optimal service (based on user-specified criteria from several semantically equivalent Web services. Such an approach may involve finding "similar" services, by first pruning the set of discovered services based on service metadata, and subsequently selecting an optimal service based on performance data. The current implementation of the prototype workflow framework is described, and demonstrated with a simple workflow. Performance results are presented that show the performance benefits of dynamic service selection. A statistical analysis based on the first order statistic is used to investigate the likely improvement in service response time arising from dynamic service selection.

  2. Nexus: A modular workflow management system for quantum simulation codes

    Science.gov (United States)

    Krogel, Jaron T.

    2016-01-01

    The management of simulation workflows represents a significant task for the individual computational researcher. Automation of the required tasks involved in simulation work can decrease the overall time to solution and reduce sources of human error. A new simulation workflow management system, Nexus, is presented to address these issues. Nexus is capable of automated job management on workstations and resources at several major supercomputing centers. Its modular design allows many quantum simulation codes to be supported within the same framework. Current support includes quantum Monte Carlo calculations with QMCPACK, density functional theory calculations with Quantum Espresso or VASP, and quantum chemical calculations with GAMESS. Users can compose workflows through a transparent, text-based interface, resembling the input file of a typical simulation code. A usage example is provided to illustrate the process.

  3. A HYBRID PETRI-NET MODEL OF GRID WORKFLOW

    Institute of Scientific and Technical Information of China (English)

    Ji Yimu; Wang Ruchuan; Ren Xunyi

    2008-01-01

    In order to effectively control the random tasks submitted and executed in grid workflow, a grid workflow model based on hybrid petri-net is presented. This model is composed of random petri-net, colored petri-net and general petri-net. Therein random petri-net declares the relationship between the number of grid users' random tasks and the size of service window and computes the server intensity of grid system. Colored petri-net sets different color for places with grid services and provides the valid interfaces for grid resource allocation and task scheduling. The experiment indicated that the model presented in this letter could compute the valve between the number of users' random tasks and the size of grid service window in grid workflow management system.

  4. Task Delegation Based Access Control Models for Workflow Systems

    Science.gov (United States)

    Gaaloul, Khaled; Charoy, François

    e-Government organisations are facilitated and conducted using workflow management systems. Role-based access control (RBAC) is recognised as an efficient access control model for large organisations. The application of RBAC in workflow systems cannot, however, grant permissions to users dynamically while business processes are being executed. We currently observe a move away from predefined strict workflow modelling towards approaches supporting flexibility on the organisational level. One specific approach is that of task delegation. Task delegation is a mechanism that supports organisational flexibility, and ensures delegation of authority in access control systems. In this paper, we propose a Task-oriented Access Control (TAC) model based on RBAC to address these requirements. We aim to reason about task from organisational perspectives and resources perspectives to analyse and specify authorisation constraints. Moreover, we present a fine grained access control protocol to support delegation based on the TAC model.

  5. Scientific Workflow Systems for 21st Century e-Science, New Bottle or New Wine?

    CERN Document Server

    Zhao, Yong; Foster, Ian

    2008-01-01

    With the advances in e-Sciences and the growing complexity of scientific analyses, more and more scientists and researchers are relying on workflow systems for process coordination, derivation automation, provenance tracking, and bookkeeping. While workflow systems have been in use for decades, it is unclear whether scientific workflows can or even should build on existing workflow technologies, or they require fundamentally new approaches. In this paper, we analyze the status and challenges of scientific workflows, investigate both existing technologies and emerging languages, platforms and systems, and identify the key challenges that must be addressed by workflow systems for e-science in the 21st century.

  6. Science Gateways, Scientific Workflows and Open Community Software

    Science.gov (United States)

    Pierce, M. E.; Marru, S.

    2014-12-01

    Science gateways and scientific workflows occupy different ends of the spectrum of user-focused cyberinfrastructure. Gateways, sometimes called science portals, provide a way for enabling large numbers of users to take advantage of advanced computing resources (supercomputers, advanced storage systems, science clouds) by providing Web and desktop interfaces and supporting services. Scientific workflows, at the other end of the spectrum, support advanced usage of cyberinfrastructure that enable "power users" to undertake computational experiments that are not easily done through the usual mechanisms (managing simulations across multiple sites, for example). Despite these different target communities, gateways and workflows share many similarities and can potentially be accommodated by the same software system. For example, pipelines to process InSAR imagery sets or to datamine GPS time series data are workflows. The results and the ability to make downstream products may be made available through a gateway, and power users may want to provide their own custom pipelines. In this abstract, we discuss our efforts to build an open source software system, Apache Airavata, that can accommodate both gateway and workflow use cases. Our approach is general, and we have applied the software to problems in a number of scientific domains. In this talk, we discuss our applications to usage scenarios specific to earth science, focusing on earthquake physics examples drawn from the QuakSim.org and GeoGateway.org efforts. We also examine the role of the Apache Software Foundation's open community model as a way to build up common commmunity codes that do not depend upon a single "owner" to sustain. Pushing beyond open source software, we also see the need to provide gateways and workflow systems as cloud services. These services centralize operations, provide well-defined programming interfaces, scale elastically, and have global-scale fault tolerance. We discuss our work providing

  7. Visualized Workflow System Based on XML and Relational Database%基于XML和关系数据库的可视化工作流系统

    Institute of Scientific and Technical Information of China (English)

    陈谊; 侯堃; 新吉乐; 陈红倩

    2012-01-01

    In order to implement a workflow management system which can support visual designing and execution of a project management workflow, a 4-layer workflow management system framework based on XML and related database was proposed, which covered the concepts, history and current advance of workflow management system, with introduction of dominant standards and technologies, and described the 4-layer system structure and system composition, data structure, the connect method of each procedure in workflow, the parsing method for XML, and implementation techniques of visual design of workflow. The workflow management system was realized in ASP.NET environment. Application shows that the system could effectively realize the project management process.%以实现一个具有可视化工作流设计和执行功能的工作流管理系统为目标,提出了一种将XML技术和关系数据库技术相结合、具有层次体系结构的工作流管理系统框架。介绍了工作流管理技术的概念、历史现状以及主要标准和技术,给出了系统的层次结构和系统组成,详细描述了系统的数据存储结构、工作流交接处理过程、XML解析方法以及利用客户端脚本技术实现工作流设计可视化的具体方法,最后在.NET平台上实现了该系统。实际应用表明,该系统能够有效实现企业项目管理中的工作流程管理。

  8. Exformatics Declarative Case Management Workflows as DCR Graphs

    DEFF Research Database (Denmark)

    Slaats, Tijs; Mukkamala, Raghava Rao; Hildebrandt, Thomas;

    2013-01-01

    Declarative workflow languages have been a growing research subject over the past ten years, but applications of the declarative approach in industry are still uncommon. Over the past two years Exformatics A/S, a Danish provider of Electronic Case Management systems, has been cooperating with...... researchers at IT University of Copenhagen (ITU) to create tools for the declarative workflow language Dynamic Condition Response Graphs (DCR Graphs) and incorporate them into their products and in teaching at ITU. In this paper we give a status report over the work. We start with an informal introduction to...

  9. Contextual cloud-based service oriented architecture for clinical workflow.

    Science.gov (United States)

    Moreno-Conde, Jesús; Moreno-Conde, Alberto; Núñez-Benjumea, Francisco J; Parra-Calderón, Carlos

    2015-01-01

    Given that acceptance of systems within the healthcare domain multiple papers highlighted the importance of integrating tools with the clinical workflow. This paper analyse how clinical context management could be deployed in order to promote the adoption of cloud advanced services and within the clinical workflow. This deployment will be able to be integrated with the eHealth European Interoperability Framework promoted specifications. Throughout this paper, it is proposed a cloud-based service-oriented architecture. This architecture will implement a context management system aligned with the HL7 standard known as CCOW. PMID:25991217

  10. A Family of RBAC- Based Workflow Authorization Models

    Institute of Scientific and Technical Information of China (English)

    HONG Fan; XING Guang-lin

    2005-01-01

    A family of RBAC-based workflow authorization models, called RWAM, are proposed. RWAM consists of a basic model and other models constructed from the basic model. The basic model provides the notion of temporal permission which means that a user can perform certain operation on a task only for a time interval, this not only ensure that only authorized users could execute a task but also ensure that the authorization flow is synchronized with workflow. The two advance models of RWAM deal with role hierarchy and constraints respectively. RWAM ranges from simple to complex and provides a general reference model for other researches and developments of such area.

  11. Biologically Inspired Execution Framework for Vulnerable Workflow Systems

    CERN Document Server

    Safdar, Sohail; Qureshi, Muhammad Aasim; Akbar, Rehan

    2009-01-01

    The main objective of the research is to introduce a biologically inspired execution framework for workflow systems under threat due to some intrusion attack. Usually vulnerable systems need to be stop and put into wait state, hence to insure the data security and privacy while being recovered. This research ensures the availability of services and data to the end user by keeping the data security, privacy and integrity intact. To achieve the specified goals, the behavior of chameleons and concept of hibernation has been considered in combination. Hence the workflow systems become more robust using biologically inspired methods and remain available to the business consumers safely even in a vulnerable state.

  12. Putting Lipstick on Pig: Enabling Database-style Workflow Provenance

    OpenAIRE

    Amsterdamer, Yael; Davidson, Susan B.; Deutch, Daniel; Milo, Tova; Stoyanovich, Julia; Tannen, Val

    2011-01-01

    Workflow provenance typically assumes that each module is a "black-box", so that each output depends on all inputs (coarse-grained dependencies). Furthermore, it does not model the internal state of a module, which can change between repeated executions. In practice, however, an output may depend on only a small subset of the inputs (fine-grained dependencies) as well as on the internal state of the module. We present a novel provenance framework that marries database-style and workflow-style...

  13. Evaluating data caching techniques in DMCF workflows using Hercules

    OpenAIRE

    Rodrigo Duro, Francisco José; Marozzo, Fabrizio; García Blas, Javier; Carretero Pérez, Jesús; Talia, Domenico; Trunfio, Paolo

    2015-01-01

    The Data Mining Cloud Framework (DMCF) is an environment for designing and executing data analysis workflows in cloud platforms. Currently, DMCF relies on the default storage of the public cloud provider for any I/O related operation. This implies that the I/O performance of DMCF is limited by the performance of the default storage. In this work we propose the usage of the Hercules system within DMCF as an ad-hoc storage system for temporary data produced inside workflow-based applications. H...

  14. Public Clouds Work Sharing Exact Workflows in Time Limits

    Directory of Open Access Journals (Sweden)

    C.Thamizhannai

    2014-12-01

    Full Text Available An algorithm that uses idle time of provisioned resources and budget surplus to replicate tasks. Deadlines being met and reduces the total execution time of applications as the budget available for replication increases. The description of tasks, data transfer time between tasks if running in different VMs (depicted in the arcs, and execution time of tasks in three different VM types (labeled S1, S2, and S3. The deadline for execution of such workflow is 30 time units and the allocation interval is 10 time units. Deadlines being met and reduces the total execution time of applications as the budget available for replication increases proposed two algorithms for cost-optimized, deadline-constrained execution of workflows in Clouds. On these settings, the IC-PCP algorithm, which is the state-of-the-art algorithm for provisioning and scheduling of workflows in Clouds. THE EIPR ALGORITHM The goal of the proposed Enhanced IC-PCP with Replication (EIPR algorithm is increasing the likelihood of completing the execution of a scientific workflow application within a user-defined deadline in a public Cloud environment. Task scheduling type of VMs to be used for workflow execution as well as start and finish time of each VM (provisioning. Placement of tasks Data transfer start and end time of scheduled tasks, but also the data transfers to the first scheduled task and from the last scheduled task. Task replication virtual machines to be ready to receive data and tasks in the moment that they are required to meet times estimated during the scheduling process. New criteria for ranking candidate tasks for replication and also workflow structure-aware scheduling of replicas, where the structure of the workflow application is considered not only during the selection of candidates for replication but also during the replica’s scheduling. We will also investigate how the replication-based approach can be used when the provisioning and scheduling process is

  15. It's All About the Data: Workflow Systems and Weather

    Science.gov (United States)

    Plale, B.

    2009-05-01

    Digital data is fueling new advances in the computational sciences, particularly geospatial research as environmental sensing grows more practical through reduced technology costs, broader network coverage, and better instruments. e-Science research (i.e., cyberinfrastructure research) has responded to data intensive computing with tools, systems, and frameworks that support computationally oriented activities such as modeling, analysis, and data mining. Workflow systems support execution of sequences of tasks on behalf of a scientist. These systems, such as Taverna, Apache ODE, and Kepler, when built as part of a larger cyberinfrastructure framework, give the scientist tools to construct task graphs of execution sequences, often through a visual interface for connecting task boxes together with arcs representing control flow or data flow. Unlike business processing workflows, scientific workflows expose a high degree of detail and control during configuration and execution. Data-driven science imposes unique needs on workflow frameworks. Our research is focused on two issues. The first is the support for workflow-driven analysis over all kinds of data sets, including real time streaming data and locally owned and hosted data. The second is the essential role metadata/provenance collection plays in data driven science, for discovery, determining quality, for science reproducibility, and for long-term preservation. The research has been conducted over the last 6 years in the context of cyberinfrastructure for mesoscale weather research carried out as part of the Linked Environments for Atmospheric Discovery (LEAD) project. LEAD has pioneered new approaches for integrating complex weather data, assimilation, modeling, mining, and cyberinfrastructure systems. Workflow systems have the potential to generate huge volumes of data. Without some form of automated metadata capture, either metadata description becomes largely a manual task that is difficult if not impossible

  16. Dynamic Profit Optimization of Composite Web Services with SLAs

    NARCIS (Netherlands)

    Zivkovic, M.; Bosman, J.W.; Berg, J.L. van den; Mei, R.D. van der; Meeuwissen, H.B.; Nunez-Queija, R.

    2011-01-01

    In this paper we investigate sequential decision mechanisms for composite web services. After executing each sub-service within a sequential workflow, decisions are made whether to terminate or continue the execution of the workflow. These decisions are based on observed response times, expected rew

  17. 一种大口径双金属复合管半自动氩弧焊接工艺%A semi - automatic TIG welding process for large - diameter bimetal composite pipe

    Institute of Scientific and Technical Information of China (English)

    王京

    2014-01-01

    采用半自动氩弧焊焊接工艺,对大口径(DN >300)双金属复合管进行焊接,包括焊前预处理、根焊、过渡焊、填充焊、盖面焊,解决了双金属复合管仅靠手工焊接施工造成的焊接速度慢、工人劳动强度大及焊接热输出量大而影响不锈钢层耐蚀性等难题。%A Semi - automatic TIG welding process for large diameter(DN > 300)bimetal composite pipe for welding,including pre-treatment before welding,root welding,soldering transition,filling welding,cosmetic welding,solved the slow speed,high labor inten-sity of workers and the welding heat output the amount is large and the effects of stainless steel corrosion resistance and other problems of the double metal composite pipe by hand welding.

  18. Styx Grid Services: Lightweight Middleware for Efficient Scientific Workflows

    Directory of Open Access Journals (Sweden)

    J.D. Blower

    2006-01-01

    Full Text Available The service-oriented approach to performing distributed scientific research is potentially very powerful but is not yet widely used in many scientific fields. This is partly due to the technical difficulties involved in creating services and workflows and the inefficiency of many workflow systems with regard to handling large datasets. We present the Styx Grid Service, a simple system that wraps command-line programs and allows them to be run over the Internet exactly as if they were local programs. Styx Grid Services are very easy to create and use and can be composed into powerful workflows with simple shell scripts or more sophisticated graphical tools. An important feature of the system is that data can be streamed directly from service to service, significantly increasing the efficiency of workflows that use large data volumes. The status and progress of Styx Grid Services can be monitored asynchronously using a mechanism that places very few demands on firewalls. We show how Styx Grid Services can interoperate with with Web Services and WS-Resources using suitable adapters.

  19. SURVEY OF WORKFLOW ANALYSIS IN PAST AND PRESENT ISSUES

    Directory of Open Access Journals (Sweden)

    SARAVANAN .M.S,

    2011-06-01

    Full Text Available This paper surveys the workflow analysis in the view of business process for all organizations. The business can be defined as an organization that provides goods and services to others, who want or need them. The concept of managing business processes is referred to as Business Process Management (BPM. A workflow is the automation of a business process, in whole or part, during which documents, information or tasks are passed from one participant to another for action, according to a set of procedural rules. The process mining aims at extracting useful and meaningful information from event logs, which is a set of real executions of business process at any organizations. This paper briefly reviews the state-or-the-art of business processes developed so far and the techniques adopted. Also presents, the survey of workflow analysis in the view of business process can be broadly classified into four major categories, they are Business Process Modeling, Ontology based Business Process Management, Workflow based Business Process Controlling and Business Process Mining.

  20. Actor-driven workflow execution in distributed environments

    NARCIS (Netherlands)

    F. Berretz; S. Skorupa; V. Sander; A. Belloum; M. Bubak

    2010-01-01

    Currently, most workflow management systems (WfMS) in Grid environments provide push-oriented task distribution strategies, where tasks are directly bound to suitable resources. In those scenarios the dedicated resources execute the submitted tasks according to the request of a WfMS or sometimes by

  1. Conceptual framework and architecture for service mediating workflow management

    NARCIS (Netherlands)

    Hu, Jinmin; Grefen, Paul

    2002-01-01

    Electronic service outsourcing creates a new paradigm for automated enterprise collaboration. The service-oriented paradigm requires a high level of flexibility of current workflow management systems and support for Business-to-Business (B2B) collaboration to realize collaborative enterprises. This

  2. Electronic Health Record-Driven Workflow for Diagnostic Radiologists.

    Science.gov (United States)

    Geeslin, Matthew G; Gaskin, Cree M

    2016-01-01

    In most settings, radiologists maintain a high-throughput practice in which efficiency is crucial. The conversion from film-based to digital study interpretation and data storage launched the era of PACS-driven workflow, leading to significant gains in speed. The advent of electronic health records improved radiologists' access to patient data; however, many still find this aspect of workflow to be relatively cumbersome. Nevertheless, the ability to guide a diagnostic interpretation with clinical information, beyond that provided in the examination indication, can add significantly to the specificity of a radiologist's interpretation. Responsibilities of the radiologist include, but are not limited to, protocoling examinations, interpreting studies, chart review, peer review, writing notes, placing orders, and communicating with referring providers. Most of the aforementioned activities are not PACS-centric and require a login to one or more additional applications. Consolidation of these tasks for completion through a single interface can simplify workflow, save time, and potentially reduce the incidence of errors. Here, the authors describe diagnostic radiology workflow that leverages the electronic health record to significantly add to a radiologist's ability to be part of the health care team, provide relevant interpretations, and improve efficiency and quality. PMID:26603098

  3. Images crossing borders: image and workflow sharing on multiple levels.

    Science.gov (United States)

    Ross, Peeter; Pohjonen, Hanna

    2011-04-01

    Digitalisation of medical data makes it possible to share images and workflows between related parties. In addition to linear data flow where healthcare professionals or patients are the information carriers, a new type of matrix of many-to-many connections is emerging. Implementation of shared workflow brings challenges of interoperability and legal clarity. Sharing images or workflows can be implemented on different levels with different challenges: inside the organisation, between organisations, across country borders, or between healthcare institutions and citizens. Interoperability issues vary according to the level of sharing and are either technical or semantic, including language. Legal uncertainty increases when crossing national borders. Teleradiology is regulated by multiple European Union (EU) directives and legal documents, which makes interpretation of the legal system complex. To achieve wider use of eHealth and teleradiology several strategic documents were published recently by the EU. Despite EU activities, responsibility for organising, providing and funding healthcare systems remains with the Member States. Therefore, the implementation of new solutions requires strong co-operation between radiologists, societies of radiology, healthcare administrators, politicians and relevant EU authorities. The aim of this article is to describe different dimensions of image and workflow sharing and to analyse legal acts concerning teleradiology in the EU. PMID:22347943

  4. Content and Workflow Management for Library Websites: Case Studies

    Science.gov (United States)

    Yu, Holly, Ed.

    2005-01-01

    Using database-driven web pages or web content management (WCM) systems to manage increasingly diverse web content and to streamline workflows is a commonly practiced solution recognized in libraries today. However, limited library web content management models and funding constraints prevent many libraries from purchasing commercially available…

  5. Images crossing borders: image and workflow sharing on multiple levels.

    Science.gov (United States)

    Ross, Peeter; Pohjonen, Hanna

    2011-04-01

    Digitalisation of medical data makes it possible to share images and workflows between related parties. In addition to linear data flow where healthcare professionals or patients are the information carriers, a new type of matrix of many-to-many connections is emerging. Implementation of shared workflow brings challenges of interoperability and legal clarity. Sharing images or workflows can be implemented on different levels with different challenges: inside the organisation, between organisations, across country borders, or between healthcare institutions and citizens. Interoperability issues vary according to the level of sharing and are either technical or semantic, including language. Legal uncertainty increases when crossing national borders. Teleradiology is regulated by multiple European Union (EU) directives and legal documents, which makes interpretation of the legal system complex. To achieve wider use of eHealth and teleradiology several strategic documents were published recently by the EU. Despite EU activities, responsibility for organising, providing and funding healthcare systems remains with the Member States. Therefore, the implementation of new solutions requires strong co-operation between radiologists, societies of radiology, healthcare administrators, politicians and relevant EU authorities. The aim of this article is to describe different dimensions of image and workflow sharing and to analyse legal acts concerning teleradiology in the EU.

  6. From Paper Based Clinical Practice Guidelines to Declarative Workflow Management

    DEFF Research Database (Denmark)

    Lyng, Karen Marie; Hildebrandt, Thomas; Mukkamala, Raghava Rao

    2009-01-01

    We present a field study of oncology workflow, involving doctors, nurses and pharmacists at Danish hospitals and discuss the obstacles, enablers and challenges for the use of computer based clinical practice guidelines. Related to the CIGDec approach of Pesic and van der Aalst we then describe how...

  7. Putting Lipstick on Pig: Enabling Database-style Workflow Provenance

    CERN Document Server

    Amsterdamer, Yael; Deutch, Daniel; Milo, Tova; Stoyanovich, Julia; Tannen, Val

    2012-01-01

    Workflow provenance typically assumes that each module is a "black-box", so that each output depends on all inputs (coarse-grained dependencies). Furthermore, it does not model the internal state of a module, which can change between repeated executions. In practice, however, an output may depend on only a small subset of the inputs (fine-grained dependencies) as well as on the internal state of the module. We present a novel provenance framework that marries database-style and workflow-style provenance, by using Pig Latin to expose the functionality of modules, thus capturing internal state and fine-grained dependencies. A critical ingredient in our solution is the use of a novel form of provenance graph that models module invocations and yields a compact representation of fine-grained workflow provenance. It also enables a number of novel graph transformation operations, allowing to choose the desired level of granularity in provenance querying (ZoomIn and ZoomOut), and supporting "what-if" workflow analyti...

  8. CrossFlow: Integrating Workflow Management and Electronic Commerce

    NARCIS (Netherlands)

    Hoffner, Y.; Ludwig, H.; Grefen, P.; Aberer, K.

    2001-01-01

    The CrossFlow1 architecture provides support for cross-organisational workflow management in dynamically established virtual enterprises. The creation of a business relationship between a service provider organisation performing a service on behalf of a consumer organisation can be made dynamic when

  9. Verification of Timed Healthcare Workflows Using Component Timed-Arc Petri Nets

    DEFF Research Database (Denmark)

    Bertolini, Cristiano; Liu, Zhiming; Srba, Jiri

    2013-01-01

    Workflows in modern healthcare systems are becoming increasingly complex and their execution involves concurrency and sharing of resources. The definition, analysis and management of collaborative healthcare workflows requires abstract model notations with a precisely defined semantics and a supp......Workflows in modern healthcare systems are becoming increasingly complex and their execution involves concurrency and sharing of resources. The definition, analysis and management of collaborative healthcare workflows requires abstract model notations with a precisely defined semantics...

  10. An integrated development workflow for community-driven FOSS-projects using continuous integration tools

    Science.gov (United States)

    Bilke, Lars; Watanabe, Norihiro; Naumov, Dmitri; Kolditz, Olaf

    2016-04-01

    A complex software project in general with high standards regarding code quality requires automated tools to help developers in doing repetitive and tedious tasks such as compilation on different platforms and configurations, doing unit testing as well as end-to-end tests and generating distributable binaries and documentation. This is known as continuous integration (CI). A community-driven FOSS-project within the Earth Sciences benefits even more from CI as time and resources regarding software development are often limited. Therefore testing developed code on more than the developers PC is a task which is often neglected and where CI can be the solution. We developed an integrated workflow based on GitHub, Travis and Jenkins for the community project OpenGeoSys - a coupled multiphysics modeling and simulation package - allowing developers to concentrate on implementing new features in a tight feedback loop. Every interested developer/user can create a pull request containing source code modifications on the online collaboration platform GitHub. The modifications are checked (compilation, compiler warnings, memory leaks, undefined behaviors, unit tests, end-to-end tests, analyzing differences in simulation run results between changes etc.) from the CI system which automatically responds to the pull request or by email on success or failure with detailed reports eventually requesting to improve the modifications. Core team developers review the modifications and merge them into the main development line once they satisfy agreed standards. We aim for efficient data structures and algorithms, self-explaining code, comprehensive documentation and high test code coverage. This workflow keeps entry barriers to get involved into the project low and permits an agile development process concentrating on feature additions rather than software maintenance procedures.

  11. Workflows for ingest of research data into digital archives - tests with Archivematica

    Science.gov (United States)

    Kirchner, I.; Bertelmann, R.; Gebauer, P.; Hasler, T.; Hirt, M.; Klump, J. F.; Peters-Kotting, W.; Rusch, B.; Ulbricht, D.

    2013-12-01

    Publication of research data and future re-use of measured data require the long-term preservation of digital objects. The ISO OAIS reference model defines responsibilities for long-term preservation of digital objects and although there is software available to support preservation of digital data, there are still problems remaining to be solved. A key task in preservation is to make the datasets ready for ingest into the archive, which is called the creation of Submission Information Packages (SIPs) in the OAIS model. This includes the creation of appropriate preservation metadata. Scientists need to be trained to deal with different types of data and to heighten their awareness for quality metadata. Other problems arise during the assembly of SIPs and during ingest into the archive because file format validators may produce conflicting output for identical data files and these conflicts are difficult to resolve automatically. Also, validation and identification tools are notorious for their poor performance. In the project EWIG Zuse-Institute Berlin acts as an infrastructure facility, while the Institute for Meteorology at FU Berlin and the German research Centre for Geosciences GFZ act as two different data producers. The aim of the project is to develop workflows for the transfer of research data into digital archives and the future re-use of data from long-term archives with emphasis on data from the geosciences. The technical work is supplemented by interviews with data practitioners at several institutions to identify problems in digital preservation workflows and by the development of university teaching materials to train students in the curation of research data and metadata. The free and open-source software Archivematica [1] is used as digital preservation system. The creation and ingest of SIPs has to meet several archival standards and be compatible to the Metadata Encoding and Transmission Standard (METS). The two data producers use different

  12. A Workflow-Oriented Approach To Propagation Models In Heliophysics

    Directory of Open Access Journals (Sweden)

    Gabriele Pierantoni

    2014-01-01

    Full Text Available The Sun is responsible for the eruption of billions of tons of plasma andthe generation of near light-speed particles that propagate throughout the solarsystem and beyond. If directed towards Earth, these events can be damaging toour tecnological infrastructure. Hence there is an effort to understand the causeof the eruptive events and how they propagate from Sun to Earth. However, thephysics governing their propagation is not well understood, so there is a need todevelop a theoretical description of their propagation, known as a PropagationModel, in order to predict when they may impact Earth. It is often difficultto define a single propagation model that correctly describes the physics ofsolar eruptive events, and even more difficult to implement models capable ofcatering for all these complexities and to validate them using real observational data.In this paper, we envisage that workflows offer both a theoretical andpractical framerwork for a novel approach to propagation models. We definea mathematical framework that aims at encompassing the different modalitieswith which workflows can be used, and provide a set of generic building blockswritten in the TAVERNA workflow language that users can use to build theirown propagation models. Finally we test both the theoretical model and thecomposite building blocks of the workflow with a real Science Use Case that wasdiscussed during the 4th CDAW (Coordinated Data Analysis Workshop eventheld by the HELIO project. We show that generic workflow building blocks canbe used to construct a propagation model that succesfully describes the transitof solar eruptive events toward Earth and predict a correct Earth-impact time

  13. Automatic multimodal real-time tracking for image plane alignment in interventional Magnetic Resonance Imaging

    International Nuclear Information System (INIS)

    Interventional magnetic resonance imaging (MRI) aims at performing minimally invasive percutaneous interventions, such as tumor ablations and biopsies, under MRI guidance. During such interventions, the acquired MR image planes are typically aligned to the surgical instrument (needle) axis and to surrounding anatomical structures of interest in order to efficiently monitor the advancement in real-time of the instrument inside the patient's body. Object tracking inside the MRI is expected to facilitate and accelerate MR-guided interventions by allowing to automatically align the image planes to the surgical instrument. In this PhD thesis, an image-based work-flow is proposed and refined for automatic image plane alignment. An automatic tracking work-flow was developed, performing detection and tracking of a passive marker directly in clinical real-time images. This tracking work-flow is designed for fully automated image plane alignment, with minimization of tracking-dedicated time. Its main drawback is its inherent dependence on the slow clinical MRI update rate. First, the addition of motion estimation and prediction with a Kalman filter was investigated and improved the work-flow tracking performance. Second, a complementary optical sensor was used for multi-sensor tracking in order to decouple the tracking update rate from the MR image acquisition rate. Performance of the work-flow was evaluated with both computer simulations and experiments using an MR compatible test bed. Results show a high robustness of the multi-sensor tracking approach for dynamic image plane alignment, due to the combination of the individual strengths of each sensor. (author)

  14. Performance prediction for Grid workflow activities based on features-ranked RBF network

    Institute of Scientific and Technical Information of China (English)

    Wang Jie; Duan Rubing; Farrukh Nadeem

    2009-01-01

    Accurate performance prediction of Grid workflow activities can help Grid schedulers map activities to appropriate Grid sites. This paper describes an approach based on features-ranked RBF neural network to predict the performance of Grid workflow activities. Experimental results for two kinds of real world Grid workflow activities are presented to show effectiveness of our approach.

  15. Automatic Fiscal Stabilizers

    Directory of Open Access Journals (Sweden)

    Narcis Eduard Mitu

    2013-11-01

    Full Text Available Policies or institutions (built into an economic system that automatically tend to dampen economic cycle fluctuations in income, employment, etc., without direct government intervention. For example, in boom times, progressive income tax automatically reduces money supply as incomes and spendings rise. Similarly, in recessionary times, payment of unemployment benefits injects more money in the system and stimulates demand. Also called automatic stabilizers or built-in stabilizers.

  16. Automatic input rectification

    OpenAIRE

    Long, Fan; Ganesh, Vijay; Carbin, Michael James; Sidiroglou, Stelios; Rinard, Martin

    2012-01-01

    We present a novel technique, automatic input rectification, and a prototype implementation, SOAP. SOAP learns a set of constraints characterizing typical inputs that an application is highly likely to process correctly. When given an atypical input that does not satisfy these constraints, SOAP automatically rectifies the input (i.e., changes the input so that it satisfies the learned constraints). The goal is to automatically convert potentially dangerous inputs into typical inputs that the ...

  17. A Community-Driven Workflow Recommendations and Reuse Infrastructure

    Science.gov (United States)

    Zhang, J.; Votava, P.; Lee, T. J.; Lee, C.; Xiao, S.; Nemani, R. R.; Foster, I.

    2013-12-01

    Aiming to connect the Earth science community to accelerate the rate of discovery, NASA Earth Exchange (NEX) has established an online repository and platform, so that researchers can publish and share their tools and models with colleagues. In recent years, workflow has become a popular technique at NEX for Earth scientists to define executable multi-step procedures for data processing and analysis. The ability to discover and reuse knowledge (sharable workflows or workflow) is critical to the future advancement of science. However, as reported in our earlier study, the reusability of scientific artifacts at current time is very low. Scientists often do not feel confident in using other researchers' tools and utilities. One major reason is that researchers are often unaware of the existence of others' data preprocessing processes. Meanwhile, researchers often do not have time to fully document the processes and expose them to others in a standard way. These issues cannot be overcome by the existing workflow search technologies used in NEX and other data projects. Therefore, this project aims to develop a proactive recommendation technology based on collective NEX user behaviors. In this way, we aim to promote and encourage process and workflow reuse within NEX. Particularly, we focus on leveraging peer scientists' best practices to support the recommendation of artifacts developed by others. Our underlying theoretical foundation is rooted in the social cognitive theory, which declares people learn by watching what others do. Our fundamental hypothesis is that sharable artifacts have network properties, much like humans in social networks. More generally, reusable artifacts form various types of social relationships (ties), and may be viewed as forming what organizational sociologists who use network analysis to study human interactions call a 'knowledge network.' In particular, we will tackle two research questions: R1: What hidden knowledge may be extracted from

  18. The Symbiotic Relationship between Scientific Workflow and Provenance (Invited)

    Science.gov (United States)

    Stephan, E.

    2010-12-01

    The purpose of this presentation is to describe the symbiotic nature of scientific workflows and provenance. We will also discuss the current trends and real world challenges facing these two distinct research areas. Although motivated differently, the needs of the international science communities are the glue that binds this relationship together. Understanding and articulating the science drivers to these communities is paramount as these technologies evolve and mature. Originally conceived for managing business processes, workflows are now becoming invaluable assets in both computational and experimental sciences. These reconfigurable, automated systems provide essential technology to perform complex analyses by coupling together geographically distributed disparate data sources and applications. As a result, workflows are capable of higher throughput in a shorter amount of time than performing the steps manually. Today many different workflow products exist; these could include Kepler and Taverna or similar products like MeDICI, developed at PNNL, that are standardized on the Business Process Execution Language (BPEL). Provenance, originating from the French term Provenir “to come from”, is used to describe the curation process of artwork as art is passed from owner to owner. The concept of provenance was adopted by digital libraries as a means to track the lineage of documents while standards such as the DublinCore began to emerge. In recent years the systems science community has increasingly expressed the need to expand the concept of provenance to formally articulate the history of scientific data. Communities such as the International Provenance and Annotation Workshop (IPAW) have formalized a provenance data model. The Open Provenance Model, and the W3C is hosting a provenance incubator group featuring the Proof Markup Language. Although both workflows and provenance have risen from different communities and operate independently, their mutual

  19. Automatic differentiation bibliography

    Energy Technology Data Exchange (ETDEWEB)

    Corliss, G.F. (comp.)

    1992-07-01

    This is a bibliography of work related to automatic differentiation. Automatic differentiation is a technique for the fast, accurate propagation of derivative values using the chain rule. It is neither symbolic nor numeric. Automatic differentiation is a fundamental tool for scientific computation, with applications in optimization, nonlinear equations, nonlinear least squares approximation, stiff ordinary differential equation, partial differential equations, continuation methods, and sensitivity analysis. This report is an updated version of the bibliography which originally appeared in Automatic Differentiation of Algorithms: Theory, Implementation, and Application.

  20. Review of Automatic Feature Extraction from High-Resolution Optical Sensor Data for UAV-Based Cadastral Mapping

    Directory of Open Access Journals (Sweden)

    Sophie Crommelinck

    2016-08-01

    Full Text Available Unmanned Aerial Vehicles (UAVs have emerged as a rapid, low-cost and flexible acquisition system that appears feasible for application in cadastral mapping: high-resolution imagery, acquired using UAVs, enables a new approach for defining property boundaries. However, UAV-derived data are arguably not exploited to its full potential: based on UAV data, cadastral boundaries are visually detected and manually digitized. A workflow that automatically extracts boundary features from UAV data could increase the pace of current mapping procedures. This review introduces a workflow considered applicable for automated boundary delineation from UAV data. This is done by reviewing approaches for feature extraction from various application fields and synthesizing these into a hypothetical generalized cadastral workflow. The workflow consists of preprocessing, image segmentation, line extraction, contour generation and postprocessing. The review lists example methods per workflow step—including a description, trialed implementation, and a list of case studies applying individual methods. Furthermore, accuracy assessment methods are outlined. Advantages and drawbacks of each approach are discussed in terms of their applicability on UAV data. This review can serve as a basis for future work on the implementation of most suitable methods in a UAV-based cadastral mapping workflow.

  1. Networked Print Production: Does JDF Provide a Perfect Workflow?

    Directory of Open Access Journals (Sweden)

    Bernd Zipper

    2004-12-01

    Full Text Available The "networked printing works" is a well-worn slogan used by many providers in the graphics industry and for the past number of years printing-works manufacturers have been working on the goal of achieving the "networked printing works". A turning point from the concept to real implementation can now be expected at drupa 2004: JDF (Job Definition Format and thus "networked production" will form the center of interest here. The first approaches towards a complete, networked workflow between prepress, print and postpress in production are already available - the products and solutions will now be presented publicly at drupa 2004. So, drupa 2004 will undoubtedly be the "JDF-drupa" - the drupa where machines learn to communicate with each other digitally - the drupa, where the dream of general system and job communication in the printing industry can be first realized. CIP3, which has since been renamed CIP4, is an international consortium of leading manufacturers from the printing and media industry who have taken on the task of integrating processes for prepress, print and postpress. The association, to which nearly all manufacturers in the graphics industry belong, has succeeded with CIP3 in developing a first international standard for the transmission of control data in the print workflow.Further development of the CIP4 standard now includes a more extensive "system language" called JDF, which will guarantee workflow communication beyond manufacturer boundaries. However, not only data for actual print production will be communicated with JDF (Job Definition Format: planning and calculation data for MIS (Management Information systems and calculation systems will also be prepared. The German printing specialist Hans-Georg Wenke defines JDF as follows: "JDF takes over data from MIS for machines, aggregates and their control desks, data exchange within office applications, and finally ensures that data can be incorporated in the technical workflow

  2. A framework for evaluating automatic indexing or classification in the context of retrieval

    DEFF Research Database (Denmark)

    Golub, Korajlka; Soergel, Dagobert; Buchanan, George;

    2016-01-01

    Tools for automatic subject assignment help deal with scale and sustainability in creating and enriching metadata, establishing more connections across and between resources and enhancing consistency. While some software vendors and experimental researchers claim the tools can replace manual...... of the literature on indexing, classification and approaches: evaluating indexing quality directly through assessment by an evaluator or through comparison with a gold standard; evaluating the quality of computer-assisted indexing directly in the context of an indexing workflow, and evaluating indexing quality...

  3. Developing integrated workflows for the digitisation of herbarium specimens using a modular and scalable approach

    Directory of Open Access Journals (Sweden)

    Elspeth Haston

    2012-07-01

    Full Text Available Digitisation programmes in many institutes frequently involve disparate and irregular funding, diverse selection criteria and scope, with different members of staff managing and operating the processes. These factors have influenced the decision at the Royal Botanic Garden Edinburgh to develop an integrated workflow for the digitisation of herbarium specimens which is modular and scalable to enable a single overall workflow to be used for all digitisation projects. This integrated workflow is comprised of three principal elements: a specimen workflow, a data workflow and an image workflow.The specimen workflow is strongly linked to curatorial processes which will impact on the prioritisation, selection and preparation of the specimens. The importance of including a conservation element within the digitisation workflow is highlighted. The data workflow includes the concept of three main categories of collection data: label data, curatorial data and supplementary data. It is shown that each category of data has its own properties which influence the timing of data capture within the workflow. Development of software has been carried out for the rapid capture of curatorial data, and optical character recognition (OCR software is being used to increase the efficiency of capturing label data and supplementary data. The large number and size of the images has necessitated the inclusion of automated systems within the image workflow.

  4. Developing integrated workflows for the digitisation of herbarium specimens using a modular and scalable approach.

    Science.gov (United States)

    Haston, Elspeth; Cubey, Robert; Pullan, Martin; Atkins, Hannah; Harris, David J

    2012-01-01

    Digitisation programmes in many institutes frequently involve disparate and irregular funding, diverse selection criteria and scope, with different members of staff managing and operating the processes. These factors have influenced the decision at the Royal Botanic Garden Edinburgh to develop an integrated workflow for the digitisation of herbarium specimens which is modular and scalable to enable a single overall workflow to be used for all digitisation projects. This integrated workflow is comprised of three principal elements: a specimen workflow, a data workflow and an image workflow.The specimen workflow is strongly linked to curatorial processes which will impact on the prioritisation, selection and preparation of the specimens. The importance of including a conservation element within the digitisation workflow is highlighted. The data workflow includes the concept of three main categories of collection data: label data, curatorial data and supplementary data. It is shown that each category of data has its own properties which influence the timing of data capture within the workflow. Development of software has been carried out for the rapid capture of curatorial data, and optical character recognition (OCR) software is being used to increase the efficiency of capturing label data and supplementary data. The large number and size of the images has necessitated the inclusion of automated systems within the image workflow. PMID:22859881

  5. Automatic Texture and Orthophoto Generation from Registered Panoramic Views

    DEFF Research Database (Denmark)

    Krispel, Ulrich; Evers, Henrik Leander; Tamke, Martin;

    2015-01-01

    Recent trends in 3D scanning are aimed at the fusion of range data and color information from images. The combination of these two outputs allows to extract novel semantic information. The workflow presented in this paper allows to detect objects, such as light switches, that are hard to identify...... from range data only. In order to detect these elements, we developed a method that utilizes range data and color information from high-resolution panoramic images of indoor scenes, taken at the scanners position. A proxy geometry is derived from the point clouds; orthographic views of the scene...... are automatically identified from the geometry and an image per view is created via projection. We combine methods of computer vision to train a classifier to detect the objects of interest from these orthographic views. Furthermore, these views can be used for automatic texturing of the proxy geometry....

  6. Workflow Modelling and Analysis Based on the Construction of Task Models

    Directory of Open Access Journals (Sweden)

    Glória Cravo

    2015-01-01

    Full Text Available We describe the structure of a workflow as a graph whose vertices represent tasks and the arcs are associated to workflow transitions in this paper. To each task an input/output logic operator is associated. Furthermore, we associate a Boolean term to each transition present in the workflow. We still identify the structure of workflows and describe their dynamism through the construction of new task models. This construction is very simple and intuitive since it is based on the analysis of all tasks present on the workflow that allows us to describe the dynamism of the workflow very easily. So, our approach has the advantage of being very intuitive, which is an important highlight of our work. We also introduce the concept of logical termination of workflows and provide conditions under which this property is valid. Finally, we provide a counter-example which shows that a conjecture presented in a previous article is false.

  7. ActiveBPEL中组合服务自动部署的研究和实现%Implementation of automatic deployment composition service on ActiveBPEL

    Institute of Scientific and Technical Information of China (English)

    杨楠; 马力; 陈彦萍

    2010-01-01

    为了把选定的单个原子服务组合成一个完整的组合服务,需要应用BPEL(Business Process Execution Language)描述整个组合服务的流程.本文通过应用原型系统中已提出的SCML(Service Composition Management Language)服务组合管理语言,对在此语言基础上自动产生BPEL的实现方法进行研究,提出一种由SCML出发自动转化BPEL并在引擎中自动部署、发布、执行的方法,并用此方法把旅游服务的模型发布在ActiveBPEL引擎上.该方法对于流程自动发布具有一定的可用性.

  8. How Workflow Systems Facilitate Business Process Reengineering and Improvement

    Directory of Open Access Journals (Sweden)

    Mohamed El Khadiri

    2012-03-01

    Full Text Available This paper investigates the relationship between workflow systems and business process reengineering and improvement. The study is based on a real case study at the “Centre Rgional dInvestissement” (CRI of Marrakech, Morocco. The CRI is entrusted to coordinate various investment projects at the regional level. Our previous work has shown that workflow system can be a basis for business process reengineering. However, for continuous process improvement, the system has shown to be insufficient as it fails to deal with exceptions and problem resolutions that informal communications provide. However, when this system is augmented with an expanded corporate memory system that includes social tools, to capture informal communication and data, we are closer to a more complete system that facilitates business process reengineering and improvement.

  9. Building Scientific Workflows for the Geosciences with Open Community Software

    Science.gov (United States)

    Pierce, M. E.; Marru, S.; Weerawarana, S. M.

    2012-12-01

    We describe the design and development of the Apache Airavata scientific workflow software and its application to problems in geosciences. Airavata is based on Service Oriented Architecture principles and is developed as general purpose software for managing large-scale science applications on supercomputing resources such as the NSF's XSEDE. Based on the NSF-funded EarthCube Workflow Working Group activities, we discuss the application of this software relative to specific requirements (such as data stream data processing, event triggering, dealing with large data sets, and advanced distributed execution patterns involved in data mining). We also consider the role of governance in EarthCube software development and present the development of Airavata software through the Apache Software Foundation's community development model. We discuss the potential impacts on software accountability and sustainability using this model.

  10. Technical Perspectives on Knowledge Management in Bioinformatics Workflow Systems

    Directory of Open Access Journals (Sweden)

    Walaa N. Ismail

    2015-01-01

    Full Text Available Workflow systems by it’s nature can help bioin-formaticians to plan for their experiments, store, capture and analysis of the runtime generated data. On the other hand, the life science research usually produces new knowledge at an increasing speed; Knowledge such as papers, databases and other systems knowledge that a researcher needs to deal with is actually a complex task that needs much of efforts and time. Thus the management of knowledge is therefore an important issue for life scientists. Approaches has been developed to organize biological knowledge sources and to record provenance knowledge of an experiment into a readily resource are presently being carried out. This article focuses on the knowledge management of in silico experimentation in bioinformatics workflow systems.

  11. CONNJUR Workflow Builder: a software integration environment for spectral reconstruction

    International Nuclear Information System (INIS)

    CONNJUR Workflow Builder (WB) is an open-source software integration environment that leverages existing spectral reconstruction tools to create a synergistic, coherent platform for converting biomolecular NMR data from the time domain to the frequency domain. WB provides data integration of primary data and metadata using a relational database, and includes a library of pre-built workflows for processing time domain data. WB simplifies maximum entropy reconstruction, facilitating the processing of non-uniformly sampled time domain data. As will be shown in the paper, the unique features of WB provide it with novel abilities to enhance the quality, accuracy, and fidelity of the spectral reconstruction process. WB also provides features which promote collaboration, education, parameterization, and non-uniform data sets along with processing integrated with the Rowland NMR Toolkit (RNMRTK) and NMRPipe software packages. WB is available free of charge in perpetuity, dual-licensed under the MIT and GPL open source licenses

  12. A framework for streamlining research workflow in neuroscience and psychology

    Directory of Open Access Journals (Sweden)

    Jonas eKubilius

    2014-01-01

    Full Text Available Successful accumulation of knowledge is critically dependent on the ability to verify and replicate every part of scientific conduct. However, such principles are difficult to enact when researchers continue to resort on ad hoc workflows and with poorly maintained code base. In this paper I examine the needs of neuroscience and psychology community, and introduce psychopy_ext, a unifying framework that seamlessly integrates popular experiment building, analysis and manuscript preparation tools by choosing reasonable defaults and implementing relatively rigid patterns of workflow. This structure allows for automation of multiple tasks, such as generated user interfaces, unit testing, control analyses of stimuli, single-command access to descriptive statistics, and publication quality plotting. Taken together, psychopy_ext opens an exciting possibility for faster, more robust code development and collaboration for researchers.

  13. Staffing and Workflow of a Maturing Institutional Repository

    Directory of Open Access Journals (Sweden)

    Debora L. Madsen

    2013-02-01

    Full Text Available Institutional repositories (IRs have become established components of many academic libraries. As an IR matures it will face the challenge of how to scale up its operations to increase the amount and types of content archived. These challenges involve staffing, systems, workflows, and promotion. In the past eight years, Kansas State University's IR (K-REx has grown from a platform for student theses, dissertations, and reports to also include faculty works. The initial workforce of a single faculty member was expanded as a part of a library-wide reorganization, resulting in a cross-departmental team that is better able to accommodate the expansion of the IR. The resultant need to define staff responsibilities and develop resources to manage the workflows has led to the innovations described here, which may prove useful to the greater library community as other IRs mature.

  14. Modular Workflow Engine for Distributed Services using Lightweight Java Clients

    CERN Document Server

    Vetter, R -M; Peetz, J -V

    2009-01-01

    In this article we introduce the concept and the first implementation of a lightweight client-server-framework as middleware for distributed computing. On the client side an installation without administrative rights or privileged ports can turn any computer into a worker node. Only a Java runtime environment and the JAR files comprising the workflow client are needed. To connect all clients to the engine one open server port is sufficient. The engine submits data to the clients and orchestrates their work by workflow descriptions from a central database. Clients request new task descriptions periodically, thus the system is robust against network failures. In the basic set-up, data up- and downloads are handled via HTTP communication with the server. The performance of the modular system could additionally be improved using dedicated file servers or distributed network file systems. We demonstrate the design features of the proposed engine in real-world applications from mechanical engineering. We have used ...

  15. CONNJUR Workflow Builder: a software integration environment for spectral reconstruction

    Energy Technology Data Exchange (ETDEWEB)

    Fenwick, Matthew; Weatherby, Gerard; Vyas, Jay; Sesanker, Colbert [UConn Health, Department of Molecular Biology and Biophysics (United States); Martyn, Timothy O. [Rensselaer at Hartford, Department of Engineering and Science (United States); Ellis, Heidi J. C. [Western New England College, Department of Computer Science and Information Technology (United States); Gryk, Michael R., E-mail: gryk@uchc.edu [UConn Health, Department of Molecular Biology and Biophysics (United States)

    2015-07-15

    CONNJUR Workflow Builder (WB) is an open-source software integration environment that leverages existing spectral reconstruction tools to create a synergistic, coherent platform for converting biomolecular NMR data from the time domain to the frequency domain. WB provides data integration of primary data and metadata using a relational database, and includes a library of pre-built workflows for processing time domain data. WB simplifies maximum entropy reconstruction, facilitating the processing of non-uniformly sampled time domain data. As will be shown in the paper, the unique features of WB provide it with novel abilities to enhance the quality, accuracy, and fidelity of the spectral reconstruction process. WB also provides features which promote collaboration, education, parameterization, and non-uniform data sets along with processing integrated with the Rowland NMR Toolkit (RNMRTK) and NMRPipe software packages. WB is available free of charge in perpetuity, dual-licensed under the MIT and GPL open source licenses.

  16. Research on Architecture of Enterprise Modeling in Workflow System

    Institute of Scientific and Technical Information of China (English)

    李伟平; 齐慧彬; 薛劲松; 朱云龙

    2002-01-01

    The market that an enterprise is faced is changing and can 't be forecastedaccurately in this information time. In order to find the chances in the marketpractitioners have focused on business processes through their re-engineeringprogramme to improve enterprise efficiency. It is necessary to manage an enterpriseusing process-based method for the requirement of enhancing work efficiency and theability of competition in the market. And information system developers haveemphasized the use of standard models to accelerate the speed of configuration andimplementation of integrated systems for enterprises. So we have to model anenterprise with process-based modeling method. An architecture of enterprise modelingis presented in this paper. This architecture is composed of four views and supportingthe whole lifecycle of enterprise model. Because workflow management system is basedon process definition, this architecture can be directly used in the workflowmanagement system. The implement method of this model was thoroughly describedmeanwhile the workflow management software supporting the building and running themodel was also given.

  17. A computational workflow for designing silicon donor qubits

    Science.gov (United States)

    Humble, Travis S.; Ericson, M. Nance; Jakowski, Jacek; Huang, Jingsong; Britton, Charles; Curtis, Franklin G.; Dumitrescu, Eugene F.; Mohiyaddin, Fahd A.; Sumpter, Bobby G.

    2016-10-01

    Developing devices that can reliably and accurately demonstrate the principles of superposition and entanglement is an on-going challenge for the quantum computing community. Modeling and simulation offer attractive means of testing early device designs and establishing expectations for operational performance. However, the complex integrated material systems required by quantum device designs are not captured by any single existing computational modeling method. We examine the development and analysis of a multi-staged computational workflow that can be used to design and characterize silicon donor qubit systems with modeling and simulation. Our approach integrates quantum chemistry calculations with electrostatic field solvers to perform detailed simulations of a phosphorus dopant in silicon. We show how atomistic details can be synthesized into an operational model for the logical gates that define quantum computation in this particular technology. The resulting computational workflow realizes a design tool for silicon donor qubits that can help verify and validate current and near-term experimental devices.

  18. Computer imaging and workflow systems in the business office.

    Science.gov (United States)

    Adams, W T; Veale, F H; Helmick, P M

    1999-05-01

    Computer imaging and workflow technology automates many business processes that currently are performed using paper processes. Documents are scanned into the imaging system and placed in electronic patient account folders. Authorized users throughout the organization, including preadmission, verification, admission, billing, cash posting, customer service, and financial counseling staff, have online access to the information they need when they need it. Such streamlining of business functions can increase collections and customer satisfaction while reducing labor, supply, and storage costs. Because the costs of a comprehensive computer imaging and workflow system can be considerable, healthcare organizations should consider implementing parts of such systems that can be cost-justified or include implementation as part of a larger strategic technology initiative.

  19. CrossFlow: Integrating Workflow Management and Electronic Commerce

    OpenAIRE

    Hoffner, Y.; Ludwig, H; Grefen, P.; Aberer, K.

    2001-01-01

    The CrossFlow1 architecture provides support for cross-organisational workflow management in dynamically established virtual enterprises. The creation of a business relationship between a service provider organisation performing a service on behalf of a consumer organisation can be made dynamic when augmented by virtual market technology, the dynamic configuration of the contract enactment infrastructures, and the provision of fine grained service monitoring and control. Standard ways of desc...

  20. A framework for streamlining research workflow in neuroscience and psychology

    OpenAIRE

    Kubilius, Jonas

    2014-01-01

    Successful accumulation of knowledge is critically dependent on the ability to verify and replicate every part of scientific conduct. However, such principles are difficult to enact when researchers continue to resort on ad-hoc workflows and with poorly maintained code base. In this paper I examine the needs of neuroscience and psychology community, and introduce psychopy_ext, a unifying framework that seamlessly integrates popular experiment building, analysis and manuscript preparation tool...

  1. Facilitating hydrological data analysis workflows in R: the RHydro package

    Science.gov (United States)

    Buytaert, Wouter; Moulds, Simon; Skoien, Jon; Pebesma, Edzer; Reusser, Dominik

    2015-04-01

    The advent of new technologies such as web-services and big data analytics holds great promise for hydrological data analysis and simulation. Driven by the need for better water management tools, it allows for the construction of much more complex workflows, that integrate more and potentially more heterogeneous data sources with longer tool chains of algorithms and models. With the scientific challenge of designing the most adequate processing workflow comes the technical challenge of implementing the workflow with a minimal risk for errors. A wide variety of new workbench technologies and other data handling systems are being developed. At the same time, the functionality of available data processing languages such as R and Python is increasing at an accelerating pace. Because of the large diversity of scientific questions and simulation needs in hydrology, it is unlikely that one single optimal method for constructing hydrological data analysis workflows will emerge. Nevertheless, languages such as R and Python are quickly gaining popularity because they combine a wide array of functionality with high flexibility and versatility. The object-oriented nature of high-level data processing languages makes them particularly suited for the handling of complex and potentially large datasets. In this paper, we explore how handling and processing of hydrological data in R can be facilitated further by designing and implementing a set of relevant classes and methods in the experimental R package RHydro. We build upon existing efforts such as the sp and raster packages for spatial data and the spacetime package for spatiotemporal data to define classes for hydrological data (HydroST). In order to handle simulation data from hydrological models conveniently, a HM class is defined. Relevant methods are implemented to allow for an optimal integration of the HM class with existing model fitting and simulation functionality in R. Lastly, we discuss some of the design challenges

  2. Enhanced Phosphoproteomic Profiling Workflow For Growth Factor Signaling Analysis

    DEFF Research Database (Denmark)

    Sylvester, Marc; Burbridge, Mike; Leclerc, Gregory;

    2010-01-01

    immobilized metal affinity chromatography (SIMAC) with TiO2 enrichment. Phosphotyrosine containing peptides were enriched by immunoprecipitation. iTRAQ™ labeling enabled multiplexed quantification of changes during stimulation and comparison of different stimuli. Several fragmentation techniques were used...... transfer dissociation adds confidence in modification site assignment. The workflow is relatively simple but the integration of complementary techniques leads to a deeper insight into cellular signaling networks and the potential pharmacological intervention thereof....

  3. Evolutionary multi-objective workflow scheduling in Cloud

    OpenAIRE

    Z. Zhu; Zhang, G.; M. Li; Liu, X.

    2015-01-01

    Cloud computing provides promising platforms for executing large applications with enormous computational resources to offer on demand. In a Cloud model, users are charged based on their usage of resources and the required quality of service (QoS) specifications. Although there are many existing workflow scheduling algorithms in traditional distributed or heterogeneous computing environments, they have difficulties in being directly applied to the Cloud environments since Cloud differs from t...

  4. Analysis of Whole Transcriptome Sequencing Data: Workflow and Software.

    Science.gov (United States)

    Yang, In Seok; Kim, Sangwoo

    2015-12-01

    RNA is a polymeric molecule implicated in various biological processes, such as the coding, decoding, regulation, and expression of genes. Numerous studies have examined RNA features using whole transcriptome sequencing (RNA-seq) approaches. RNA-seq is a powerful technique for characterizing and quantifying the transcriptome and accelerates the development of bioinformatics software. In this review, we introduce routine RNA-seq workflow together with related software, focusing particularly on transcriptome reconstruction and expression quantification. PMID:26865842

  5. a Standardized Approach to Topographic Data Processing and Workflow Management

    Science.gov (United States)

    Wheaton, J. M.; Bailey, P.; Glenn, N. F.; Hensleigh, J.; Hudak, A. T.; Shrestha, R.; Spaete, L.

    2013-12-01

    An ever-increasing list of options exist for collecting high resolution topographic data, including airborne LIDAR, terrestrial laser scanners, bathymetric SONAR and structure-from-motion. An equally rich, arguably overwhelming, variety of tools exists with which to organize, quality control, filter, analyze and summarize these data. However, scientists are often left to cobble together their analysis as a series of ad hoc steps, often using custom scripts and one-time processes that are poorly documented and rarely shared with the community. Even when literature-cited software tools are used, the input and output parameters differ from tool to tool. These parameters are rarely archived and the steps performed lost, making the analysis virtually impossible to replicate precisely. What is missing is a coherent, robust, framework for combining reliable, well-documented topographic data-processing steps into a workflow that can be repeated and even shared with others. We have taken several popular topographic data processing tools - including point cloud filtering and decimation as well as DEM differencing - and defined a common protocol for passing inputs and outputs between them. This presentation describes a free, public online portal that enables scientists to create custom workflows for processing topographic data using a number of popular topographic processing tools. Users provide the inputs required for each tool and in what sequence they want to combine them. This information is then stored for future reuse (and optionally sharing with others) before the user then downloads a single package that contains all the input and output specifications together with the software tools themselves. The user then launches the included batch file that executes the workflow on their local computer against their topographic data. This ZCloudTools architecture helps standardize, automate and archive topographic data processing. It also represents a forum for discovering and

  6. Hybrid Workflow Policy Management for Heart Disease Identification

    OpenAIRE

    Dong-Hyun Kim; Woo-Ram Jung; Chan-Hyun Youn.

    2010-01-01

    As science technology grows, medical application is becoming more complex to solve the physiological problems within expected time. Workflow management systems (WMS) in Grid computing are promising solution to solve the sophisticated problem such as genomic analysis, drug discovery, disease identification, etc. Although existing WMS can provide basic management functionality in Grid environment, consideration of user requirements such as performance, reliability and interaction with user is m...

  7. DNA Qualification Workflow for Next Generation Sequencing of Histopathological Samples

    OpenAIRE

    Michele Simbolo; Marisa Gottardi; Vincenzo Corbo; Matteo Fassan; Andrea Mafficini; Giorgio Malpeli; Lawlor, Rita T; Aldo Scarpa

    2013-01-01

    Histopathological samples are a treasure-trove of DNA for clinical research. However, the quality of DNA can vary depending on the source or extraction method applied. Thus a standardized and cost-effective workflow for the qualification of DNA preparations is essential to guarantee interlaboratory reproducible results. The qualification process consists of the quantification of double strand DNA (dsDNA) and the assessment of its suitability for downstream applications, such as high-throughpu...

  8. A graph model of data and workflow provenance

    OpenAIRE

    Acar, U.; Buneman, P.; J. Cheney; Van den Bussche, Jan; Kwasnikowska, Natalia; Vansummeren, Stijn

    2010-01-01

    Provenance has been studied extensively in both database and workflow management systems, so far with little convergence of definitions or models. Provenance in databases has generally been defined for relational or complex object data, by propagating fine-grained annotations or algebraic expressions from the input to the output. This kind of provenance has been found useful in other areas of computer science: annotation databases, probabilistic databases, schema and data integration, etc. In...

  9. Bioinformatics Workflow for Clinical Whole Genome Sequencing at Partners HealthCare Personalized Medicine

    Directory of Open Access Journals (Sweden)

    Ellen A. Tsai

    2016-02-01

    Full Text Available Effective implementation of precision medicine will be enhanced by a thorough understanding of each patient’s genetic composition to better treat his or her presenting symptoms or mitigate the onset of disease. This ideally includes the sequence information of a complete genome for each individual. At Partners HealthCare Personalized Medicine, we have developed a clinical process for whole genome sequencing (WGS with application in both healthy individuals and those with disease. In this manuscript, we will describe our bioinformatics strategy to efficiently process and deliver genomic data to geneticists for clinical interpretation. We describe the handling of data from FASTQ to the final variant list for clinical review for the final report. We will also discuss our methodology for validating this workflow and the cost implications of running WGS.

  10. Sufficient and Necessary Condition to Decide Compatibility for a Class of Interorganizational Workflow Nets

    Directory of Open Access Journals (Sweden)

    Guanjun Liu

    2015-01-01

    Full Text Available Interorganizational Workflow nets (IWF-nets can well model many concurrent systems such as web service composition, in which multiple processes interact via sending/receiving messages. Compatibility of IWF-nets is a crucial criterion for the correctness of these systems. It guarantees that a system has no deadlock, livelock, or dead tasks. In our previous work we proved that the compatibility problem is PSPACE-complete for safe IWF-nets. This paper defines a subclass of IWF-nets that can model many cases about interactions. Necessary and sufficient condition is presented to decide their compatibility, and it depends on the net structures only. Finally, an algorithm is developed based on the condition.

  11. Bioinformatics Workflow for Clinical Whole Genome Sequencing at Partners HealthCare Personalized Medicine.

    Science.gov (United States)

    Tsai, Ellen A; Shakbatyan, Rimma; Evans, Jason; Rossetti, Peter; Graham, Chet; Sharma, Himanshu; Lin, Chiao-Feng; Lebo, Matthew S

    2016-01-01

    Effective implementation of precision medicine will be enhanced by a thorough understanding of each patient's genetic composition to better treat his or her presenting symptoms or mitigate the onset of disease. This ideally includes the sequence information of a complete genome for each individual. At Partners HealthCare Personalized Medicine, we have developed a clinical process for whole genome sequencing (WGS) with application in both healthy individuals and those with disease. In this manuscript, we will describe our bioinformatics strategy to efficiently process and deliver genomic data to geneticists for clinical interpretation. We describe the handling of data from FASTQ to the final variant list for clinical review for the final report. We will also discuss our methodology for validating this workflow and the cost implications of running WGS. PMID:26927186

  12. Automated quality control in a file-based broadcasting workflow

    Science.gov (United States)

    Zhang, Lina

    2014-04-01

    Benefit from the development of information and internet technologies, television broadcasting is transforming from inefficient tape-based production and distribution to integrated file-based workflows. However, no matter how many changes have took place, successful broadcasting still depends on the ability to deliver a consistent high quality signal to the audiences. After the transition from tape to file, traditional methods of manual quality control (QC) become inadequate, subjective, and inefficient. Based on China Central Television's full file-based workflow in the new site, this paper introduces an automated quality control test system for accurate detection of hidden troubles in media contents. It discusses the system framework and workflow control when the automated QC is added. It puts forward a QC criterion and brings forth a QC software followed this criterion. It also does some experiments on QC speed by adopting parallel processing and distributed computing. The performance of the test system shows that the adoption of automated QC can make the production effective and efficient, and help the station to achieve a competitive advantage in the media market.

  13. a Workflow for UAV's Integration Into a Geodesign Platform

    Science.gov (United States)

    Anca, P.; Calugaru, A.; Alixandroae, I.; Nazarie, R.

    2016-06-01

    This paper presents a workflow for the development of various Geodesign scenarios. The subject is important in the context of identifying patterns and designing solutions for a Smart City with optimized public transportation, efficient buildings, efficient utilities, recreational facilities a.s.o.. The workflow describes the procedures starting with acquiring data in the field, data processing, orthophoto generation, DTM generation, integration into a GIS platform and analyzing for a better support for Geodesign. Esri's City Engine is used mostly for 3D modeling capabilities that enable the user to obtain 3D realistic models. The workflow uses as inputs information extracted from images acquired using UAVs technologies, namely eBee, existing 2D GIS geodatabases, and a set of CGA rules. The method that we used further, is called procedural modeling, and uses rules in order to extrude buildings, the street network, parcel zoning and side details, based on the initial attributes from the geodatabase. The resulted products are various scenarios for redesigning, for analyzing new exploitation sites. Finally, these scenarios can be published as interactive web scenes for internal, groups or pubic consultation. In this way, problems like the impact of new constructions being build, re-arranging green spaces or changing routes for public transportation, etc. are revealed through impact and visibility analysis or shadowing analysis and are brought to the citizen's attention. This leads to better decisions.

  14. IT-benchmarking of clinical workflows: concept, implementation, and evaluation.

    Science.gov (United States)

    Thye, Johannes; Straede, Matthias-Christopher; Liebe, Jan-David; Hübner, Ursula

    2014-01-01

    Due to the emerging evidence of health IT as opportunity and risk for clinical workflows, health IT must undergo a continuous measurement of its efficacy and efficiency. IT-benchmarks are a proven means for providing this information. The aim of this study was to enhance the methodology of an existing benchmarking procedure by including, in particular, new indicators of clinical workflows and by proposing new types of visualisation. Drawing on the concept of information logistics, we propose four workflow descriptors that were applied to four clinical processes. General and specific indicators were derived from these descriptors and processes. 199 chief information officers (CIOs) took part in the benchmarking. These hospitals were assigned to reference groups of a similar size and ownership from a total of 259 hospitals. Stepwise and comprehensive feedback was given to the CIOs. Most participants who evaluated the benchmark rated the procedure as very good, good, or rather good (98.4%). Benchmark information was used by CIOs for getting a general overview, advancing IT, preparing negotiations with board members, and arguing for a new IT project. PMID:24825693

  15. The MPO API: A tool for recording scientific workflows

    Energy Technology Data Exchange (ETDEWEB)

    Wright, John C., E-mail: jcwright@mit.edu [MIT Plasma Science and Fusion Center, Cambridge, MA (United States); Greenwald, Martin; Stillerman, Joshua [MIT Plasma Science and Fusion Center, Cambridge, MA (United States); Abla, Gheni; Chanthavong, Bobby; Flanagan, Sean; Schissel, David; Lee, Xia [General Atomics, San Diego, CA (United States); Romosan, Alex; Shoshani, Arie [Lawrence Berkeley Laboratory, Berkeley, CA (United States)

    2014-05-15

    Highlights: • A description of a new framework and tool for recording scientific workflows, especially those resulting from simulation and analysis. • An explanation of the underlying technologies used to implement this web based tool. • Several examples of using the tool. - Abstract: Data from large-scale experiments and extreme-scale computing is expensive to produce and may be used for high-consequence applications. The Metadata, Provenance and Ontology (MPO) project builds on previous work [M. Greenwald, Fusion Eng. Des. 87 (2012) 2205–2208] and is focused on providing documentation of workflows, data provenance and the ability to data-mine large sets of results. While there are important design and development aspects to the data structures and user interfaces, we concern ourselves in this paper with the application programming interface (API) – the set of functions that interface with the data server. Our approach for the data server is to follow the Representational State Transfer (RESTful) software architecture style for client–server communication. At its core, the API uses the POST and GET methods of the HTTP protocol to transfer workflow information in message bodies to targets specified in the URL to and from the database via a web server. Higher level API calls are built upon this core API. This design facilitates implementation on different platforms and in different languages and is robust to changes in the underlying technologies used. The command line client implementation can communicate with the data server from any machine with HTTP access.

  16. AnalyzeThis: An Analysis Workflow-Aware Storage System

    Energy Technology Data Exchange (ETDEWEB)

    Sim, Hyogi [ORNL; Kim, Youngjae [ORNL; Vazhkudai, Sudharshan S [ORNL; Tiwari, Devesh [ORNL; Anwar, Ali [Virginia Tech, Blacksburg, VA; Butt, Ali R [Virginia Tech, Blacksburg, VA; Ramakrishnan, Lavanya [Lawrence Berkeley National Laboratory (LBNL)

    2015-01-01

    The need for novel data analysis is urgent in the face of a data deluge from modern applications. Traditional approaches to data analysis incur significant data movement costs, moving data back and forth between the storage system and the processor. Emerging Active Flash devices enable processing on the flash, where the data already resides. An array of such Active Flash devices allows us to revisit how analysis workflows interact with storage systems. By seamlessly blending together the flash storage and data analysis, we create an analysis workflow-aware storage system, AnalyzeThis. Our guiding principle is that analysis-awareness be deeply ingrained in each and every layer of the storage, elevating data analyses as first-class citizens, and transforming AnalyzeThis into a potent analytics-aware appliance. We implement the AnalyzeThis storage system atop an emulation platform of the Active Flash array. Our results indicate that AnalyzeThis is viable, expediting workflow execution and minimizing data movement.

  17. Optimal Workflow Scheduling in Critical Infrastructure Systems with Neural Networks

    Directory of Open Access Journals (Sweden)

    S. Vukmirović

    2012-04-01

    Full Text Available Critical infrastructure systems (CISs, such as power grids, transportation systems, communication networks and water systems are the backbone of a country’s national security and industrial prosperity. These CISs execute large numbers of workflows with very high resource requirements that can span through different systems and last for a long time. The proper functioning and synchronization of these workflows is essential since humanity’s well-being is connected to it. Because of this, the challenge of ensuring availability and reliability of these services in the face of a broad range of operating conditions is very complicated. This paper proposes an architecture which dynamically executes a scheduling algorithm using feedback about the current status of CIS nodes. Different artificial neural networks (ANNs were created in order to solve the scheduling problem. Their performances were compared and as the main result of this paper, an optimal ANN architecture for workflow scheduling in CISs is proposed. A case study is shown for a meter data management system with measurements from a power distribution management system in Serbia. Performance tests show that significant improvement of the overall execution time can be achieved by ANNs.

  18. Research on a dynamic workflow access control model

    Science.gov (United States)

    Liu, Yiliang; Deng, Jinxia

    2007-12-01

    In recent years, the access control technology has been researched widely in workflow system, two typical technologies of that are RBAC (Role-Based Access Control) and TBAC (Task-Based Access Control) model, which has been successfully used in the role authorizing and assigning in a certain extent. However, during the process of complicating a system's structure, these two types of technology can not be used in minimizing privileges and separating duties, and they are inapplicable when users have a request of frequently changing on the workflow's process. In order to avoid having these weakness during the applying, a variable flow dynamic role_task_view (briefly as DRTVBAC) of fine-grained access control model is constructed on the basis existed model. During the process of this model applying, an algorithm is constructed to solve users' requirements of application and security needs on fine-grained principle of privileges minimum and principle of dynamic separation of duties. The DRTVBAC model is implemented in the actual system, the figure shows that the task associated with the dynamic management of role and the role assignment is more flexible on authority and recovery, it can be met the principle of least privilege on the role implement of a specific task permission activated; separated the authority from the process of the duties completing in the workflow; prevented sensitive information discovering from concise and dynamic view interface; satisfied with the requirement of the variable task-flow frequently.

  19. The MPO API: A tool for recording scientific workflows

    International Nuclear Information System (INIS)

    Highlights: • A description of a new framework and tool for recording scientific workflows, especially those resulting from simulation and analysis. • An explanation of the underlying technologies used to implement this web based tool. • Several examples of using the tool. - Abstract: Data from large-scale experiments and extreme-scale computing is expensive to produce and may be used for high-consequence applications. The Metadata, Provenance and Ontology (MPO) project builds on previous work [M. Greenwald, Fusion Eng. Des. 87 (2012) 2205–2208] and is focused on providing documentation of workflows, data provenance and the ability to data-mine large sets of results. While there are important design and development aspects to the data structures and user interfaces, we concern ourselves in this paper with the application programming interface (API) – the set of functions that interface with the data server. Our approach for the data server is to follow the Representational State Transfer (RESTful) software architecture style for client–server communication. At its core, the API uses the POST and GET methods of the HTTP protocol to transfer workflow information in message bodies to targets specified in the URL to and from the database via a web server. Higher level API calls are built upon this core API. This design facilitates implementation on different platforms and in different languages and is robust to changes in the underlying technologies used. The command line client implementation can communicate with the data server from any machine with HTTP access

  20. Composites

    Science.gov (United States)

    Taylor, John G.

    The Composites market is arguably the most challenging and profitable market for phenolic resins aside from electronics. The variety of products and processes encountered creates the challenges, and the demand for high performance in critical operations brings value. Phenolic composite materials are rendered into a wide range of components to supply a diverse and fragmented commercial base that includes customers in aerospace (Space Shuttle), aircraft (interiors and brakes), mass transit (interiors), defense (blast protection), marine, mine ducting, off-shore (ducts and grating) and infrastructure (architectural) to name a few. For example, phenolic resin is a critical adhesive in the manufacture of honeycomb sandwich panels. Various solvent and water based resins are described along with resin characteristics and the role of metal ions for enhanced thermal stability of the resin used to coat the honeycomb. Featured new developments include pultrusion of phenolic grating, success in RTM/VARTM fabricated parts, new ballistic developments for military vehicles and high char yield carbon-carbon composites along with many others. Additionally, global regional market resin volumes and sales are presented and compared with other thermosetting resin systems.

  1. Workflow improvements for digital breast tomosynthesis: computerized generation of enhanced synthetic images

    Science.gov (United States)

    Fotin, Sergei V.; Yin, Yin; Haldankar, Hrishikesh; Hoffmeister, Jeffrey W.; Periaswamy, Senthil

    2016-03-01

    In a typical 2D mammography workflow scenario, a computer-aided detection (CAD) algorithm is used as a second reader producing marks for a radiologist to review. In the case of 3D digital breast tomosynthesis (DBT), the display of CAD detections at multiple reconstruction heights would lead to an increased image browsing and interpretation time. We propose an alternative approach in which an algorithm automatically identifies suspicious regions of interest from 3D reconstructed DBT slices and then merges the findings with the corresponding 2D synthetic projection image which is then reviewed. The resultant enhanced synthetic 2D image combines the benefits of a familiar 2D breast view with superior appearance of suspicious locations from 3D slices. Moreover, clicking on 2D suspicious locations brings up the display of the corresponding 3D regions in a DBT volume allowing navigation between 2D and 3D images. We explored the use of these enhanced synthetic images in a concurrent read paradigm by conducting a study with 5 readers and 30 breast exams. We observed that the introduction of the enhanced synthetic view reduced radiologist's average interpretation time by 5.4%, increased sensitivity by 6.7% and increased specificity by 15.6%.

  2. PROTEOMER: A workflow-optimized laboratory information management system for 2-D electrophoresis-centered proteomics.

    Science.gov (United States)

    Nebrich, Grit; Herrmann, Marion; Hartl, Daniela; Diedrich, Madeleine; Kreitler, Thomas; Wierling, Christoph; Klose, Joachim; Giavalisco, Patrick; Zabel, Claus; Mao, Lei

    2009-04-01

    In recent years proteomics became increasingly important to functional genomics. Although a large amount of data is generated by high throughput large-scale techniques, a connection of these mostly heterogeneous data from different analytical platforms and of different experiments is limited. Data mining procedures and algorithms are often insufficient to extract meaningful results from large datasets and therefore limit the exploitation of the generated biological information. In our proteomic core facility, which almost exclusively focuses on 2-DE/MS-based proteomics, we developed a proteomic database custom tailored to our needs aiming at connecting MS protein identification information to 2-DE derived protein expression profiles. The tools developed should not only enable an automatic evaluation of single experiments, but also link multiple 2-DE experiments with MS-data on different levels and thereby helping to create a comprehensive network of our proteomics data. Therefore the key feature of our "PROTEOMER" database is its high cross-referencing capacity, enabling integration of a wide range of experimental data. To illustrate the workflow and utility of the system, two practical examples are provided to demonstrate that proper data cross-referencing can transform information into biological knowledge. PMID:19259999

  3. Information Management Workflow and Tools Enabling Multiscale Modeling Within ICME Paradigm

    Science.gov (United States)

    Arnold, Steven M.; Bednarcyk, Brett A.; Austin, Nic; Terentjev, Igor; Cebon, Dave; Marsden, Will

    2016-01-01

    With the increased emphasis on reducing the cost and time to market of new materials, the need for analytical tools that enable the virtual design and optimization of materials throughout their processing - internal structure - property - performance envelope, along with the capturing and storing of the associated material and model information across its lifecycle, has become critical. This need is also fueled by the demands for higher efficiency in material testing; consistency, quality and traceability of data; product design; engineering analysis; as well as control of access to proprietary or sensitive information. Fortunately, material information management systems and physics-based multiscale modeling methods have kept pace with the growing user demands. Herein, recent efforts to establish workflow for and demonstrate a unique set of web application tools for linking NASA GRC's Integrated Computational Materials Engineering (ICME) Granta MI database schema and NASA GRC's Integrated multiscale Micromechanics Analysis Code (ImMAC) software toolset are presented. The goal is to enable seamless coupling between both test data and simulation data, which is captured and tracked automatically within Granta MI®, with full model pedigree information. These tools, and this type of linkage, are foundational to realizing the full potential of ICME, in which materials processing, microstructure, properties, and performance are coupled to enable application-driven design and optimization of materials and structures.

  4. The BEL information extraction workflow (BELIEF): evaluation in the BioCreative V BEL and IAT track

    Science.gov (United States)

    Madan, Sumit; Hodapp, Sven; Senger, Philipp; Ansari, Sam; Szostak, Justyna; Hoeng, Julia; Peitsch, Manuel; Fluck, Juliane

    2016-01-01

    Network-based approaches have become extremely important in systems biology to achieve a better understanding of biological mechanisms. For network representation, the Biological Expression Language (BEL) is well designed to collate findings from the scientific literature into biological network models. To facilitate encoding and biocuration of such findings in BEL, a BEL Information Extraction Workflow (BELIEF) was developed. BELIEF provides a web-based curation interface, the BELIEF Dashboard, that incorporates text mining techniques to support the biocurator in the generation of BEL networks. The underlying UIMA-based text mining pipeline (BELIEF Pipeline) uses several named entity recognition processes and relationship extraction methods to detect concepts and BEL relationships in literature. The BELIEF Dashboard allows easy curation of the automatically generated BEL statements and their context annotations. Resulting BEL statements and their context annotations can be syntactically and semantically verified to ensure consistency in the BEL network. In summary, the workflow supports experts in different stages of systems biology network building. Based on the BioCreative V BEL track evaluation, we show that the BELIEF Pipeline automatically extracts relationships with an F-score of 36.4% and fully correct statements can be obtained with an F-score of 30.8%. Participation in the BioCreative V Interactive task (IAT) track with BELIEF revealed a systems usability scale (SUS) of 67. Considering the complexity of the task for new users—learning BEL, working with a completely new interface, and performing complex curation—a score so close to the overall SUS average highlights the usability of BELIEF. Database URL: BELIEF is available at http://www.scaiview.com/belief/

  5. The BEL information extraction workflow (BELIEF): evaluation in the BioCreative V BEL and IAT track

    Science.gov (United States)

    Madan, Sumit; Hodapp, Sven; Senger, Philipp; Ansari, Sam; Szostak, Justyna; Hoeng, Julia; Peitsch, Manuel; Fluck, Juliane

    2016-01-01

    Network-based approaches have become extremely important in systems biology to achieve a better understanding of biological mechanisms. For network representation, the Biological Expression Language (BEL) is well designed to collate findings from the scientific literature into biological network models. To facilitate encoding and biocuration of such findings in BEL, a BEL Information Extraction Workflow (BELIEF) was developed. BELIEF provides a web-based curation interface, the BELIEF Dashboard, that incorporates text mining techniques to support the biocurator in the generation of BEL networks. The underlying UIMA-based text mining pipeline (BELIEF Pipeline) uses several named entity recognition processes and relationship extraction methods to detect concepts and BEL relationships in literature. The BELIEF Dashboard allows easy curation of the automatically generated BEL statements and their context annotations. Resulting BEL statements and their context annotations can be syntactically and semantically verified to ensure consistency in the BEL network. In summary, the workflow supports experts in different stages of systems biology network building. Based on the BioCreative V BEL track evaluation, we show that the BELIEF Pipeline automatically extracts relationships with an F-score of 36.4% and fully correct statements can be obtained with an F-score of 30.8%. Participation in the BioCreative V Interactive task (IAT) track with BELIEF revealed a systems usability scale (SUS) of 67. Considering the complexity of the task for new users—learning BEL, working with a completely new interface, and performing complex curation—a score so close to the overall SUS average highlights the usability of BELIEF. Database URL: BELIEF is available at http://www.scaiview.com/belief/ PMID:27694210

  6. Automatic Payroll Deposit System.

    Science.gov (United States)

    Davidson, D. B.

    1979-01-01

    The Automatic Payroll Deposit System in Yakima, Washington's Public School District No. 7, directly transmits each employee's salary amount for each pay period to a bank or other financial institution. (Author/MLF)

  7. Introducing Concurrency to Workflows: Theory and A Real-World Case Study

    Directory of Open Access Journals (Sweden)

    Laird Burns

    2014-11-01

    Full Text Available Making use of the concepts of the activity diagrams of the Unified Modeling Language, this paper defines an important class of workflows, called flow independent workflows, which are deterministic in the sense that if a flow independent workflow is given the same multi-set of resources as input over and over again, it will produce the same output every time. After which, this paper provides a methodology, and its accompanying algorithms, that introduces concurrency to flow independent workflows by rearranging the action nodes in every flow of control. It then applies the methodology to a real-world case to demonstrate its usefulness. It concludes with future research possibilities that might extend the methodology to general workflows, i.e., not necessarily flow independent workflows.

  8. Restructuring of workflows to minimise errors via stochastic model checking: An automated evolutionary approach

    DEFF Research Database (Denmark)

    Herbert, Luke Thomas; Hansen, Zaza Nadja Lee

    2016-01-01

    This article presents a framework for the automated restructuring of stochastic workflows to reduce the impact of faults. The framework allows for the modelling of workflows by means of a formalised subset of the BPMN workflow language. We extend this modelling formalism to describe faults...... to model resources, associated with a workflow. The approach is fully automated and only the modelling of the production workflows, potential faults and the expression of the goals require manual input. We present the design of a software tool implementing this framework and explore the practical utility...... of this approach through an industrial case study in which the risk of production failures and their impact are reduced by restructuring the workflow....

  9. An Adaptable Seismic Data Format for Modern Scientific Workflows

    Science.gov (United States)

    Smith, J. A.; Bozdag, E.; Krischer, L.; Lefebvre, M.; Lei, W.; Podhorszki, N.; Tromp, J.

    2013-12-01

    Data storage, exchange, and access play a critical role in modern seismology. Current seismic data formats, such as SEED, SAC, and SEG-Y, were designed with specific applications in mind and are frequently a major bottleneck in implementing efficient workflows. We propose a new modern parallel format that can be adapted for a variety of seismic workflows. The Adaptable Seismic Data Format (ASDF) features high-performance parallel read and write support and the ability to store an arbitrary number of traces of varying sizes. Provenance information is stored inside the file so that users know the origin of the data as well as the precise operations that have been applied to the waveforms. The design of the new format is based on several real-world use cases, including earthquake seismology and seismic interferometry. The metadata is based on the proven XML schemas StationXML and QuakeML. Existing time-series analysis tool-kits are easily interfaced with this new format so that seismologists can use robust, previously developed software packages, such as ObsPy and the SAC library. ADIOS, netCDF4, and HDF5 can be used as the underlying container format. At Princeton University, we have chosen to use ADIOS as the container format because it has shown superior scalability for certain applications, such as dealing with big data on HPC systems. In the context of high-performance computing, we have implemented ASDF into the global adjoint tomography workflow on Oak Ridge National Laboratory's supercomputer Titan.

  10. Introducing OAWAL: crowdsourcing best practices for open access workflows in academic libraries

    OpenAIRE

    Emery, Jill; Stone, Graham

    2014-01-01

    Currently in the formative stage, the intent of OAWAL is to create an openly accessible wiki for librarians working on the management of open access workflow within their given institutions. At is point, the team has developed significant areas of focus for workflow management and will be building upon the current structure as informed through in-person and online crowdsourcing. The current sections to be developed are: advocacy, Creative Commons, the Library as Publisher, standards, workflow...

  11. Context-oriented scientific workflow system and its application in virtual screening

    OpenAIRE

    Fan, Xiaoliang; Brézillon, Patrick; Zhang, Ruisheng; Li, Lian

    2010-01-01

    Scientific workflow (SWF) system is gradually liberating the computational scientists from burden of data-centric operations to concentration on their decision making. However, contemporary SWF systems fail to address the variables when scientists urge to deliver new outcomes through reproduction of workflow, including not only workflow representation, but also its "context" of use. Thus, current failure is mainly due to lack of representing and managing the "context". We propose a context-or...

  12. The Workflow Specification of Process Definition%工作流过程定义规范

    Institute of Scientific and Technical Information of China (English)

    缪晓阳; 石文俊; 吴朝晖

    2000-01-01

    This paper discusses the representation of a business process in a form.There are three basic aspects:the concept of workflow process definition,on which the idea of process definition interchange is raised;the meta-model of workflow,which is used to describe the entities and attributes of entities within the process definition;the workflow process definition language(WPDL),which is used to implement the Process definition.

  13. Design and Implementation of Visualized Workflow Modeling System Based on B/S Structure

    Institute of Scientific and Technical Information of China (English)

    WANG Jian; LI wei-li

    2007-01-01

    According to the necessity of flexible workflow management system, the solution to set up the visualized workflow modelling system based on B/S structure is put forward, which conforms to the relevant specifications of WfMC and the workflow process definition meta-modei. The design for system structure is presented in detail, and the key technologies for system implementation are also introduced. Additionally, an example is illustrated to demonstrate the validity of system.

  14. High performance workflow implementation for protein surface characterization using grid technology

    OpenAIRE

    Clematis Andrea; D'Agostino Daniele; Morra Giulia; Merelli Ivan; Milanesi Luciano

    2005-01-01

    Abstract Background This study concerns the development of a high performance workflow that, using grid technology, correlates different kinds of Bioinformatics data, starting from the base pairs of the nucleotide sequence to the exposed residues of the protein surface. The implementation of this workflow is based on the Italian Grid.it project infrastructure, that is a network of several computational resources and storage facilities distributed at different grid sites. Methods Workflows are...

  15. CMS Data Processing Workflows during an Extended Cosmic Ray Run

    Energy Technology Data Exchange (ETDEWEB)

    2009-11-01

    The CMS Collaboration conducted a month-long data taking exercise, the Cosmic Run At Four Tesla, during October-November 2008, with the goal of commissioning the experiment for extended operation. With all installed detector systems participating, CMS recorded 270 million cosmic ray events with the solenoid at a magnetic field strength of 3.8 T. This paper describes the data flow from the detector through the various online and offline computing systems, as well as the workflows used for recording the data, for aligning and calibrating the detector, and for analysis of the data.

  16. Reference and PDF-manager software: complexities, support and workflow.

    Science.gov (United States)

    Mead, Thomas L; Berryman, Donna R

    2010-10-01

    In the past, librarians taught reference management by training library users to use established software programs such as RefWorks or EndNote. In today's environment, there is a proliferation of Web-based programs that are being used by library clientele that offer a new twist on the well-known reference management programs. Basically, these new programs are PDF-manager software (e.g., Mendeley or Papers). Librarians are faced with new questions, issues, and concerns, given the new workflows and pathways that these PDF-manager programs present. This article takes a look at some of those.

  17. PhyloGrid: a development for a workflow in Phylogeny

    CERN Document Server

    Montes, Esther; Mayo, Rafael

    2010-01-01

    In this work we present the development of a workflow based on Taverna which is going to be implemented for calculations in Phylogeny by means of the MrBayes tool. It has a friendly interface developed with the Gridsphere framework. The user is able to define the parameters for doing the Bayesian calculation, determine the model of evolution, check the accuracy of the results in the intermediate stages as well as do a multiple alignment of the sequences previously to the final result. To do this, no knowledge from his/her side about the computational procedure is required.

  18. Integrating workflow and project management systems for PLM applications

    Directory of Open Access Journals (Sweden)

    Fabio Fonseca Pereira de Paula

    2008-07-01

    Full Text Available The adoption of Product Life-cycle Management Systems (PLMs concept is fundamental to improve the product development, mainly to small and medium enterprises (SMEs. One of the challenges is the integration between project management and product data management functions. The paper presents an analysis of the potential integration strategies for a specifics product data management system (SMARTEAM and a project management system (Microsoft Project, which are commonly used for SMEs. Finally the article presents some considerations about the study of Project Management solutions in SMB’s companies, considering the PLM approach. Key-words: integration, project management (PM, workflow, PDM, PLM.

  19. WooW-II: Workshop on open workflows

    Directory of Open Access Journals (Sweden)

    Daniel Arribas-Bel

    2015-07-01

    Full Text Available This resource describes WooW-II, a two-day workshop on open workflows for quantitative social scientists. The workshop is broken down in five main parts, where each of them typically consists of an introductionary tutorial and a hands-on assignment. The specific tools discussed in this workshop are Markdown, Pandoc, Git, Github, R, and Rstudio, but the theoretical approach applies to a wider range of tools (e.g., LATEX and Python. By the end of the workshop, participants should be able to reproduce a paper of their own and make it available in an open form applying the concepts and tools introduced.

  20. Conflict detection and resolution for authorization policies in workflow systems

    Institute of Scientific and Technical Information of China (English)

    Chen-hua MA; Guo-dong LU; Jiong QIU

    2009-01-01

    The specification of authorization policies in access control models proposed so far cannot satisfy the requirements in workflow management systems (WFMSs). Furthermore, existing approaches have not provided effective conflict detection and resolution methods to maintain the consistency of authorization polices in WFMSs. To address these concerns, we propose the definition of authorization policies in which context constraints are considered and the complicated requirements in WFMSs can be satisfied. Based on the definition, we put forward static and dynamic conflict detection methods for authorization policies. By defining two new concepts, the precedence establishment rule and the confict resolution policy, we provide a flexible approach to resolving conflicts.

  1. CMS Data Processing Workflows during an Extended Cosmic Ray Run

    CERN Document Server

    Chatrchyan, S; Sirunyan, A M; Adam, W; Arnold, B; Bergauer, H; Bergauer, T; Dragicevic, M; Eichberger, M; Erö, J; Friedl, M; Frühwirth, R; Ghete, V M; Hammer, J; Hänsel, S; Hoch, M; Hörmann, N; Hrubec, J; Jeitler, M; Kasieczka, G; Kastner, K; Krammer, M; Liko, D; Magrans de Abril, I; Mikulec, I; Mittermayr, F; Neuherz, B; Oberegger, M; Padrta, M; Pernicka, M; Rohringer, H; Schmid, S; Schöfbeck, R; Schreiner, T; Stark, R; Steininger, H; Strauss, J; Taurok, A; Teischinger, F; Themel, T; Uhl, D; Wagner, P; Waltenberger, W; Walzel, G; Widl, E; Wulz, C E; Chekhovsky, V; Dvornikov, O; Emeliantchik, I; Litomin, A; Makarenko, V; Marfin, I; Mossolov, V; Shumeiko, N; Solin, A; Stefanovitch, R; Suarez Gonzalez, J; Tikhonov, A; Fedorov, A; Karneyeu, A; Korzhik, M; Panov, V; Zuyeuski, R; Kuchinsky, P; Beaumont, W; Benucci, L; Cardaci, M; De Wolf, E A; Delmeire, E; Druzhkin, D; Hashemi, M; Janssen, X; Maes, T; Mucibello, L; Ochesanu, S; Rougny, R; Selvaggi, M; Van Haevermaet, H; Van Mechelen, P; Van Remortel, N; Adler, V; Beauceron, S; Blyweert, S; D'Hondt, J; De Weirdt, S; Devroede, O; Heyninck, J; Kalogeropoulos, A; Maes, J; Maes, M; Mozer, M U; Tavernier, S; Van Doninck, W; Van Mulders, P; Villella, I; Bouhali, O; Chabert, E C; Charaf, O; Clerbaux, B; De Lentdecker, G; Dero, V; Elgammal, S; Gay, A P R; Hammad, G H; Marage, P E; Rugovac, S; Vander Velde, C; Vanlaer, P; Wickens, J; Grunewald, M; Klein, B; Marinov, A; Ryckbosch, D; Thyssen, F; Tytgat, M; Vanelderen, L; Verwilligen, P; Basegmez, S; Bruno, G; Caudron, J; Delaere, C; Demin, P; Favart, D; Giammanco, A; Grégoire, G; Lemaitre, V; Militaru, O; Ovyn, S; Piotrzkowski, K; Quertenmont, L; Schul, N; Beliy, N; Daubie, E; Alves, G A; Pol, M E; Souza, M H G; Carvalho, W; De Jesus Damiao, D; De Oliveira Martins, C; Fonseca De Souza, S; Mundim, L; Oguri, V; Santoro, A; Silva Do Amaral, S M; Sznajder, A; Fernandez Perez Tomei, T R; Ferreira Dias, M A; Gregores, E M; Novaes, S F; Abadjiev, K; Anguelov, T; Damgov, J; Darmenov, N; Dimitrov, L; Genchev, V; Iaydjiev, P; Piperov, S; Stoykova, S; Sultanov, G; Trayanov, R; Vankov, I; Dimitrov, A; Dyulendarova, M; Kozhuharov, V; Litov, L; Marinova, E; Mateev, M; Pavlov, B; Petkov, P; Toteva, Z; Chen, G M; Chen, H S; Guan, W; Jiang, C H; Liang, D; Liu, B; Meng, X; Tao, J; Wang, J; Wang, Z; Xue, Z; Zhang, Z; Ban, Y; Cai, J; Ge, Y; Guo, S; Hu, Z; Mao, Y; Qian, S J; Teng, H; Zhu, B; Avila, C; Baquero Ruiz, M; Carrillo Montoya, C A; Gomez, A; Gomez Moreno, B; Ocampo Rios, A A; Osorio Oliveros, A F; Reyes Romero, D; Sanabria, J C; Godinovic, N; Lelas, K; Plestina, R; Polic, D; Puljak, I; Antunovic, Z; Dzelalija, M; Brigljevic, V; Duric, S; Kadija, K; Morovic, S; Fereos, R; Galanti, M; Mousa, J; Papadakis, A; Ptochos, F; Razis, P A; Tsiakkouri, D; Zinonos, Z; Hektor, A; Kadastik, M; Kannike, K; Müntel, M; Raidal, M; Rebane, L; Anttila, E; Czellar, S; Härkönen, J; Heikkinen, A; Karimäki, V; Kinnunen, R; Klem, J; Kortelainen, M J; Lampén, T; Lassila-Perini, K; Lehti, S; Lindén, T; Luukka, P; Mäenpää, T; Nysten, J; Tuominen, E; Tuominiemi, J; Ungaro, D; Wendland, L; Banzuzi, K; Korpela, A; Tuuva, T; Nedelec, P; Sillou, D; Besancon, M; Chipaux, R; Dejardin, M; Denegri, D; Descamps, J; Fabbro, B; Faure, J L; Ferri, F; Ganjour, S; Gentit, F X; Givernaud, A; Gras, P; Hamel de Monchenault, G; Jarry, P; Lemaire, M C; Locci, E; Malcles, J; Marionneau, M; Millischer, L; Rander, J; Rosowsky, A; Rousseau, D; Titov, M; Verrecchia, P; Baffioni, S; Bianchini, L; Bluj, M; Busson, P; Charlot, C; Dobrzynski, L; Granier de Cassagnac, R; Haguenauer, M; Miné, P; Paganini, P; Sirois, Y; Thiebaux, C; Zabi, A; Agram, J L; Besson, A; Bloch, D; Bodin, D; Brom, J M; Conte, E; Drouhin, F; Fontaine, J C; Gelé, D; Goerlach, U; Gross, L; Juillot, P; Le Bihan, A C; Patois, Y; Speck, J; Van Hove, P; Baty, C; Bedjidian, M; Blaha, J; Boudoul, G; Brun, H; Chanon, N; Chierici, R; Contardo, D; Depasse, P; Dupasquier, T; El Mamouni, H; Fassi, F; Fay, J; Gascon, S; Ille, B; Kurca, T; Le Grand, T; Lethuillier, M; Lumb, N; Mirabito, L; Perries, S; Vander Donckt, M; Verdier, P; Djaoshvili, N; Roinishvili, N; Roinishvili, V; Amaglobeli, N; Adolphi, R; Anagnostou, G; Brauer, R; Braunschweig, W; Edelhoff, M; Esser, H; Feld, L; Karpinski, W; Khomich, A; Klein, K; Mohr, N; Ostaptchouk, A; Pandoulas, D; Pierschel, G; Raupach, F; Schael, S; Schultz von Dratzig, A; Schwering, G; Sprenger, D; Thomas, M; Weber, M; Wittmer, B; Wlochal, M; Actis, O; Altenhöfer, G; Bender, W; Biallass, P; Erdmann, M; Fetchenhauer, G; Frangenheim, J; Hebbeker, T; Hilgers, G; Hinzmann, A; Hoepfner, K; Hof, C; Kirsch, M; Klimkovich, T; Kreuzer, P; Lanske, D; Merschmeyer, M; Meyer, A; Philipps, B; Pieta, H; Reithler, H; Schmitz, S A; Sonnenschein, L; Sowa, M; Steggemann, J; Szczesny, H; Teyssier, D; Zeidler, C; Bontenackels, M; Davids, M; Duda, M; Flügge, G; Geenen, H; Giffels, M; Haj Ahmad, W; Hermanns, T; Heydhausen, D; Kalinin, S; Kress, T; Linn, A; Nowack, A; Perchalla, L; Poettgens, M; Pooth, O; Sauerland, P; Stahl, A; Tornier, D; Zoeller, M H; Aldaya Martin, M; Behrens, U; Borras, K; Campbell, A; Castro, E; Dammann, D; Eckerlin, G; Flossdorf, A; Flucke, G; Geiser, A; Hatton, D; Hauk, J; Jung, H; Kasemann, M; Katkov, I; Kleinwort, C; Kluge, H; Knutsson, A; Kuznetsova, E; Lange, W; Lohmann, W; Mankel, R; Marienfeld, M; Meyer, A B; Miglioranzi, S; Mnich, J; Ohlerich, M; Olzem, J; Parenti, A; Rosemann, C; Schmidt, R; Schoerner-Sadenius, T; Volyanskyy, D; Wissing, C; Zeuner, W D; Autermann, C; Bechtel, F; Draeger, J; Eckstein, D; Gebbert, U; Kaschube, K; Kaussen, G; Klanner, R; Mura, B; Naumann-Emme, S; Nowak, F; Pein, U; Sander, C; Schleper, P; Schum, T; Stadie, H; Steinbrück, G; Thomsen, J; Wolf, R; Bauer, J; Blüm, P; Buege, V; Cakir, A; Chwalek, T; De Boer, W; Dierlamm, A; Dirkes, G; Feindt, M; Felzmann, U; Frey, M; Furgeri, A; Gruschke, J; Hackstein, C; Hartmann, F; Heier, S; Heinrich, M; Held, H; Hirschbuehl, D; Hoffmann, K H; Honc, S; Jung, C; Kuhr, T; Liamsuwan, T; Martschei, D; Mueller, S; Müller, Th; Neuland, M B; 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Cline, D; Cousins, R; Erhan, S; Hauser, J; Ignatenko, M; Jarvis, C; Mumford, J; Plager, C; Rakness, G; Schlein, P; Tucker, J; Valuev, V; Wallny, R; Yang, X; Babb, J; Bose, M; Chandra, A; Clare, R; Ellison, J A; Gary, J W; Hanson, G; Jeng, G Y; Kao, S C; Liu, F; Liu, H; Luthra, A; Nguyen, H; Pasztor, G; Satpathy, A; Shen, B C; Stringer, R; Sturdy, J; Sytnik, V; Wilken, R; Wimpenny, S; Branson, J G; Dusinberre, E; Evans, D; Golf, F; Kelley, R; Lebourgeois, M; Letts, J; Lipeles, E; Mangano, B; Muelmenstaedt, J; Norman, M; Padhi, S; Petrucci, A; Pi, H; Pieri, M; Ranieri, R; Sani, M; Sharma, V; Simon, S; Würthwein, F; Yagil, A; Campagnari, C; D'Alfonso, M; Danielson, T; Garberson, J; Incandela, J; Justus, C; Kalavase, P; Koay, S A; Kovalskyi, D; Krutelyov, V; Lamb, J; Lowette, S; Pavlunin, V; Rebassoo, F; Ribnik, J; Richman, J; Rossin, R; Stuart, D; To, W; Vlimant, J R; Witherell, M; Apresyan, A; Bornheim, A; Bunn, J; Chiorboli, M; Gataullin, M; Kcira, D; Litvine, V; Ma, Y; Newman, H B; Rogan, C; Timciuc, V; Veverka, J; Wilkinson, R; Yang, Y; Zhang, L; Zhu, K; Zhu, R Y; Akgun, B; Carroll, R; Ferguson, T; Jang, D W; Jun, S Y; Paulini, M; Russ, J; Terentyev, N; Vogel, H; Vorobiev, I; Cumalat, J P; Dinardo, M E; Drell, B R; Ford, W T; Heyburn, B; Luiggi Lopez, E; Nauenberg, U; Stenson, K; Ulmer, K; Wagner, S R; Zang, S L; Agostino, L; Alexander, J; Blekman, F; Cassel, D; Chatterjee, A; Das, S; Gibbons, L K; Heltsley, B; Hopkins, W; Khukhunaishvili, A; Kreis, B; Kuznetsov, V; Patterson, J R; Puigh, D; Ryd, A; Shi, X; Stroiney, S; Sun, W; Teo, W D; Thom, J; Vaughan, J; Weng, Y; Wittich, P; Beetz, C P; Cirino, G; Sanzeni, C; Winn, D; Abdullin, S; Afaq, M A; Albrow, M; Ananthan, B; Apollinari, G; Atac, M; Badgett, W; Bagby, L; Bakken, J A; Baldin, B; Banerjee, S; Banicz, K; Bauerdick, L A T; Beretvas, A; Berryhill, J; Bhat, P C; Biery, K; Binkley, M; Bloch, I; Borcherding, F; Brett, A M; Burkett, K; Butler, J N; Chetluru, V; Cheung, H W K; Chlebana, F; Churin, I; Cihangir, S; Crawford, M; Dagenhart, W; Demarteau, M; Derylo, G; Dykstra, D; Eartly, D P; Elias, J E; Elvira, V D; Evans, D; Feng, L; Fischler, M; Fisk, I; Foulkes, S; Freeman, J; Gartung, P; Gottschalk, E; Grassi, T; Green, D; Guo, Y; Gutsche, O; Hahn, A; Hanlon, J; Harris, R M; Holzman, B; Howell, J; Hufnagel, D; James, E; Jensen, H; Johnson, M; Jones, C D; Joshi, U; Juska, E; Kaiser, J; Klima, B; Kossiakov, S; Kousouris, K; Kwan, S; Lei, C M; Limon, P; Lopez Perez, J A; Los, S; Lueking, L; Lukhanin, G; Lusin, S; Lykken, J; Maeshima, K; Marraffino, J M; Mason, D; McBride, P; Miao, T; Mishra, K; Moccia, S; Mommsen, R; Mrenna, S; Muhammad, A S; Newman-Holmes, C; Noeding, C; O'Dell, V; Prokofyev, O; Rivera, R; Rivetta, C H; Ronzhin, A; Rossman, P; Ryu, S; Sekhri, V; Sexton-Kennedy, E; Sfiligoi, I; Sharma, S; Shaw, T M; Shpakov, D; Skup, E; Smith, R P; Soha, A; Spalding, W J; Spiegel, L; Suzuki, I; Tan, P; Tanenbaum, W; Tkaczyk, S; Trentadue, R; Uplegger, L; Vaandering, E W; Vidal, R; Whitmore, J; Wicklund, E; Wu, W; Yarba, J; Yumiceva, F; Yun, J C; Acosta, D; Avery, P; Barashko, V; Bourilkov, D; Chen, M; Di Giovanni, G P; Dobur, D; Drozdetskiy, A; Field, R D; Fu, Y; Furic, I K; Gartner, J; Holmes, D; Kim, B; Klimenko, S; Konigsberg, J; Korytov, A; Kotov, K; Kropivnitskaya, A; Kypreos, T; Madorsky, A; Matchev, K; Mitselmakher, G; Pakhotin, Y; Piedra Gomez, J; Prescott, C; Rapsevicius, V; Remington, R; Schmitt, M; Scurlock, B; Wang, D; Yelton, J; Ceron, C; Gaultney, V; Kramer, L; Lebolo, L M; Linn, S; Markowitz, P; Martinez, G; Rodriguez, J L; Adams, T; Askew, A; Baer, H; Bertoldi, M; Chen, J; Dharmaratna, W G D; Gleyzer, S V; Haas, J; Hagopian, S; Hagopian, V; Jenkins, M; Johnson, K F; Prettner, E; Prosper, H; Sekmen, S; Baarmand, M M; Guragain, S; Hohlmann, M; Kalakhety, H; Mermerkaya, H; Ralich, R; Vodopiyanov, I; Abelev, B; Adams, M R; Anghel, I M; Apanasevich, L; Bazterra, V E; Betts, R R; Callner, J; Castro, M A; Cavanaugh, R; Dragoiu, C; Garcia-Solis, E J; Gerber, C E; Hofman, D J; Khalatian, S; Mironov, C; Shabalina, E; Smoron, A; Varelas, N; Akgun, U; Albayrak, E A; Ayan, A S; Bilki, B; Briggs, R; Cankocak, K; Chung, K; Clarida, W; Debbins, P; Duru, F; Ingram, F D; Lae, C K; McCliment, E; Merlo, J P; Mestvirishvili, A; Miller, M J; Moeller, A; Nachtman, J; Newsom, C R; Norbeck, E; Olson, J; Onel, Y; Ozok, F; Parsons, J; Schmidt, I; Sen, S; Wetzel, J; Yetkin, T; Yi, K; Barnett, B A; Blumenfeld, B; Bonato, A; Chien, C Y; Fehling, D; Giurgiu, G; Gritsan, A V; Guo, Z J; Maksimovic, P; Rappoccio, S; Swartz, M; Tran, N V; Zhang, Y; Baringer, P; Bean, A; Grachov, O; Murray, M; Radicci, V; Sanders, S; Wood, J S; Zhukova, V; Bandurin, D; Bolton, T; Kaadze, K; Liu, A; Maravin, Y; Onoprienko, D; Svintradze, I; Wan, Z; Gronberg, J; Hollar, J; Lange, D; Wright, D; Baden, D; Bard, R; Boutemeur, M; Eno, S C; Ferencek, D; Hadley, N J; Kellogg, R G; Kirn, M; Kunori, S; Rossato, K; Rumerio, P; Santanastasio, F; Skuja, A; Temple, J; Tonjes, M B; Tonwar, S C; Toole, T; Twedt, E; Alver, B; Bauer, G; Bendavid, J; Busza, W; Butz, E; Cali, I A; Chan, M; D'Enterria, D; Everaerts, P; Gomez Ceballos, G; Hahn, K A; Harris, P; Jaditz, S; Kim, Y; Klute, M; Lee, Y J; Li, W; Loizides, C; Ma, T; Miller, M; Nahn, S; Paus, C; Roland, C; Roland, G; Rudolph, M; Stephans, G; Sumorok, K; Sung, K; Vaurynovich, S; Wenger, E A; Wyslouch, B; Xie, S; Yilmaz, Y; Yoon, A S; Bailleux, D; Cooper, S I; Cushman, P; Dahmes, B; De Benedetti, A; Dolgopolov, A; Dudero, P R; Egeland, R; Franzoni, G; Haupt, J; Inyakin, A; Klapoetke, K; Kubota, Y; Mans, J; Mirman, N; Petyt, D; Rekovic, V; Rusack, R; Schroeder, M; Singovsky, A; Zhang, J; Cremaldi, L M; Godang, R; Kroeger, R; Perera, L; Rahmat, R; Sanders, D A; Sonnek, P; Summers, D; Bloom, K; Bockelman, B; Bose, S; Butt, J; Claes, D R; Dominguez, A; Eads, M; Keller, J; Kelly, T; Kravchenko, I; Lazo-Flores, J; Lundstedt, C; Malbouisson, H; Malik, S; Snow, G R; Baur, U; Iashvili, I; Kharchilava, A; Kumar, A; Smith, K; Strang, M; Alverson, G; Barberis, E; Boeriu, O; Eulisse, G; Govi, G; McCauley, T; Musienko, Y; Muzaffar, S; Osborne, I; Paul, T; Reucroft, S; Swain, J; Taylor, L; Tuura, L; Anastassov, A; Gobbi, B; Kubik, A; Ofierzynski, R A; Pozdnyakov, A; Schmitt, M; Stoynev, S; Velasco, M; Won, S; Antonelli, L; Berry, D; Hildreth, M; Jessop, C; Karmgard, D J; Kolberg, T; Lannon, K; Lynch, S; Marinelli, N; Morse, D M; Ruchti, R; Slaunwhite, J; Warchol, J; Wayne, M; Bylsma, B; Durkin, L S; Gilmore, J; Gu, J; Killewald, P; Ling, T Y; Williams, G; Adam, N; Berry, E; Elmer, P; Garmash, A; Gerbaudo, D; Halyo, V; Hunt, A; Jones, J; Laird, E; Marlow, D; Medvedeva, T; Mooney, M; Olsen, J; Piroué, P; Stickland, D; Tully, C; Werner, J S; Wildish, T; Xie, Z; Zuranski, A; Acosta, J G; Bonnett Del Alamo, M; Huang, X T; Lopez, A; Mendez, H; Oliveros, S; Ramirez Vargas, J E; Santacruz, N; Zatzerklyany, A; Alagoz, E; Antillon, E; Barnes, V E; Bolla, G; Bortoletto, D; Everett, A; Garfinkel, A F; Gecse, Z; Gutay, L; Ippolito, N; Jones, M; Koybasi, O; Laasanen, A T; Leonardo, N; Liu, C; Maroussov, V; Merkel, P; Miller, D H; Neumeister, N; Sedov, A; Shipsey, I; Yoo, H D; Zheng, Y; Jindal, P; Parashar, N; Cuplov, V; Ecklund, K M; Geurts, F J M; Liu, J H; Maronde, D; Matveev, M; Padley, B P; Redjimi, R; Roberts, J; Sabbatini, L; Tumanov, A; Betchart, B; Bodek, A; Budd, H; Chung, Y S; de Barbaro, P; Demina, R; Flacher, H; Gotra, Y; Harel, A; Korjenevski, S; Miner, D C; Orbaker, D; Petrillo, G; Vishnevskiy, D; Zielinski, M; Bhatti, A; Demortier, L; Goulianos, K; Hatakeyama, K; Lungu, G; Mesropian, C; Yan, M; Atramentov, O; Bartz, E; Gershtein, Y; Halkiadakis, E; Hits, D; Lath, A; Rose, K; Schnetzer, S; Somalwar, S; Stone, R; Thomas, S; Watts, T L; Cerizza, G; Hollingsworth, M; Spanier, S; Yang, Z C; York, A; Asaadi, J; Aurisano, A; Eusebi, R; Golyash, A; Gurrola, A; Kamon, T; Nguyen, C N; Pivarski, J; Safonov, A; Sengupta, S; Toback, D; Weinberger, M; Akchurin, N; Berntzon, L; Gumus, K; Jeong, C; Kim, H; Lee, S W; Popescu, S; Roh, Y; Sill, A; Volobouev, I; Washington, E; Wigmans, R; Yazgan, E; Engh, D; Florez, C; Johns, W; Pathak, S; Sheldon, P; Andelin, D; Arenton, M W; Balazs, M; Boutle, S; Buehler, M; Conetti, S; Cox, B; Hirosky, R; Ledovskoy, A; Neu, C; Phillips II, D; Ronquest, M; Yohay, R; Gollapinni, S; Gunthoti, K; Harr, R; Karchin, P E; Mattson, M; Sakharov, A; Anderson, M; Bachtis, M; Bellinger, J N; Carlsmith, D; Crotty, I; Dasu, S; Dutta, S; Efron, J; Feyzi, F; Flood, K; Gray, L; Grogg, K S; Grothe, M; Hall-Wilton, R; Jaworski, M; Klabbers, P; Klukas, J; Lanaro, A; Lazaridis, C; Leonard, J; Loveless, R; Magrans de Abril, M; Mohapatra, A; Ott, G; Polese, G; Reeder, D; Savin, A; Smith, W H; Sourkov, A; Swanson, J; Weinberg, M; Wenman, D; Wensveen, M; White, A

    2010-01-01

    The CMS Collaboration conducted a month-long data taking exercise, the Cosmic Run At Four Tesla, during October-November 2008, with the goal of commissioning the experiment for extended operation. With all installed detector systems participating, CMS recorded 270 million cosmic ray events with the solenoid at a magnetic field strength of 3.8 T. This paper describes the data flow from the detector through the various online and offline computing systems, as well as the workflows used for recording the data, for aligning and calibrating the detector, and for analysis of the data.

  2. Big data analytics workflow management for eScience

    Science.gov (United States)

    Fiore, Sandro; D'Anca, Alessandro; Palazzo, Cosimo; Elia, Donatello; Mariello, Andrea; Nassisi, Paola; Aloisio, Giovanni

    2015-04-01

    In many domains such as climate and astrophysics, scientific data is often n-dimensional and requires tools that support specialized data types and primitives if it is to be properly stored, accessed, analysed and visualized. Currently, scientific data analytics relies on domain-specific software and libraries providing a huge set of operators and functionalities. However, most of these software fail at large scale since they: (i) are desktop based, rely on local computing capabilities and need the data locally; (ii) cannot benefit from available multicore/parallel machines since they are based on sequential codes; (iii) do not provide declarative languages to express scientific data analysis tasks, and (iv) do not provide newer or more scalable storage models to better support the data multidimensionality. Additionally, most of them: (v) are domain-specific, which also means they support a limited set of data formats, and (vi) do not provide a workflow support, to enable the construction, execution and monitoring of more complex "experiments". The Ophidia project aims at facing most of the challenges highlighted above by providing a big data analytics framework for eScience. Ophidia provides several parallel operators to manipulate large datasets. Some relevant examples include: (i) data sub-setting (slicing and dicing), (ii) data aggregation, (iii) array-based primitives (the same operator applies to all the implemented UDF extensions), (iv) data cube duplication, (v) data cube pivoting, (vi) NetCDF-import and export. Metadata operators are available too. Additionally, the Ophidia framework provides array-based primitives to perform data sub-setting, data aggregation (i.e. max, min, avg), array concatenation, algebraic expressions and predicate evaluation on large arrays of scientific data. Bit-oriented plugins have also been implemented to manage binary data cubes. Defining processing chains and workflows with tens, hundreds of data analytics operators is the

  3. The robust schedule - a link to improved workflow

    DEFF Research Database (Denmark)

    Lindhard, Søren Munch; Wandahl, Søren

    2012-01-01

    In today’s construction, there is a paramount focus on time, and on the scheduling and control of time. Everything is organized with respect to time. The construction project has to be completed within a fixed and often tight deadline. Otherwise a daily penalty often has to be paid. This pins down...... is a chaotic, complex and uncontrolled construction site. Furthermore, strict time limits entail the workflow to be optimized under sub-optimal conditions. Even though productivity overall seems to be increasing, productivity per man-hour is decreasing resulting in increased cost. To increase productivity...

  4. The robust schedule - A link to improved workflow

    DEFF Research Database (Denmark)

    Lindhard, Søren; Wandahl, Søren

    2012-01-01

    In today’s construction, there is a paramount focus on time, and on the scheduling and control of time. Everything is organized with respect to time. The construction project has to be completed within a fixed and often tight deadline. Otherwise a daily penalty often has to be paid. This pin....... The result is a chaotic, complex and uncontrolled construction site. Furthermore, strict time limits entail the workflow to be optimized under non-optimal conditions. Even though productivity seems to be increasing, productivity per man-hour is decreasing resulting in increased cost. To increase productivity...

  5. PhyloGrid: a development for a workflow in Phylogeny

    OpenAIRE

    Montes, Esther; Isea, Raul; Mayo, Rafael

    2010-01-01

    In this work we present the development of a workflow based on Taverna which is going to be implemented for calculations in Phylogeny by means of the MrBayes tool. It has a friendly interface developed with the Gridsphere framework. The user is able to define the parameters for doing the Bayesian calculation, determine the model of evolution, check the accuracy of the results in the intermediate stages as well as do a multiple alignment of the sequences previously to the final result. To do t...

  6. Workflow for High Throughput Screening of Gas Sensing Materials

    Directory of Open Access Journals (Sweden)

    Ulrich Simon

    2006-04-01

    Full Text Available The workflow of a high throughput screening setup for the rapid identification ofnew and improved sensor materials is presented. The polyol method was applied to preparenanoparticular metal oxides as base materials, which were functionalised by surface doping.Using multi-electrode substrates and high throughput impedance spectroscopy (HT-IS awide range of materials could be screened in a short time. Applying HT-IS in search of newselective gas sensing materials a NO2-tolerant NO sensing material with reducedsensitivities towards other test gases was identified based on iridium doped zinc oxide.Analogous behaviour was observed for iridium doped indium oxide.

  7. Workflow for large-scale analysis of melanoma tissue samples

    Directory of Open Access Journals (Sweden)

    Maria E. Yakovleva

    2015-09-01

    Full Text Available The aim of the present study was to create an optimal workflow for analysing a large cohort of malignant melanoma tissue samples. Samples were lysed with urea and enzymatically digested with trypsin or trypsin/Lys C. Buffer exchange or dilution was used to reduce urea concentration prior to digestion. The tissue digests were analysed directly or following strong cation exchange (SCX fractionation by nano LC–MS/MS. The approach which resulted in the largest number of protein IDs involved a buffer exchange step before enzymatic digestion with trypsin and chromatographic separation in 120 min gradient followed by SCX–RP separation of peptides.

  8. Understanding the Potential of Digital Intraoral and Benchtop Scanning Workflows.

    Science.gov (United States)

    Jansen, Curtis E

    2015-01-01

    Although the overwhelming majority of dental offices now use digital radiography and patient records, relatively few yet use either stand-alone intraoral scanning systems (6%) or complete systems that combine intraoral scanning with computer-aided design and computer-aided manufacturing (12%). This should change as dentists become more aware of the numerous advantages scanning systems offer in terms of patient care and communication of patient information, particularly with the dental laboratory. This article reviews the various types of scanner architecture as well as potential workflow models. PMID:26625165

  9. Time-efficient CT colonography interpretation using an advanced image-gallery-based, computer-aided ''first-reader'' workflow for the detection of colorectal adenomas

    International Nuclear Information System (INIS)

    To assess the performance of an advanced ''first-reader'' workflow for computer-aided detection (CAD) of colorectal adenomas ≥ 6 mm at computed tomographic colonography (CTC) in a low-prevalence cohort. A total of 616 colonoscopy-validated CTC patient-datasets were retrospectively reviewed by a radiologist using a ''first-reader'' CAD workflow. CAD detections were presented as galleries of six automatically generated two-dimensional (2D) and three-dimensional (3D) images together with interactive 3D target views and 2D multiplanar views of the complete dataset. Each patient-dataset was interpreted by initially using CAD image-galleries followed by a fast 2D review to address unprompted colonic areas. Per-patient, per-polyp, and per-adenoma sensitivities were calculated for lesions ≥ 6 mm. Statistical testing employed Fisher's exact and McNemar tests. In 91/616 patients, 131 polyps (92 adenomas, 39 non-adenomas) ≥ 6 mm and two cancers were identified by reference standard. Using the CAD gallery-based first-reader workflow, the radiologist detected all adenomas ≥ 10 mm (34/34) and cancers. Per-patient and polyp sensitivities for lesions ≥ 6 mm were 84.3 % (75/89), and 83.2 % (109/131), respectively, with 89.1 % (57/64) and 85.9 % (79/92) for adenomas. Overall specificity was 95.6 % (504/527). Mean interpretation time was 3.1 min per patient. A CAD algorithm, applied in an image-gallery-based first-reader workflow, can substantially decrease reading times while enabling accurate detection of colorectal adenomas in a low-prevalence population. (orig.)

  10. Design and implementation of a secure workflow system based on PKI/PMI

    Science.gov (United States)

    Yan, Kai; Jiang, Chao-hui

    2013-03-01

    As the traditional workflow system in privilege management has the following weaknesses: low privilege management efficiency, overburdened for administrator, lack of trust authority etc. A secure workflow model based on PKI/PMI is proposed after studying security requirements of the workflow systems in-depth. This model can achieve static and dynamic authorization after verifying user's ID through PKC and validating user's privilege information by using AC in workflow system. Practice shows that this system can meet the security requirements of WfMS. Moreover, it can not only improve system security, but also ensures integrity, confidentiality, availability and non-repudiation of the data in the system.

  11. Bandwidth-Aware Scheduling of Workflow Application on Multiple Grid Sites

    Directory of Open Access Journals (Sweden)

    Harshadkumar B. Prajapati

    2014-01-01

    Full Text Available Bandwidth-aware workflow scheduling is required to improve the performance of a workflow application in a multisite Grid environment, as the data movement cost between two low-bandwidth sites can adversely affect the makespan of the application. Pegasus WMS, an open-source and freely available WMS, cannot fully utilize its workflow mapping capability due to unavailability of integration of any bandwidth monitoring infrastructure in it. This paper develops the integration of Network Weather Service (NWS in Pegasus WMS to enable the bandwidth-aware mapping of scientific workflows. Our work demonstrates the applicability of the integration of NWS by making existing Heft site-selector of Pegasus WMS bandwidth aware. Furthermore, this paper proposes and implements a new workflow scheduling algorithm—Level based Highest Input and Processing Weight First. The results of the performed experiments indicate that the bandwidth-aware workflow scheduling algorithms perform better than bandwidth-unaware algorithms: Random and Heft of Pegasus WMS. Moreover, our proposed workflow scheduling algorithm performs better than the bandwidth-aware Heft algorithms. Thus, the proposed bandwidth-aware workflow scheduling enhances capability of Pegasus WMS and can increase performance of workflow applications.

  12. Definition of astronomical data analysis workflows on a service-oriented Grid architecture using Business Process Execution Language

    Science.gov (United States)

    Manna, V.; Cascone, E.; Capasso, G.; Tortone, G.

    2006-07-01

    Many international Grid projects have been launched recently in order to face the enormous amount of astronomical data which is produced and/or will be produced in the next years by the new generation of large telescopes and CCD mosaic detectors. Grid is the effective and natural solution for the CCD mosaic data processing but due to complex composition of astronomical applications a Grid workflow management system is required in order to simplify the description of nested tasks execution, monitoring and data handling. The recently released Business Process Execution Language for Web Services (BPEL4WS) specification is positioned to become the standard for Web services composition. It allows you to create complex processes by creating and wiring together different activities that can, for example, perform Web services invocations, manipulate data, throw faults, or terminate a process. The evolution towards a service-oriented architecture, supported by emerging standard, is an activity that has many attention. This issue is being tackled within the EU-funded EGEE project (Enabling Grids for E-science in Europe) whose primary goals are the provision of robust middleware components and the creation of reliable and dependable Grid infrastructure to support e-Science applications, using an architecture that offers a Web Service interface. In this paper we present a proposal for the execution of astronomical data analysis workflow on a service-oriented Grid architecture using the new standard language BPEL4WS.

  13. A High Throughput Workflow Environment for Cosmological Simulations

    CERN Document Server

    Erickson, Brandon M S; Evrard, August E; Becker, Matthew R; Busha, Michael T; Kravtsov, Andrey V; Marru, Suresh; Pierce, Marlon; Wechsler, Risa H

    2012-01-01

    The next generation of wide-area sky surveys offer the power to place extremely precise constraints on cosmological parameters and to test the source of cosmic acceleration. These observational programs will employ multiple techniques based on a variety of statistical signatures of galaxies and large-scale structure. These techniques have sources of systematic error that need to be understood at the percent-level in order to fully leverage the power of next-generation catalogs. Simulations of large-scale structure provide the means to characterize these uncertainties. We are using XSEDE resources to produce multiple synthetic sky surveys of galaxies and large-scale structure in support of science analysis for the Dark Energy Survey. In order to scale up our production to the level of fifty 10^10-particle simulations, we are working to embed production control within the Apache Airavata workflow environment. We explain our methods and report how the workflow has reduced production time by 40% compared to manua...

  14. Automation and workflow considerations for embedding Digimarc Barcodes at scale

    Science.gov (United States)

    Rodriguez, Tony; Haaga, Don; Calhoon, Sean

    2015-03-01

    The Digimarc® Barcode is a digital watermark applied to packages and variable data labels that carries GS1 standard GTIN-14 data traditionally carried by a 1-D barcode. The Digimarc Barcode can be read with smartphones and imaging-based barcode readers commonly used in grocery and retail environments. Using smartphones, consumers can engage with products and retailers can materially increase the speed of check-out, increasing store margins and providing a better experience for shoppers. Internal testing has shown an average of 53% increase in scanning throughput, enabling 100's of millions of dollars in cost savings [1] for retailers when deployed at scale. To get to scale, the process of embedding a digital watermark must be automated and integrated within existing workflows. Creating the tools and processes to do so represents a new challenge for the watermarking community. This paper presents a description and an analysis of the workflow implemented by Digimarc to deploy the Digimarc Barcode at scale. An overview of the tools created and lessons learned during the introduction of technology to the market are provided.

  15. Designing Collaborative Healthcare Technology for the Acute Care Workflow

    Directory of Open Access Journals (Sweden)

    Michael Gonzales

    2015-10-01

    Full Text Available Preventable medical errors in hospitals are the third leading cause of death in the United States. Many of these are caused by poor situational awareness, especially in acute care resuscitation scenarios. While a number of checklists and technological interventions have been developed to reduce cognitive load and improve situational awareness, these tools often do not fit the clinical workflow. To better understand the challenges faced by clinicians in acute care codes, we conducted a qualitative study with interprofessional clinicians at three regional hospitals. Our key findings are: Current documentation processes are inadequate (with information recorded on paper towels; reference guides can serve as fixation points, reducing rather than enhancing situational awareness; the physical environment imposes significant constraints on workflow; homegrown solutions may be used often to solve unstandardized processes; simulation scenarios do not match real-world practice. We present a number of considerations for collaborative healthcare technology design and discuss the implications of our findings on current work for the development of more effective interventions for acute care resuscitation scenarios.

  16. Autonomic Management of Application Workflows on Hybrid Computing Infrastructure

    Directory of Open Access Journals (Sweden)

    Hyunjoo Kim

    2011-01-01

    Full Text Available In this paper, we present a programming and runtime framework that enables the autonomic management of complex application workflows on hybrid computing infrastructures. The framework is designed to address system and application heterogeneity and dynamics to ensure that application objectives and constraints are satisfied. The need for such autonomic system and application management is becoming critical as computing infrastructures become increasingly heterogeneous, integrating different classes of resources from high-end HPC systems to commodity clusters and clouds. For example, the framework presented in this paper can be used to provision the appropriate mix of resources based on application requirements and constraints. The framework also monitors the system/application state and adapts the application and/or resources to respond to changing requirements or environment. To demonstrate the operation of the framework and to evaluate its ability, we employ a workflow used to characterize an oil reservoir executing on a hybrid infrastructure composed of TeraGrid nodes and Amazon EC2 instances of various types. Specifically, we show how different applications objectives such as acceleration, conservation and resilience can be effectively achieved while satisfying deadline and budget constraints, using an appropriate mix of dynamically provisioned resources. Our evaluations also demonstrate that public clouds can be used to complement and reinforce the scheduling and usage of traditional high performance computing infrastructure.

  17. Project Report: Automatic Sequence Processor Software Analysis

    Science.gov (United States)

    Benjamin, Brandon

    2011-01-01

    The Mission Planning and Sequencing (MPS) element of Multi-Mission Ground System and Services (MGSS) provides space missions with multi-purpose software to plan spacecraft activities, sequence spacecraft commands, and then integrate these products and execute them on spacecraft. Jet Propulsion Laboratory (JPL) is currently is flying many missions. The processes for building, integrating, and testing the multi-mission uplink software need to be improved to meet the needs of the missions and the operations teams that command the spacecraft. The Multi-Mission Sequencing Team is responsible for collecting and processing the observations, experiments and engineering activities that are to be performed on a selected spacecraft. The collection of these activities is called a sequence and ultimately a sequence becomes a sequence of spacecraft commands. The operations teams check the sequence to make sure that no constraints are violated. The workflow process involves sending a program start command, which activates the Automatic Sequence Processor (ASP). The ASP is currently a file-based system that is comprised of scripts written in perl, c-shell and awk. Once this start process is complete, the system checks for errors and aborts if there are any; otherwise the system converts the commands to binary, and then sends the resultant information to be radiated to the spacecraft.

  18. Automatic text summarization

    CERN Document Server

    Torres Moreno, Juan Manuel

    2014-01-01

    This new textbook examines the motivations and the different algorithms for automatic document summarization (ADS). We performed a recent state of the art. The book shows the main problems of ADS, difficulties and the solutions provided by the community. It presents recent advances in ADS, as well as current applications and trends. The approaches are statistical, linguistic and symbolic. Several exemples are included in order to clarify the theoretical concepts.  The books currently available in the area of Automatic Document Summarization are not recent. Powerful algorithms have been develop

  19. Automatic utilities auditing

    Energy Technology Data Exchange (ETDEWEB)

    Smith, Colin Boughton [Energy Metering Technology (United Kingdom)

    2000-08-01

    At present, energy audits represent only snapshot situations of the flow of energy. The normal pattern of energy audits as seen through the eyes of an experienced energy auditor is described. A brief history of energy auditing is given. It is claimed that the future of energy auditing lies in automatic meter reading with expert data analysis providing continuous automatic auditing thereby reducing the skill element. Ultimately, it will be feasible to carry out auditing at intervals of say 30 minutes rather than five years.

  20. Automatic Camera Control

    DEFF Research Database (Denmark)

    Burelli, Paolo; Preuss, Mike

    2014-01-01

    Automatically generating computer animations is a challenging and complex problem with applications in games and film production. In this paper, we investigate howto translate a shot list for a virtual scene into a series of virtual camera configurations — i.e automatically controlling the virtual...... camera. We approach this problem by modelling it as a dynamic multi-objective optimisation problem and show how this metaphor allows a much richer expressiveness than a classical single objective approach. Finally, we showcase the application of a multi-objective evolutionary algorithm to generate a shot...

  1. Service Based Cooperation Patterns to Support Flexible Inter-Organizational Workflows

    Directory of Open Access Journals (Sweden)

    Saida Boukhedouma

    2014-03-01

    Full Text Available Service Oriented Architecture (SOA is a paradigm that provides important advantages like interoperability, reusability and flexibility, particularly beneficial for B2B applications. In the current paper, we consider specific architectures of inter-organizational workflows (IOWF fairly widespread in the B2B area and implementing different cooperation schemas. Our aim is to propose new generic IOWF-architectures by using the SOA paradigm in order to obtain IOWF models flexible enough to ease their adaptation, evolution and reuse. For that, we introduce the concept of Service-Based Cooperation Pattern (SBCP that supports the definition of IOWF models based on services. A SBCP is defined by three main dimensions: the distribution of services, the control of execution and the structure of interaction between services. Also, we define a concept of composite cooperation pattern based on the combination of elementary patterns. We illustrate our approach by a general description of our cooperation framework called “S-IOFLOW” that supports the implementation of IOWF models obeying to the described SBCP. Three main points characterize our approach: (i the use of a pattern-based approach; (ii the definition of composite patterns by reusing elementary ones and (iii the support of several cooperation schemas with different types of control.

  2. Automatic atlas based electron density and structure contouring for MRI-based prostate radiation therapy on the cloud

    International Nuclear Information System (INIS)

    Our group have been developing methods for MRI-alone prostate cancer radiation therapy treatment planning. To assist with clinical validation of the workflow we are investigating a cloud platform solution for research purposes. Benefits of cloud computing can include increased scalability, performance and extensibility while reducing total cost of ownership. In this paper we demonstrate the generation of DICOM-RT directories containing an automatic average atlas based electron density image and fast pelvic organ contouring from whole pelvis MR scans.

  3. Automatic Atlas Based Electron Density and Structure Contouring for MRI-based Prostate Radiation Therapy on the Cloud

    Science.gov (United States)

    Dowling, J. A.; Burdett, N.; Greer, P. B.; Sun, J.; Parker, J.; Pichler, P.; Stanwell, P.; Chandra, S.; Rivest-Hénault, D.; Ghose, S.; Salvado, O.; Fripp, J.

    2014-03-01

    Our group have been developing methods for MRI-alone prostate cancer radiation therapy treatment planning. To assist with clinical validation of the workflow we are investigating a cloud platform solution for research purposes. Benefits of cloud computing can include increased scalability, performance and extensibility while reducing total cost of ownership. In this paper we demonstrate the generation of DICOM-RT directories containing an automatic average atlas based electron density image and fast pelvic organ contouring from whole pelvis MR scans.

  4. Integrated Enterprise Modeling Method Based on Workflow Model and Multiviews%Integrated Enterprise Modeling Method Based on Workflow Model and Multiviews

    Institute of Scientific and Technical Information of China (English)

    林慧苹; 范玉顺; 吴澄

    2001-01-01

    Many enterprise modeling methods are proposed to model thebusiness process of enterprises and to implement CIM systems. But difficulties are still encountered when these methods are applied to the CIM system design and implementation. This paper proposes a new integrated enterprise modeling methodology based on the workflow model. The system architecture and the integrated modeling environment are described with a new simulation strategy. The modeling process and the relationship between the workflow model and the views are discussed.

  5. Scheduling Multilevel Deadline-Constrained Scientific Workflows on Clouds Based on Cost Optimization

    Directory of Open Access Journals (Sweden)

    Maciej Malawski

    2015-01-01

    Full Text Available This paper presents a cost optimization model for scheduling scientific workflows on IaaS clouds such as Amazon EC2 or RackSpace. We assume multiple IaaS clouds with heterogeneous virtual machine instances, with limited number of instances per cloud and hourly billing. Input and output data are stored on a cloud object store such as Amazon S3. Applications are scientific workflows modeled as DAGs as in the Pegasus Workflow Management System. We assume that tasks in the workflows are grouped into levels of identical tasks. Our model is specified using mathematical programming languages (AMPL and CMPL and allows us to minimize the cost of workflow execution under deadline constraints. We present results obtained using our model and the benchmark workflows representing real scientific applications in a variety of domains. The data used for evaluation come from the synthetic workflows and from general purpose cloud benchmarks, as well as from the data measured in our own experiments with Montage, an astronomical application, executed on Amazon EC2 cloud. We indicate how this model can be used for scenarios that require resource planning for scientific workflows and their ensembles.

  6. Performance engineering method for workflow systems : an integrated view of human and computerised work processes

    OpenAIRE

    Brataas, Gunnar

    1996-01-01

    A method for designing workflow systems which satisfy performance requirements is proposed in this thesis. Integration of human and computerised performance is particularly useful for workflow systems where human and computerised processes are intertwined. The proposed framework encompasses human and computerised resources. Even though systematic performance engineering is not common practice in information system development, current, best practice shows that performance engineering of softw...

  7. Soundness of Timed-Arc Workflow Nets in Discrete and Continuous-Time Semantics

    DEFF Research Database (Denmark)

    Mateo, Jose Antonio; Srba, Jiri; Sørensen, Mathias Grund

    2015-01-01

    Analysis of workflow processes with quantitative aspectslike timing is of interest in numerous time-critical applications. We suggest a workflow model based on timed-arc Petri nets and studythe foundational problems of soundness and strong (time-bounded) soundness.We first consider the discrete-t...

  8. CrossFlow: Cross-Organizational Workflow Management in Dynamic Virtual Enterprises

    NARCIS (Netherlands)

    Grefen, Paul; Aberer, Karl; Hoffner, Yigal; Ludwig, Heiko

    2000-01-01

    In this report, we present the approach to cross-organizational workflow management of the CrossFlow project. CrossFlow is a European research project aiming at the support of cross-organizational workflows in dynamic virtual enterprises. The cooperation in these virtual enterprises is based on dyna

  9. CrossFlow: Cross-Organizational Workflow Management in Dynamic Virtual Enterprises

    NARCIS (Netherlands)

    Grefen, Paul; Aberer, Karl; Hoffner, Yigal; Ludwig, Heiko

    2000-01-01

    This paper gives a detailed overview of the approach to cross-organizational workflow management developed in the CrossFlow project. CrossFlow is a European research project aiming at the support of cross-organizational workflows in dynamic virtual enterprises. The cooperation in these virtual enter

  10. CrossFlow: Cross-Organizational Workflow Management for Service Outsourcing in Dynamic Virtual Enterprises

    NARCIS (Netherlands)

    Grefen, Paul; Aberer, Karl; Ludwig, Heiko; Hoffner, Yigal

    2001-01-01

    In this report, we present the approach to cross-organizational workflow management of the CrossFlow project. CrossFlow is a European research project aiming at the support of cross-organizational workflows in dynamic virtual enterprises. The cooperation in these virtual enterprises is based on dyna

  11. The Impact of Computerized Provider Order Entry Systems on Inpatient Clinical Workflow: A Literature Review

    NARCIS (Netherlands)

    Z. Niazkhani (Zahra); H. Pirnejad (Habibollah); M. Berg (Marc); J.E.C.M. Aarts (Jos)

    2009-01-01

    textabstractPrevious studies have shown the importance of workflow issues in the implementation of CPOE systems and patient safety practices. To understand the impact of CPOE on clinical workflow, we developed a conceptual framework and conducted a literature search for CPOE evaluations between 1990

  12. A Six‐Stage Workflow for Robust Application of Systems Pharmacology

    Science.gov (United States)

    Gadkar, K; Kirouac, DC; Mager, DE; van der Graaf, PH

    2016-01-01

    Quantitative and systems pharmacology (QSP) is increasingly being applied in pharmaceutical research and development. One factor critical to the ultimate success of QSP is the establishment of commonly accepted language, technical criteria, and workflows. We propose an integrated workflow that bridges conceptual objectives with underlying technical detail to support the execution, communication, and evaluation of QSP projects. PMID:27299936

  13. Fault tolerant workflow scheduling based on replication and resubmission of tasks in Cloud Computing

    Directory of Open Access Journals (Sweden)

    Jayadivya S K

    2012-06-01

    Full Text Available The aim of workflow scheduling system is to schedule the workflows within the user given deadline to achieve a good success rate. Workflow is a set of tasks processed in a predefined order based on its data and control dependency. Scheduling these workflows in a computing environment, like cloud environment, is an NP-Complete problem and it becomes more challenging when failures of tasks areconsidered. To overcome these failures, the workflow scheduling system should be fault tolerant. In this paper, the proposed Fault Tolerant Workflow Scheduling algorithm (FTWS provides fault tolerance by using replication and resubmission of tasks based on priority of the tasks. The replication of tasks depends on a heuristic metric which is calculated by finding the tradeoff between the replication factor and resubmission factor. The heuristic metric is considered because replication alone may lead to resource wastage and resubmission alone may increase makespan. Tasks are prioritized based on the criticality of the task which is calculated by using parameters like out degree, earliest deadline and high resubmission impact. Priority helps in meeting the deadline of a task and thereby reducing wastage of resources. FTWS schedules workflows within a deadline even in the presence of failures without using any history of information. The experiments were conducted in a simulated cloud environment by scheduling workflows in the presence of failures which are generated randomly. The experimental results of the proposed work demonstrate the effective success rate in-spite of various failures.

  14. Provenance for Runtime Workflow Steering and Validation in Computational Seismology

    Science.gov (United States)

    Spinuso, A.; Krischer, L.; Krause, A.; Filgueira, R.; Magnoni, F.; Muraleedharan, V.; David, M.

    2014-12-01

    Provenance systems may be offered by modern workflow engines to collect metadata about the data transformations at runtime. If combined with effective visualisation and monitoring interfaces, these provenance recordings can speed up the validation process of an experiment, suggesting interactive or automated interventions with immediate effects on the lifecycle of a workflow run. For instance, in the field of computational seismology, if we consider research applications performing long lasting cross correlation analysis and high resolution simulations, the immediate notification of logical errors and the rapid access to intermediate results, can produce reactions which foster a more efficient progress of the research. These applications are often executed in secured and sophisticated HPC and HTC infrastructures, highlighting the need for a comprehensive framework that facilitates the extraction of fine grained provenance and the development of provenance aware components, leveraging the scalability characteristics of the adopted workflow engines, whose enactment can be mapped to different technologies (MPI, Storm clusters, etc). This work looks at the adoption of W3C-PROV concepts and data model within a user driven processing and validation framework for seismic data, supporting also computational and data management steering. Validation needs to balance automation with user intervention, considering the scientist as part of the archiving process. Therefore, the provenance data is enriched with community-specific metadata vocabularies and control messages, making an experiment reproducible and its description consistent with the community understandings. Moreover, it can contain user defined terms and annotations. The current implementation of the system is supported by the EU-Funded VERCE (http://verce.eu). It provides, as well as the provenance generation mechanisms, a prototypal browser-based user interface and a web API built on top of a NoSQL storage

  15. Automatic Complexity Analysis

    DEFF Research Database (Denmark)

    Rosendahl, Mads

    1989-01-01

    One way to analyse programs is to to derive expressions for their computational behaviour. A time bound function (or worst-case complexity) gives an upper bound for the computation time as a function of the size of input. We describe a system to derive such time bounds automatically using abstract...

  16. An Improvement on Algorithm of Grid-Workflow Based on QoS

    Institute of Scientific and Technical Information of China (English)

    ZHANG Yun-feng; GE Wei

    2004-01-01

    With the emergence of grid computing, new challenges have arisen in workflow tasks scheduling.The goal of grid-workflow task scheduling is to achieve high system throughput and to match the application needs with the available computing resources.This matching of resources in a non-deterministically share heterogeneous environment leads to concerns on quality of service (QoS).Grid concept is presented in this paper, coupled with the QoS requirement of workflow task and an improved algorithm-ILGSS algorithm, has been brought out.The complexity of the improved scheduling algorithm has been analyzed.The experiment results show that the improved algorithm can lead to significant performance gain in various applications.An important research domain-adaptive workflow transaction in grid computing environment, has been explored and a new solution for the scheduling of distribute workflow has been bring forward in grid environment.

  17. Domain-Specific Languages For Developing and Deploying Signature Discovery Workflows

    Energy Technology Data Exchange (ETDEWEB)

    Jacob, Ferosh; Wynne, Adam S.; Liu, Yan; Gray, Jeff

    2013-12-02

    Domain-agnostic Signature Discovery entails scientific investigation across multiple domains through the re-use of existing algorithms into workflows. The existing algorithms may be written in any programming language for various hardware architectures (e.g., desktops, commodity clusters, and specialized parallel hardware platforms). This raises an engineering issue in generating Web services for heterogeneous algorithms so that they can be composed into a scientific workflow environment (e.g., Taverna). In this paper, we present our software tool that defines two simple Domain-Specific Languages (DSLs) to automate these processes: SDL and WDL. Our Service Description Language (SDL) describes key elements of a signature discovery algorithm and generates the service code. The Workflow Description Language (WDL) describes the pipeline of services and generates deployable artifacts for the Taverna workflow management system. We demonstrate our tool with a landscape classification example that is represented by BLAST workflows composed of services that wrap original scripts.

  18. Automatic Generation of Building Models with Levels of Detail 1-3

    Science.gov (United States)

    Nguatem, W.; Drauschke, M.; Mayer, H.

    2016-06-01

    We present a workflow for the automatic generation of building models with levels of detail (LOD) 1 to 3 according to the CityGML standard (Gröger et al., 2012). We start with orienting unsorted image sets employing (Mayer et al., 2012), we compute depth maps using semi-global matching (SGM) (Hirschmüller, 2008), and fuse these depth maps to reconstruct dense 3D point clouds (Kuhn et al., 2014). Based on planes segmented from these point clouds, we have developed a stochastic method for roof model selection (Nguatem et al., 2013) and window model selection (Nguatem et al., 2014). We demonstrate our workflow up to the export into CityGML.

  19. Automatic Texture Mapping of Architectural and Archaeological 3d Models

    Science.gov (United States)

    Kersten, T. P.; Stallmann, D.

    2012-07-01

    Today, detailed, complete and exact 3D models with photo-realistic textures are increasingly demanded for numerous applications in architecture and archaeology. Manual texture mapping of 3D models by digital photographs with software packages, such as Maxon Cinema 4D, Autodesk 3Ds Max or Maya, still requires a complex and time-consuming workflow. So, procedures for automatic texture mapping of 3D models are in demand. In this paper two automatic procedures are presented. The first procedure generates 3D surface models with textures by web services, while the second procedure textures already existing 3D models with the software tmapper. The program tmapper is based on the Multi Layer 3D image (ML3DImage) algorithm and developed in the programming language C++. The studies showing that the visibility analysis using the ML3DImage algorithm is not sufficient to obtain acceptable results of automatic texture mapping. To overcome the visibility problem the Point Cloud Painter algorithm in combination with the Z-buffer-procedure will be applied in the future.

  20. A Component Based Approach to Scientific Workflow Management

    CERN Document Server

    Le Goff, Jean-Marie; Baker, Nigel; Brooks, Peter; McClatchey, Richard

    2001-01-01

    CRISTAL is a distributed scientific workflow system used in the manufacturing and production phases of HEP experiment construction at CERN. The CRISTAL project has studied the use of a description driven approach, using meta- modelling techniques, to manage the evolving needs of a large physics community. Interest from such diverse communities as bio-informatics and manufacturing has motivated the CRISTAL team to re-engineer the system to customize functionality according to end user requirements but maximize software reuse in the process. The next generation CRISTAL vision is to build a generic component architecture from which a complete software product line can be generated according to the particular needs of the target enterprise. This paper discusses the issues of adopting a component product line based approach and our experiences of software reuse.

  1. Optimizing perioperative decision making: improved information for clinical workflow planning.

    Science.gov (United States)

    Doebbeling, Bradley N; Burton, Matthew M; Wiebke, Eric A; Miller, Spencer; Baxter, Laurence; Miller, Donald; Alvarez, Jorge; Pekny, Joseph

    2012-01-01

    Perioperative care is complex and involves multiple interconnected subsystems. Delayed starts, prolonged cases and overtime are common. Surgical procedures account for 40-70% of hospital revenues and 30-40% of total costs. Most planning and scheduling in healthcare is done without modern planning tools, which have potential for improving access by assisting in operations planning support. We identified key planning scenarios of interest to perioperative leaders, in order to examine the feasibility of applying combinatorial optimization software solving some of those planning issues in the operative setting. Perioperative leaders desire a broad range of tools for planning and assessing alternate solutions. Our modeled solutions generated feasible solutions that varied as expected, based on resource and policy assumptions and found better utilization of scarce resources. Combinatorial optimization modeling can effectively evaluate alternatives to support key decisions for planning clinical workflow and improving care efficiency and satisfaction. PMID:23304284

  2. The Distributed Workflow Management System--FlowAgent

    Institute of Scientific and Technical Information of China (English)

    王文军; 仲萃豪

    2000-01-01

    While mainframe or 2-tier client/server system have serious problems in flexibility and scalability for the large-scale business processes, 3-tier client/server architecture and object-oriented system modeling which construct business process on service components seem to bring software system some scalability. As enabling infrastructure for object-oriented methodology, distributed WFMS (Work-flow Management System) can flexibly describe business rules among autonomous 'service tasks', and support scalability of large-scale business process. But current distributed WFMS still have difficulty to manage a large number of distributed tasks, the 'multi-TaskDomain' architecture of FlowAgent will try to solve this problem, and bring a dynamic and distributed environment for task-scheduling.

  3. Using Simulations to Integrate Technology into Health Care Aidesཿ Workflow

    Directory of Open Access Journals (Sweden)

    Sharla King

    2013-07-01

    Full Text Available Health care aides (HCAs are critical to home care, providing a range of services to people with chronic conditions, aging or are unable to care for themselves independently. The current HCA supply will not keep up with this increasing demand without fundamental changes in their work environment. One possible solution to some of the workflow challenges and workplace stress of HCAs is hand-held tablet technology. In order to introduce the use of tablets with HCAs, simulations were developed. Once an HCA was comfortable with the tablet, a simulated client was introduced. The HCA interacted with the simulated client and used the tablet applications to assist with providing care. After the simulations, the HCAs participated in a focus group. HCAs completed a survey before and after the tablet training and simulation to determine their perception and acceptance of the tablet. Future deployment and implementation of technologies in home care should be further evaluated for outcomes.

  4. Translating Unstructured Workflow Processes to Readable BPEL: Theory and Implementation

    DEFF Research Database (Denmark)

    van der Aalst, Willibrordus Martinus Pancratius; Lassen, Kristian Bisgaard

    2008-01-01

    The Business Process Execution Language for Web Services (BPEL) has emerged as the de-facto standard for implementing processes. Although intended as a language for connecting web services, its application is not limited to cross-organizational processes. It is expected that in the near future...... a wide variety of process-aware information systems will be realized using BPEL. While being a powerful language, BPEL is difficult to use. Its XML representation is very verbose and only readable for the trained eye. It offers many constructs and typically things can be implemented in many ways, e...... and not easy to use by end-users. Therefore, we provide a mapping from Workflow Nets (WF-nets) to BPEL. This mapping builds on the rich theory of Petri nets and can also be used to map other languages (e.g., UML, EPC, BPMN, etc.) onto BPEL. In addition to this we have implemented the algorithm in a tool called...

  5. A Model of Workflow-oriented Attributed Based Access Control

    Directory of Open Access Journals (Sweden)

    Guoping Zhang

    2011-02-01

    Full Text Available the emergence of “Internet of Things” breaks previous traditional thinking, which integrates physical infrastructure and network infrastructure into unified infrastructure. There will be a lot of resources or information in IoT, so computing and processing of information is the core supporting of IoT. In this paper, we introduce “Service-Oriented Computing” to solve the problem where each device can offer its functionality as standard services. Here we mainly discuss the access control issue of service-oriented computing in Internet of Things. This paper puts forward a model of Workflow-oriented Attributed Based Access Control (WABAC, and design an access control framework based on WABAC model. The model grants permissions to subjects according to subject atttribute, resource attribute, environment attribute and current task, meeting access control request of SOC. Using the approach presented can effectively enhance the access control security for SOC applications, and prevent the abuse of subject permissions.

  6. Approach for workflow modeling using π-calculus

    Institute of Scientific and Technical Information of China (English)

    杨东; 张申生

    2003-01-01

    As a variant of process algebra, π-calculus can describe the interactions between evolving processes. By modeling activity as a process interacting with other processes through ports, this paper presents a new approach: representing workilow models using ~-calculus. As a result, the model can characterize the dynamic behaviors of the workflow process in terms of the LTS ( Labeled Transition Semantics) semantics of π-calculus. The main advantage of the worktlow model's formal semantic is that it allows for verification of the model's properties, such as deadlock-free and normal termination. Moreover, the equivalence of worktlow models can be checked thlx)ugh weak bisimulation theorem in the π-caleulus, thus facilitating the optimizationof business processes.

  7. Towards better digital pathology workflows: programming libraries for high-speed sharpness assessment of Whole Slide Images

    Science.gov (United States)

    2014-01-01

    Background Since microscopic slides can now be automatically digitized and integrated in the clinical workflow, quality assessment of Whole Slide Images (WSI) has become a crucial issue. We present a no-reference quality assessment method that has been thoroughly tested since 2010 and is under implementation in multiple sites, both public university-hospitals and private entities. It is part of the FlexMIm R&D project which aims to improve the global workflow of digital pathology. For these uses, we have developed two programming libraries, in Java and Python, which can be integrated in various types of WSI acquisition systems, viewers and image analysis tools. Methods Development and testing have been carried out on a MacBook Pro i7 and on a bi-Xeon 2.7GHz server. Libraries implementing the blur assessment method have been developed in Java, Python, PHP5 and MySQL5. For web applications, JavaScript, Ajax, JSON and Sockets were also used, as well as the Google Maps API. Aperio SVS files were converted into the Google Maps format using VIPS and Openslide libraries. Results We designed the Java library as a Service Provider Interface (SPI), extendable by third parties. Analysis is computed in real-time (3 billion pixels per minute). Tests were made on 5000 single images, 200 NDPI WSI, 100 Aperio SVS WSI converted to the Google Maps format. Conclusions Applications based on our method and libraries can be used upstream, as calibration and quality control tool for the WSI acquisition systems, or as tools to reacquire tiles while the WSI is being scanned. They can also be used downstream to reacquire the complete slides that are below the quality threshold for surgical pathology analysis. WSI may also be displayed in a smarter way by sending and displaying the regions of highest quality before other regions. Such quality assessment scores could be integrated as WSI's metadata shared in clinical, research or teaching contexts, for a more efficient medical informatics

  8. Workflow Management Application Programming Interface Specification%工作流管理应用编程接口规范

    Institute of Scientific and Technical Information of China (English)

    刘华伟; 吴朝晖

    2000-01-01

    The document 'Workflow Management Application Programming Interface Specification'is distributed by the Workflow Management Coalition to specify stadard APIs which can be supported by workflow management products.In this paper,we first introduce two parts of this interface,then discuss the standardized data structure and functions definition,finally address the future work.

  9. A Review on Scientific Workflows%科学工作流技术研究综述

    Institute of Scientific and Technical Information of China (English)

    张卫民; 刘灿灿; 骆志刚

    2011-01-01

    Scientific Workflow Management Systems ( SWfMS) has become an effective platform for representing and managing large-scale complex scientific computing processes, which glue together a large number of complex applications for data management, analysis, simulation, and visualization, and then assist the scientists for scientific discovery. In this paper, the current studies of Scientific Workflow (SWF) are reviewed firstly, including SWF models, presentations, languages, composition, validation, scheduling and provenance, as well as fault tolerance and system security. Then, the latest studies in recent years are also discussed. Based on the analysis of the key technologies and the latest development, the drawbacks in this domain are pointed out and some suggestions towards the future development are made. Finally, the recent research status quo in China is presented and some suggestions are given.%科学工作流管理系统(Scientific Workflow Management Systems,SWfMS)为科学家提供一个管理大规模复杂科学计算的有效平台,通过管理复杂应用程序对海量科学数据进行管理、分析、仿真和可视化以帮助科学家进行科学发现.本文首先对科学工作流(Scientific Workflow,SWF)的关键技术和研究现状进行全面综述,包括SWF模型、表示、语言、组合、验证、调度、数据来源管理以及系统的容错性与安全性等;然后对近两年的最新研究进行分析,并在此基础上指出该领域目前存在的不足和未来发展方向;最后对我国目前的研究现状进行分析并给出建议.

  10. Automatic trend estimation

    CERN Document Server

    Vamos¸, C˘alin

    2013-01-01

    Our book introduces a method to evaluate the accuracy of trend estimation algorithms under conditions similar to those encountered in real time series processing. This method is based on Monte Carlo experiments with artificial time series numerically generated by an original algorithm. The second part of the book contains several automatic algorithms for trend estimation and time series partitioning. The source codes of the computer programs implementing these original automatic algorithms are given in the appendix and will be freely available on the web. The book contains clear statement of the conditions and the approximations under which the algorithms work, as well as the proper interpretation of their results. We illustrate the functioning of the analyzed algorithms by processing time series from astrophysics, finance, biophysics, and paleoclimatology. The numerical experiment method extensively used in our book is already in common use in computational and statistical physics.

  11. 基于数据驱动的工作流引擎的设计与实现%Design and Implementation of Data-Driven Based Workflow Engine

    Institute of Scientific and Technical Information of China (English)

    陈义松; 汪芸

    2012-01-01

    Workflow is a computerized business process.Workflow engine provides the runtime environment for workflow processes,playing a key role in the implementation of processes.The traditional workflow technology reflects a number of deficiencies in dealing with complicated and changing process.This paper proposes a data-driven based mode to achieve loose coupling between activities,and designs and implements workflow engine with the purpose of supporting this kind of data-driven mode.The engine copes with the complicated business processes with strong processing capabilities and can automatically mode the processes.%工作流是计算机化的业务流程.工作流引擎为工作流流程提供运行环境,在流程的执行过程中起着关键性作用.传统的工作流技术在处理复杂多变的流程时,缺乏良好的建模以及适应机制.本文提出一种基于数据驱动的工作流运行方式,实现了活动与活动之间的松散耦合,并以此为基础设计并实现支持这种数据驱动方式的工作流引擎.该引擎在应对复杂多变的业务流程时具有较强的处理能力,并能够实现流程的自动建模.

  12. Automatic Program Reports

    OpenAIRE

    Lígia Maria da Silva Ribeiro; Gabriel de Sousa Torcato David

    2007-01-01

    To profit from the data collected by the SIGARRA academic IS, a systematic setof graphs and statistics has been added to it and are available on-line. Thisanalytic information can be automatically included in a flexible yearly report foreach program as well as in a synthesis report for the whole school. Somedifficulties in the interpretation of some graphs led to the definition of new keyindicators and the development of a data warehouse across the university whereeffective data consolidation...

  13. Automatic food decisions

    DEFF Research Database (Denmark)

    Mueller Loose, Simone

    Consumers' food decisions are to a large extent shaped by automatic processes, which are either internally directed through learned habits and routines or externally influenced by context factors and visual information triggers. Innovative research methods such as eye tracking, choice experiments...... and food diaries allow us to better understand the impact of unconscious processes on consumers' food choices. Simone Mueller Loose will provide an overview of recent research insights into the effects of habit and context on consumers' food choices....

  14. Automatic Differentiation Variational Inference

    OpenAIRE

    Kucukelbir, Alp; Tran, Dustin; Ranganath, Rajesh; Gelman, Andrew; Blei, David M.

    2016-01-01

    Probabilistic modeling is iterative. A scientist posits a simple model, fits it to her data, refines it according to her analysis, and repeats. However, fitting complex models to large data is a bottleneck in this process. Deriving algorithms for new models can be both mathematically and computationally challenging, which makes it difficult to efficiently cycle through the steps. To this end, we develop automatic differentiation variational inference (ADVI). Using our method, the scientist on...

  15. Measuring Semantic and Structural Information for Data Oriented Workflow Retrieval with Cost Constraints

    Directory of Open Access Journals (Sweden)

    Yinglong Ma

    2014-01-01

    Full Text Available The reuse of data oriented workflows (DOWs can reduce the cost of workflow system development and control the risk of project failure and therefore is crucial for accelerating the automation of business processes. Reusing workflows can be achieved by measuring the similarity among candidate workflows and selecting the workflow satisfying requirements of users from them. However, due to DOWs being often developed based on an open, distributed, and heterogeneous environment, different users often can impose diverse cost constraints on data oriented workflows. This makes the reuse of DOWs challenging. There is no clear solution for retrieving DOWs with cost constraints. In this paper, we present a novel graph based model of DOWs with cost constraints, called constrained data oriented workflow (CDW, which can express cost constraints that users are often concerned about. An approach is proposed for retrieving CDWs, which seamlessly combines semantic and structural information of CDWs. A distance measure based on matrix theory is adopted to seamlessly combine semantic and structural similarities of CDWs for selecting and reusing them. Finally, the related experiments are made to show the effectiveness and efficiency of our approach.

  16. Bioconductor workflow for microbiome data analysis: from raw reads to community analyses.

    Science.gov (United States)

    Callahan, Ben J; Sankaran, Kris; Fukuyama, Julia A; McMurdie, Paul J; Holmes, Susan P

    2016-01-01

    High-throughput sequencing of PCR-amplified taxonomic markers (like the 16S rRNA gene) has enabled a new level of analysis of complex bacterial communities known as microbiomes. Many tools exist to quantify and compare abundance levels or microbial composition of communities in different conditions. The sequencing reads have to be denoised and assigned to the closest taxa from a reference database. Common approaches use a notion of 97% similarity and normalize the data by subsampling to equalize library sizes. In this paper, we show that statistical models allow more accurate abundance estimates. By providing a complete workflow in R, we enable the user to do sophisticated downstream statistical analyses, including both parameteric and nonparametric methods. We provide examples of using the R packages dada2, phyloseq, DESeq2, ggplot2 and vegan to filter, visualize and test microbiome data. We also provide examples of supervised analyses using random forests, partial least squares and linear models as well as nonparametric testing using community networks and the ggnetwork package.

  17. Bioconductor workflow for microbiome data analysis: from raw reads to community analyses

    Science.gov (United States)

    Callahan, Ben J.; Sankaran, Kris; Fukuyama, Julia A.; McMurdie, Paul J.; Holmes, Susan P.

    2016-01-01

    High-throughput sequencing of PCR-amplified taxonomic markers (like the 16S rRNA gene) has enabled a new level of analysis of complex bacterial communities known as microbiomes. Many tools exist to quantify and compare abundance levels or microbial composition of communities in different conditions. The sequencing reads have to be denoised and assigned to the closest taxa from a reference database. Common approaches use a notion of 97% similarity and normalize the data by subsampling to equalize library sizes. In this paper, we show that statistical models allow more accurate abundance estimates. By providing a complete workflow in R, we enable the user to do sophisticated downstream statistical analyses, including both parameteric and nonparametric methods. We provide examples of using the R packages dada2, phyloseq, DESeq2, ggplot2 and vegan to filter, visualize and test microbiome data. We also provide examples of supervised analyses using random forests, partial least squares and linear models as well as nonparametric testing using community networks and the ggnetwork package. PMID:27508062

  18. Bioconductor workflow for microbiome data analysis: from raw reads to community analyses.

    Science.gov (United States)

    Callahan, Ben J; Sankaran, Kris; Fukuyama, Julia A; McMurdie, Paul J; Holmes, Susan P

    2016-01-01

    High-throughput sequencing of PCR-amplified taxonomic markers (like the 16S rRNA gene) has enabled a new level of analysis of complex bacterial communities known as microbiomes. Many tools exist to quantify and compare abundance levels or microbial composition of communities in different conditions. The sequencing reads have to be denoised and assigned to the closest taxa from a reference database. Common approaches use a notion of 97% similarity and normalize the data by subsampling to equalize library sizes. In this paper, we show that statistical models allow more accurate abundance estimates. By providing a complete workflow in R, we enable the user to do sophisticated downstream statistical analyses, including both parameteric and nonparametric methods. We provide examples of using the R packages dada2, phyloseq, DESeq2, ggplot2 and vegan to filter, visualize and test microbiome data. We also provide examples of supervised analyses using random forests, partial least squares and linear models as well as nonparametric testing using community networks and the ggnetwork package. PMID:27508062

  19. Inheritance Optimization of Extend Case Transfer Model of Interoganization Workflows Management

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    Extend case transfer architecture inter-organization workflow management fits the needs of Collaboration commerce. However, during the third step of extend case transfer architecture, modifications of private workflows might cause some fatal problems, such as dead locks, live locks and dead tasks. These problems could change the soundness and efficiency of overall work flow. This paper presents a Petri net based approach to protect the inheritance of public work flows in private domains, and discusses an implementation of our collaboration commerce workflow model.

  20. An Inter-enterprise Workflow Model for Supply Chain and B2B E-commerce

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    The goals of B2B electronic commerce and supply chain management system are to implement interoperability of independent enterprises, to smooth the information flow between them and to deploy business processes over multiple enterprises. The inherent characteristics of workflow system make it suitable to implement the cross organization management. This paper, firstly, proposes an inter-enterprises workflow model based on the agreement to support the construction of supply chain management system and B2B electronic commerce. This model has extended the standard workflow model. After that, an architecture which supports the model has been introduced, especially it details the structure and implementation of interfaces between enterprises.

  1. Un modelo de referencia para definir la perspectiva organizacional de modelos de workflows

    OpenAIRE

    Stroppi, Luis Jesús Ramón; Villarreal, Pablo David

    2009-01-01

    El soporte que las herramientas de modelado y sistemas de gestión de workflows brindan a la perspectiva organizacional es limitado. Esto se debe a la falta de herramientas que permitan entender los requerimientos de distribución de trabajo definidos en un modelo de workflow. Este trabajo presenta un modelo de referencia que da soporte a la definición de la perspectiva organizacional de los modelos de workflows. El modelo provee un conjunto de atributos de actividad que permiten identificar lo...

  2. DOMstudio: an integrated workflow for Digital Outcrop Model reconstruction and interpretation

    Science.gov (United States)

    Bistacchi, Andrea

    2015-04-01

    ). This dataset can be used as-is (PC-DOM), or a 3D triangulated surface can be interpolated from the point cloud, and images can be used to associate a texture to this surface (TS-DOM). In the DOMstudio workflow we use both PC-DOMs and TS-DOMs. Particularly, the latter are obtained projecting the original images onto the triangulated surface, without any downsampling, thus retaining the original resolution and quality of images collected in the field. In the DOMstudio interpretation step, PC-DOM is considered the best option for fracture analysis in outcrops where facets corresponding to fractures are present. This allows obtaining orientation statistics (e.g. stereoplots, Fisher statistics, etc.) directly from a point cloud where, for each point, the unit vector normal to the outcrop surface has been calculated. A recent development in this kind of processing is represented by the possibility to automatically select (segment) subset point clouds representing single fracture surfaces, which can be used for studies on fracture length, spacing, etc., allowing to obtain parameters like the frequency-length distribution, P21, etc. PC-DOM interpretation can be combined or complemented, depending on the outcrop morphology, with an interpretation carried out on a TS-DOM in terms of traces, which are the linear intersection of "geological" surfaces (fractures, faults, bedding, etc.) with the outcrop surface. This kind of interpretation is very well suited for outcrops with smooth surfaces, and can be performed either by manual picking, or by applying image analysis techniques on the images associated with the DOM. In this case, a huge mass of data, with very high resolution, can be collected very effectively. If we consider applications like lithological or mineral map-ping, TS-DOM datasets are the only suitable support. Finally, the DOMstudio workflow produces output in formats that are compatible with all common geomodelling packages (e.g. Gocad/Skua, Petrel, Move), allowing

  3. DOMstudio: an integrated workflow for Digital Outcrop Model reconstruction and interpretation

    Science.gov (United States)

    Bistacchi, Andrea

    2015-04-01

    ). This dataset can be used as-is (PC-DOM), or a 3D triangulated surface can be interpolated from the point cloud, and images can be used to associate a texture to this surface (TS-DOM). In the DOMstudio workflow we use both PC-DOMs and TS-DOMs. Particularly, the latter are obtained projecting the original images onto the triangulated surface, without any downsampling, thus retaining the original resolution and quality of images collected in the field. In the DOMstudio interpretation step, PC-DOM is considered the best option for fracture analysis in outcrops where facets corresponding to fractures are present. This allows obtaining orientation statistics (e.g. stereoplots, Fisher statistics, etc.) directly from a point cloud where, for each point, the unit vector normal to the outcrop surface has been calculated. A recent development in this kind of processing is represented by the possibility to automatically select (segment) subset point clouds representing single fracture surfaces, which can be used for studies on fracture length, spacing, etc., allowing to obtain parameters like the frequency-length distribution, P21, etc. PC-DOM interpretation can be combined or complemented, depending on the outcrop morphology, with an interpretation carried out on a TS-DOM in terms of traces, which are the linear intersection of "geological" surfaces (fractures, faults, bedding, etc.) with the outcrop surface. This kind of interpretation is very well suited for outcrops with smooth surfaces, and can be performed either by manual picking, or by applying image analysis techniques on the images associated with the DOM. In this case, a huge mass of data, with very high resolution, can be collected very effectively. If we consider applications like lithological or mineral map-ping, TS-DOM datasets are the only suitable support. Finally, the DOMstudio workflow produces output in formats that are compatible with all common geomodelling packages (e.g. Gocad/Skua, Petrel, Move), allowing

  4. DNA qualification workflow for next generation sequencing of histopathological samples.

    Science.gov (United States)

    Simbolo, Michele; Gottardi, Marisa; Corbo, Vincenzo; Fassan, Matteo; Mafficini, Andrea; Malpeli, Giorgio; Lawlor, Rita T; Scarpa, Aldo

    2013-01-01

    Histopathological samples are a treasure-trove of DNA for clinical research. However, the quality of DNA can vary depending on the source or extraction method applied. Thus a standardized and cost-effective workflow for the qualification of DNA preparations is essential to guarantee interlaboratory reproducible results. The qualification process consists of the quantification of double strand DNA (dsDNA) and the assessment of its suitability for downstream applications, such as high-throughput next-generation sequencing. We tested the two most frequently used instrumentations to define their role in this process: NanoDrop, based on UV spectroscopy, and Qubit 2.0, which uses fluorochromes specifically binding dsDNA. Quantitative PCR (qPCR) was used as the reference technique as it simultaneously assesses DNA concentration and suitability for PCR amplification. We used 17 genomic DNAs from 6 fresh-frozen (FF) tissues, 6 formalin-fixed paraffin-embedded (FFPE) tissues, 3 cell lines, and 2 commercial preparations. Intra- and inter-operator variability was negligible, and intra-methodology variability was minimal, while consistent inter-methodology divergences were observed. In fact, NanoDrop measured DNA concentrations higher than Qubit and its consistency with dsDNA quantification by qPCR was limited to high molecular weight DNA from FF samples and cell lines, where total DNA and dsDNA quantity virtually coincide. In partially degraded DNA from FFPE samples, only Qubit proved highly reproducible and consistent with qPCR measurements. Multiplex PCR amplifying 191 regions of 46 cancer-related genes was designated the downstream application, using 40 ng dsDNA from FFPE samples calculated by Qubit. All but one sample produced amplicon libraries suitable for next-generation sequencing. NanoDrop UV-spectrum verified contamination of the unsuccessful sample. In conclusion, as qPCR has high costs and is labor intensive, an alternative effective standard workflow for

  5. DNA qualification workflow for next generation sequencing of histopathological samples.

    Directory of Open Access Journals (Sweden)

    Michele Simbolo

    Full Text Available Histopathological samples are a treasure-trove of DNA for clinical research. However, the quality of DNA can vary depending on the source or extraction method applied. Thus a standardized and cost-effective workflow for the qualification of DNA preparations is essential to guarantee interlaboratory reproducible results. The qualification process consists of the quantification of double strand DNA (dsDNA and the assessment of its suitability for downstream applications, such as high-throughput next-generation sequencing. We tested the two most frequently used instrumentations to define their role in this process: NanoDrop, based on UV spectroscopy, and Qubit 2.0, which uses fluorochromes specifically binding dsDNA. Quantitative PCR (qPCR was used as the reference technique as it simultaneously assesses DNA concentration and suitability for PCR amplification. We used 17 genomic DNAs from 6 fresh-frozen (FF tissues, 6 formalin-fixed paraffin-embedded (FFPE tissues, 3 cell lines, and 2 commercial preparations. Intra- and inter-operator variability was negligible, and intra-methodology variability was minimal, while consistent inter-methodology divergences were observed. In fact, NanoDrop measured DNA concentrations higher than Qubit and its consistency with dsDNA quantification by qPCR was limited to high molecular weight DNA from FF samples and cell lines, where total DNA and dsDNA quantity virtually coincide. In partially degraded DNA from FFPE samples, only Qubit proved highly reproducible and consistent with qPCR measurements. Multiplex PCR amplifying 191 regions of 46 cancer-related genes was designated the downstream application, using 40 ng dsDNA from FFPE samples calculated by Qubit. All but one sample produced amplicon libraries suitable for next-generation sequencing. NanoDrop UV-spectrum verified contamination of the unsuccessful sample. In conclusion, as qPCR has high costs and is labor intensive, an alternative effective standard

  6. DNA qualification workflow for next generation sequencing of histopathological samples.

    Science.gov (United States)

    Simbolo, Michele; Gottardi, Marisa; Corbo, Vincenzo; Fassan, Matteo; Mafficini, Andrea; Malpeli, Giorgio; Lawlor, Rita T; Scarpa, Aldo

    2013-01-01

    Histopathological samples are a treasure-trove of DNA for clinical research. However, the quality of DNA can vary depending on the source or extraction method applied. Thus a standardized and cost-effective workflow for the qualification of DNA preparations is essential to guarantee interlaboratory reproducible results. The qualification process consists of the quantification of double strand DNA (dsDNA) and the assessment of its suitability for downstream applications, such as high-throughput next-generation sequencing. We tested the two most frequently used instrumentations to define their role in this process: NanoDrop, based on UV spectroscopy, and Qubit 2.0, which uses fluorochromes specifically binding dsDNA. Quantitative PCR (qPCR) was used as the reference technique as it simultaneously assesses DNA concentration and suitability for PCR amplification. We used 17 genomic DNAs from 6 fresh-frozen (FF) tissues, 6 formalin-fixed paraffin-embedded (FFPE) tissues, 3 cell lines, and 2 commercial preparations. Intra- and inter-operator variability was negligible, and intra-methodology variability was minimal, while consistent inter-methodology divergences were observed. In fact, NanoDrop measured DNA concentrations higher than Qubit and its consistency with dsDNA quantification by qPCR was limited to high molecular weight DNA from FF samples and cell lines, where total DNA and dsDNA quantity virtually coincide. In partially degraded DNA from FFPE samples, only Qubit proved highly reproducible and consistent with qPCR measurements. Multiplex PCR amplifying 191 regions of 46 cancer-related genes was designated the downstream application, using 40 ng dsDNA from FFPE samples calculated by Qubit. All but one sample produced amplicon libraries suitable for next-generation sequencing. NanoDrop UV-spectrum verified contamination of the unsuccessful sample. In conclusion, as qPCR has high costs and is labor intensive, an alternative effective standard workflow for

  7. SU-E-J-15: Automatically Detect Patient Treatment Position and Orientation in KV Portal Images

    International Nuclear Information System (INIS)

    Purpose: In the course of radiation therapy, the complex information processing workflow will Result in potential errors, such as incorrect or inaccurate patient setups. With automatic image check and patient identification, such errors could be effectively reduced. For this purpose, we developed a simple and rapid image processing method, to automatically detect the patient position and orientation in 2D portal images, so to allow automatic check of positions and orientations for patient daily RT treatments. Methods: Based on the principle of portal image formation, a set of whole body DRR images were reconstructed from multiple whole body CT volume datasets, and fused together to be used as the matching template. To identify the patient setup position and orientation shown in a 2D portal image, the 2D portal image was preprocessed (contrast enhancement, down-sampling and couch table detection), then matched to the template image so to identify the laterality (left or right), position, orientation and treatment site. Results: Five day’s clinical qualified portal images were gathered randomly, then were processed by the automatic detection and matching method without any additional information. The detection results were visually checked by physicists. 182 images were correct detection in a total of 200kV portal images. The correct rate was 91%. Conclusion: The proposed method can detect patient setup and orientation quickly and automatically. It only requires the image intensity information in KV portal images. This method can be useful in the framework of Electronic Chart Check (ECCK) to reduce the potential errors in workflow of radiation therapy and so to improve patient safety. In addition, the auto-detection results, as the patient treatment site position and patient orientation, could be useful to guide the sequential image processing procedures, e.g. verification of patient daily setup accuracy. This work was partially supported by research grant from

  8. AGENT-BASED WORKFLOW COORDINATION FOR SUPPLY CHAIN MANAGEMENT%基于Agent的供应链工作流协调管理

    Institute of Scientific and Technical Information of China (English)

    徐琪; Qiu-Ro-bin; 徐福缘

    2003-01-01

    To align customer demand with suppliers for reducing work-in-process and supply costs and increasing responsiveness to customer requirements, a real time collaborative supply chain management system is essential. A solution to the realization of supply chain management capable of timely responding to customer requirements is proposed. Workflow automation is used to manage process interaction across enterprises; Agents can be automatically invoked by supply chain workflow process and are used to promote the flexibility and reconfigurability by providing the mechanism in support of distributed compution in an enterprises to meet the requirements of performance and business dynamics. An approach that supports agent-based workflow process in a supply chain is proposed. And the coordination mechanism between agents is also discussed.%通过agent技术和工作流技术的集成,本文提出了一个实时响应顾客需求的供应链协调管理解决方案.在该方案中,工作流系统以中央协调方式支持企业业务过程;agent由过程事件激发,动态地执行具体的过程任务.由于agent的特性,它不局限于环境,可以在分布的、跨平台的异构环境中自动地完成任务.因此集成了工作流与agent 技术的协调管理方法,具有良好的可重构性和柔性机制,能够充分满足供应链管理分布性和动态性特点,为供应链跨组织的企业业务过程管理提供了有力的技术支持.

  9. Documenting scientific workflow: the metadata, provenance and ontology project

    Science.gov (United States)

    Greenwald, Martin; Stillerman, J.; Wright, J.; Abla, G.; Chanthavong, R.; Schissel, D.; Romosan, A.; Shoshani, A.

    2014-10-01

    Careful management of data, its creation and transformation (provenance) and associated metadata is a critical part of any scientific enterprise. Traditionally this was the role of the lab notebook, but the digital era has resulted instead in the fragmentation of data, processing and annotation. This paper describes an ongoing multi-institutional project aimed at remedying this problem by developing tools to automate documentation of scientific workflows and associated information. Data and all processes that create or modify that data are represented mathematically as a directed acyclic graph, providing explicit information about the relationships between elements with all elements having globally unique and persistent IDs. The export of data, for publication, presentation or external databases would be recorded, allowing traceability in either direction - answering the questions ``Where was this data used?'' or ``Where did the data in this figure come from.'' Namespace management is provided through a well structured ``ontology,'' which can be customized for any particular community or application. Supported by DOE Contract DE-SC0008736.

  10. A Workflow for Global Sensitivity Analysis of PBPK Models

    Directory of Open Access Journals (Sweden)

    Kevin eMcNally

    2011-06-01

    Full Text Available Physiologically based pharmacokinetic models have a potentially significant role in the development of a reliable predictive toxicity testing strategy. The structure of PBPK models are ideal frameworks into which disparate in vitro and in vivo data can be integrated and utilised to translate information generated, using alternative to animal measures of toxicity and human biological monitoring data, into plausible corresponding exposures. However, these models invariably include the description of well known non-linear biological processes such as, enzyme saturation and interactions between parameters such as, organ mass and body mass. Therefore, an appropriate sensitivity analysis technique is required which can quantify the influences associated with individual parameters, interactions between parameters and any non-linear processes. In this report we have defined a workflow for sensitivity analysis of PBPK models that is computationally feasible, accounts for interactions between parameters, and can be displayed in the form of a bar chart and cumulative sum line (Lowry plot, which we believe is intuitive and appropriate for toxicologists, risk assessors and regulators.

  11. Enabling Efficient Climate Science Workflows in High Performance Computing Environments

    Science.gov (United States)

    Krishnan, H.; Byna, S.; Wehner, M. F.; Gu, J.; O'Brien, T. A.; Loring, B.; Stone, D. A.; Collins, W.; Prabhat, M.; Liu, Y.; Johnson, J. N.; Paciorek, C. J.

    2015-12-01

    A typical climate science workflow often involves a combination of acquisition of data, modeling, simulation, analysis, visualization, publishing, and storage of results. Each of these tasks provide a myriad of challenges when running on a high performance computing environment such as Hopper or Edison at NERSC. Hurdles such as data transfer and management, job scheduling, parallel analysis routines, and publication require a lot of forethought and planning to ensure that proper quality control mechanisms are in place. These steps require effectively utilizing a combination of well tested and newly developed functionality to move data, perform analysis, apply statistical routines, and finally, serve results and tools to the greater scientific community. As part of the CAlibrated and Systematic Characterization, Attribution and Detection of Extremes (CASCADE) project we highlight a stack of tools our team utilizes and has developed to ensure that large scale simulation and analysis work are commonplace and provide operations that assist in everything from generation/procurement of data (HTAR/Globus) to automating publication of results to portals like the Earth Systems Grid Federation (ESGF), all while executing everything in between in a scalable environment in a task parallel way (MPI). We highlight the use and benefit of these tools by showing several climate science analysis use cases they have been applied to.

  12. Clinical workflow for personalized foot pressure ulcer prevention.

    Science.gov (United States)

    Bucki, M; Luboz, V; Perrier, A; Champion, E; Diot, B; Vuillerme, N; Payan, Y

    2016-09-01

    Foot pressure ulcers are a common complication of diabetes because of patient's lack of sensitivity due to neuropathy. Deep pressure ulcers appear internally when pressures applied on the foot create high internal strains nearby bony structures. Monitoring tissue strains in persons with diabetes is therefore important for an efficient prevention. We propose to use personalized biomechanical foot models to assess strains within the foot and to determine the risk of ulcer formation. Our workflow generates a foot model adapted to a patient's morphology by deforming an atlas model to conform it to the contours of segmented medical images of the patient's foot. Our biomechanical model is composed of rigid bodies for the bones, joined by ligaments and muscles, and a finite element mesh representing the soft tissues. Using our registration algorithm to conform three datasets, three new patient models were created. After applying a pressure load below these foot models, the Von Mises equivalent strains and "cluster volumes" (i.e. volumes of contiguous elements with strains above a given threshold) were measured within eight functionally meaningful foot regions. The results show the variability of both location and strain values among the three considered patients. This study also confirms that the anatomy of the foot has an influence on the risk of pressure ulcer. PMID:27212210

  13. Accelerating Science Impact through Big Data Workflow Management and Supercomputing

    Science.gov (United States)

    De, K.; Klimentov, A.; Maeno, T.; Mashinistov, R.; Nilsson, P.; Oleynik, D.; Panitkin, S.; Ryabinkin, E.; Wenaus, T.

    2016-02-01

    The Large Hadron Collider (LHC), operating at the international CERN Laboratory in Geneva, Switzerland, is leading Big Data driven scientific explorations. ATLAS, one of the largest collaborations ever assembled in the the history of science, is at the forefront of research at the LHC. To address an unprecedented multi-petabyte data processing challenge, the ATLAS experiment is relying on a heterogeneous distributed computational infrastructure. To manage the workflow for all data processing on hundreds of data centers the PanDA (Production and Distributed Analysis)Workload Management System is used. An ambitious program to expand PanDA to all available computing resources, including opportunistic use of commercial and academic clouds and Leadership Computing Facilities (LCF), is realizing within BigPanDA and megaPanDA projects. These projects are now exploring how PanDA might be used for managing computing jobs that run on supercomputers including OLCF's Titan and NRC-KI HPC2. The main idea is to reuse, as much as possible, existing components of the PanDA system that are already deployed on the LHC Grid for analysis of physics data. The next generation of PanDA will allow many data-intensive sciences employing a variety of computing platforms to benefit from ATLAS experience and proven tools in highly scalable processing.

  14. A novel workflow for seismic net pay estimation with uncertainty

    CERN Document Server

    Glinsky, Michael E; Unaldi, Muhlis; Nagassar, Vishal

    2016-01-01

    This paper presents a novel workflow for seismic net pay estimation with uncertainty. It is demonstrated on the Cassra/Iris Field. The theory for the stochastic wavelet derivation (which estimates the seismic noise level along with the wavelet, time-to-depth mapping, and their uncertainties), the stochastic sparse spike inversion, and the net pay estimation (using secant areas) along with its uncertainty; will be outlined. This includes benchmarking of this methodology on a synthetic model. A critical part of this process is the calibration of the secant areas. This is done in a two step process. First, a preliminary calibration is done with the stochastic reflection response modeling using rock physics relationships derived from the well logs. Second, a refinement is made to the calibration to account for the encountered net pay at the wells. Finally, a variogram structure is estimated from the extracted secant area map, then used to build in the lateral correlation to the ensemble of net pay maps while matc...

  15. Anima: Modular workflow system for comprehensive image data analysis

    Directory of Open Access Journals (Sweden)

    Ville eRantanen

    2014-07-01

    Full Text Available Modern microscopes produce vast amounts of image data, and computational methods are needed to analyze and interpret these data. Furthermore, a single image analysis project may require tens or hundreds of analysis steps starting from data import and preprocessing to segmentation and statistical analysis; and ending with visualization and reporting. To manage such large-scale image data analysis projects, we present here a modular workflow system called Anima. Anima is designed for comprehensive and efficient image data analysis, and it contains several features that are crucial in high-throughput image data analysis: programming language independence, batch processing, easily customized data processing, interoperability with other software via application programming interfaces, and advanced multivariate statistical analysis. The utility of Anima is shown with two case studies focusing on testing different algorithms developed in different imaging platforms and an automated prediction of alive/dead C. elegans worms by integrating several analysis environmens. Anima is fully open source and available with documentation at http://www.anduril.org/anima

  16. A workflow model to analyse pediatric emergency overcrowding.

    Science.gov (United States)

    Zgaya, Hayfa; Ajmi, Ines; Gammoudi, Lotfi; Hammadi, Slim; Martinot, Alain; Beuscart, Régis; Renard, Jean-Marie

    2014-01-01

    The greatest source of delay in patient flow is the waiting time from the health care request, and especially the bed request to exit from the Pediatric Emergency Department (PED) for hospital admission. It represents 70% of the time that these patients occupied in the PED waiting rooms. Our objective in this study is to identify tension indicators and bottlenecks that contribute to overcrowding. Patient flow mapping through the PED was carried out in a continuous 2 years period from January 2011 to December 2012. Our method is to use the collected real data, basing on accurate visits made in the PED of the Regional University Hospital Center (CHRU) of Lille (France), in order to construct an accurate and complete representation of the PED processes. The result of this representation is a Workflow model of the patient journey in the PED representing most faithfully possible the reality of the PED of CHRU of Lille. This model allowed us to identify sources of delay in patient flow and aspects of the PED activity that could be improved. It must be enough retailed to produce an analysis allowing to identify the dysfunctions of the PED and also to propose and to estimate prevention indicators of tensions. Our survey is integrated into the French National Research Agency project, titled: "Hospital: optimization, simulation and avoidance of strain" (ANR HOST).

  17. Accelerating Science Impact through Big Data Workflow Management and Supercomputing

    Directory of Open Access Journals (Sweden)

    De K.

    2016-01-01

    Full Text Available The Large Hadron Collider (LHC, operating at the international CERN Laboratory in Geneva, Switzerland, is leading Big Data driven scientific explorations. ATLAS, one of the largest collaborations ever assembled in the the history of science, is at the forefront of research at the LHC. To address an unprecedented multi-petabyte data processing challenge, the ATLAS experiment is relying on a heterogeneous distributed computational infrastructure. To manage the workflow for all data processing on hundreds of data centers the PanDA (Production and Distributed AnalysisWorkload Management System is used. An ambitious program to expand PanDA to all available computing resources, including opportunistic use of commercial and academic clouds and Leadership Computing Facilities (LCF, is realizing within BigPanDA and megaPanDA projects. These projects are now exploring how PanDA might be used for managing computing jobs that run on supercomputers including OLCF’s Titan and NRC-KI HPC2. The main idea is to reuse, as much as possible, existing components of the PanDA system that are already deployed on the LHC Grid for analysis of physics data. The next generation of PanDA will allow many data-intensive sciences employing a variety of computing platforms to benefit from ATLAS experience and proven tools in highly scalable processing.

  18. Automatic Configuration in NTP

    Institute of Scientific and Technical Information of China (English)

    Jiang Zongli(蒋宗礼); Xu Binbin

    2003-01-01

    NTP is nowadays the most widely used distributed network time protocol, which aims at synchronizing the clocks of computers in a network and keeping the accuracy and validation of the time information which is transmitted in the network. Without automatic configuration mechanism, the stability and flexibility of the synchronization network built upon NTP protocol are not satisfying. P2P's resource discovery mechanism is used to look for time sources in a synchronization network, and according to the network environment and node's quality, the synchronization network is constructed dynamically.

  19. A cross-package Bioconductor workflow for analysing methylation array data [version 2; referees: 3 approved, 1 approved with reservations

    Directory of Open Access Journals (Sweden)

    Jovana Maksimovic

    2016-07-01

    Full Text Available Methylation in the human genome is known to be associated with development and disease. The Illumina Infinium methylation arrays are by far the most common way to interrogate methylation across the human genome. This paper provides a Bioconductor workflow using multiple packages for the analysis of methylation array data. Specifically, we demonstrate the steps involved in a typical differential methylation analysis pipeline including: quality control, filtering, normalization, data exploration and statistical testing for probe-wise differential methylation. We further outline other analyses such as differential methylation of regions, differential variability analysis, estimating cell type composition and gene ontology testing. Finally, we provide some examples of how to visualise methylation array data.

  20. A cross-package Bioconductor workflow for analysing methylation array data [version 1; referees: 3 approved, 1 approved with reservations

    Directory of Open Access Journals (Sweden)

    Jovana Maksimovic

    2016-06-01

    Full Text Available Methylation in the human genome is known to be associated with development and disease. The Illumina Infinium methylation arrays are by far the most common way to interrogate methylation across the human genome. This paper provides a Bioconductor workflow using multiple packages for the analysis of methylation array data. Specifically, we demonstrate the steps involved in a typical differential methylation analysis pipeline including: quality control, filtering, normalization, data exploration and statistical testing for probe-wise differential methylation. We further outline other analyses such as differential methylation of regions, differential variability analysis, estimating cell type composition and gene ontology testing. Finally, we provide some examples of how to visualise methylation array data.

  1. A mixed methods approach for measuring the impact of delivery-centric interventions on clinician workflow.

    Science.gov (United States)

    Cady, Rhonda G; Finkelstein, Stanley M

    2012-01-01

    Health interventions vary widely. Pharmaceuticals, medical devices and wellness promotion are defined as 'outcome-centric.' They are implemented by clinicians for the use and benefit of consumers, and intervention effectiveness is measured by a change in health outcome. Electronic health records, computerized physician order entry systems and telehealth technologies are defined as 'delivery-centric.' They are implemented by organizations for use by clinicians to manage and facilitate consumer health, and the impact of these interventions on clinician workflow has become increasingly important. The methodological framework introduced in this paper uses a two-phase sequential mixed methods design that qualitatively explores clinician workflow before and after implementation of a delivery-centric intervention, and uses this information to quantitatively measure changes to workflow activities. The mixed methods protocol provides a standardized approach for understanding and determining the impact of delivery-centric interventions on clinician workflow. PMID:23304393

  2. Task-driven equipment inspection system based on safe workflow model

    Science.gov (United States)

    Guo, Xinyou; Liu, Yangguang

    2010-12-01

    An equipment inspection system is one that contains a number of equipment queues served in cyclic order. In order to satisfy multi-task scheduling and multi-task combination requirements for equipment inspection system, we propose a model based on inspection workflow in this paper. On the one hand, the model organizes all kinds of equipments according to inspection workflow, elemental work units according to inspection tasks, combination elements according to the task defined by users. We proposed a 3-dimensional workflow model for equipments inspection system including organization sub-model, process sub-model and data sub-model. On the other hand, the model is based on the security authorization which defined by relation between roles, tasks, pre-defined business workflows and inspection data. The system based on proposed framework is safe and efficient. Our implement shows that the system is easy to operate and manage according to the basic performance.

  3. A framework for service enterprise workflow simulation with multi-agents cooperation

    Science.gov (United States)

    Tan, Wenan; Xu, Wei; Yang, Fujun; Xu, Lida; Jiang, Chuanqun

    2013-11-01

    Process dynamic modelling for service business is the key technique for Service-Oriented information systems and service business management, and the workflow model of business processes is the core part of service systems. Service business workflow simulation is the prevalent approach to be used for analysis of service business process dynamically. Generic method for service business workflow simulation is based on the discrete event queuing theory, which is lack of flexibility and scalability. In this paper, we propose a service workflow-oriented framework for the process simulation of service businesses using multi-agent cooperation to address the above issues. Social rationality of agent is introduced into the proposed framework. Adopting rationality as one social factor for decision-making strategies, a flexible scheduling for activity instances has been implemented. A system prototype has been developed to validate the proposed simulation framework through a business case study.

  4. Visual compression of workflow visualizations with automated detection of macro motifs.

    Science.gov (United States)

    Maguire, Eamonn; Rocca-Serra, Philippe; Sansone, Susanna-Assunta; Davies, Jim; Chen, Min

    2013-12-01

    This paper is concerned with the creation of 'macros' in workflow visualization as a support tool to increase the efficiency of data curation tasks. We propose computation of candidate macros based on their usage in large collections of workflows in data repositories. We describe an efficient algorithm for extracting macro motifs from workflow graphs. We discovered that the state transition information, used to identify macro candidates, characterizes the structural pattern of the macro and can be harnessed as part of the visual design of the corresponding macro glyph. This facilitates partial automation and consistency in glyph design applicable to a large set of macro glyphs. We tested this approach against a repository of biological data holding some 9,670 workflows and found that the algorithmically generated candidate macros are in keeping with domain expert expectations.

  5. Formal Verification of Temporal Properties for Reduced Overhead in Grid Scientific Workflows

    Institute of Scientific and Technical Information of China (English)

    Jun-Wei Cao; Fan Zhang; Ke Xu; Lian-Chcn Liu; Chcng Wu

    2011-01-01

    With quick development of grid techniques and growing complexity of grid applications,it is becoming critical for reasoning temporal properties of grid workflows to probe potential pitfalls and errors,in order to ensure reliability and trustworthiness at the initial design phase.A state Pi calculus is proposed and implemented in this work,which not only enables flexible abstraction and management of historical grid system events,but also facilitates modeling and temporal verification of grid workflows.Furthermore,a relaxed region analysis (RRA) approach is proposed to decompose large scale grid workflows into sequentially composed regions with relaxation of parallel workflow branches,and corresponding verification strategies are also decomposed following modular verification principles.Performance evaluation results show that the RRA approach can dramatically reduce CPU time and memory usage of formal verification.

  6. Database supported electronic retrospective analyses in radiation oncology. Establishing a workflow using the example of pancreatic cancer; Datenbankbasierte digitale retrospektive Auswertung von Patientenkollektiven in der Radioonkologie. Etablierung eines Workflows am Beispiel des Pankreaskarzinoms

    Energy Technology Data Exchange (ETDEWEB)

    Kessel, K.A.; Habermehl, D.; Bougatf, N.; Debus, J.; Combs, S.E. [Universitatesklinikum Heidelberg (Germany). Abt. fuer Radioonkologie und Strahlentherapie; Bohn, C. [CHILI GmbH, Dossenheim (Germany); Jaeger, A.; Floca, R.O.; Zhang, L. [Deutsches Krebsforschungszentrum (DKFZ), Heidelberg (Germany); Bendl, R. [Hochschule Heilbronn (Germany). Fakultaet fuer Medizinische Informatik

    2012-12-15

    Purpose: Especially in the field of radiation oncology, handling a large variety of voluminous datasets from various information systems in different documentation styles efficiently is crucial for patient care and research. To date, conducting retrospective clinical analyses is rather difficult and time consuming. With the example of patients with pancreatic cancer treated with radio-chemotherapy, we performed a therapy evaluation by using an analysis system connected with a documentation system. Materials and methods: A total number of 783 patients have been documented into a professional, database-based documentation system. Information about radiation therapy, diagnostic images and dose distributions have been imported into the web-based system. Results: For 36 patients with disease progression after neoadjuvant chemoradiation, we designed and established an analysis workflow. After an automatic registration of the radiation plans with the follow-up images, the recurrence volumes are segmented manually. Based on these volumes the DVH (dose volume histogram) statistic is calculated, followed by the determination of the dose applied to the region of recurrence. All results are saved in the database and included in statistical calculations. Conclusion: The main goal of using an automatic analysis tool is to reduce time and effort conducting clinical analyses, especially with large patient groups. We showed a first approach and use of some existing tools, however manual interaction is still necessary. Further steps need to be taken to enhance automation. Already, it has become apparent that the benefits of digital data management and analysis lie in the central storage of data and reusability of the results. Therefore, we intend to adapt the analysis system to other types of tumors in radiation oncology. (orig.)

  7. Nanocuration workflows: Establishing best practices for identifying, inputting, and sharing data to inform decisions on nanomaterials

    Directory of Open Access Journals (Sweden)

    Christina M. Powers

    2015-09-01

    Full Text Available There is a critical opportunity in the field of nanoscience to compare and integrate information across diverse fields of study through informatics (i.e., nanoinformatics. This paper is one in a series of articles on the data curation process in nanoinformatics (nanocuration. Other articles in this series discuss key aspects of nanocuration (temporal metadata, data completeness, database integration, while the focus of this article is on the nanocuration workflow, or the process of identifying, inputting, and reviewing nanomaterial data in a data repository. In particular, the article discusses: 1 the rationale and importance of a defined workflow in nanocuration, 2 the influence of organizational goals or purpose on the workflow, 3 established workflow practices in other fields, 4 current workflow practices in nanocuration, 5 key challenges for workflows in emerging fields like nanomaterials, 6 examples to make these challenges more tangible, and 7 recommendations to address the identified challenges. Throughout the article, there is an emphasis on illustrating key concepts and current practices in the field. Data on current practices in the field are from a group of stakeholders active in nanocuration. In general, the development of workflows for nanocuration is nascent, with few individuals formally trained in data curation or utilizing available nanocuration resources (e.g., ISA-TAB-Nano. Additional emphasis on the potential benefits of cultivating nanomaterial data via nanocuration processes (e.g., capability to analyze data from across research groups and providing nanocuration resources (e.g., training will likely prove crucial for the wider application of nanocuration workflows in the scientific community.

  8. Cross-organizational Service-based Workflows - Solution Strategies for Quality of Service Optimization

    OpenAIRE

    Eckert, Julian

    2009-01-01

    By the application of the Service-oriented Architecture (SOA) paradigm on business processes, workflows can be decomposed into basic activities that can be realized by reusable services offering a specific business functionality. In order to compose cross-organizational service-based workflows, services can be sourced from internal as well as from external providers. On a large service market, services are offered with varying Quality of Service (QoS) levels and several pricing models. Provid...

  9. Characterizing Strain Variation in Engineered E. coli Using a Multi-Omics-Based Workflow

    DEFF Research Database (Denmark)

    Brunk, Elizabeth; George, Kevin W.; Alonso-Gutierrez, Jorge;

    2016-01-01

    Understanding the complex interactions that occur between heterologous and native biochemical pathways represents a major challenge in metabolic engineering and synthetic biology. We present a workflow that integrates metabolomics, proteomics, and genome-scale models of Escherichia coli metabolism...... to study the effects of introducing a heterologous pathway into a microbial host. This workflow incorporates complementary approaches from computational systems biology, metabolic engineering, and synthetic biology; provides molecular insight into how the host organism microenvironment changes due...

  10. Towards Efficient Service Delivery: The Role Of Workflow Systems In Public Sector In Kenya

    OpenAIRE

    Thuku, Lawrence Xavier Waweru; Mwangi, Karanja Evanson

    2015-01-01

    Current challenges in Electronic Government initiatives include performance management, effective and efficient means of sharing information between different stakeholders e.g. government departments in order to improve the quality of service delivery to the citizens. To address these challenges, this paper addresses an application domain of workflow systems in public institutions and proposes a framework that can be effectively used in implementing workflow systems in public institutions

  11. Modelling Task Delegation for Human-Centric eGovernment Workflows

    OpenAIRE

    Gaaloul, Khaled; Charoy, François; Schaad, Andreas

    2009-01-01

    International audience The execution of cross-domain eGovernment applications is a challenging topic. eGovernment organisations are facilitated and conducted using workflow management systems. Workflows automates the management and coordination of organisational or business processes. In the context of eGovernment, what is in many cases described as collaboration appears, however, to be coordination and synchronisation of processes ignoring human-centric interactions. In addition, we obser...

  12. Agent-based inter-organizational workflow management system for electronic institutions

    OpenAIRE

    Leitão, Paulo; Mendes, João M.

    2008-01-01

    Indexado Inspec An Electronic Institution is a computational framework that provides a set of services supporting the Virtual Organization lifecycle, namely its formation, operation and dissolution. A crucial service is related to the coordination of the corresponding inter-organizational workflow defined by the established contract. This paper introduces an agent-based interorganizational workflow management system, part of an Electronic Institution, aiming to coordinate the contract exec...

  13. Re-thinking Workflow Provenance against Data-Oriented Investigation Lifecycle

    OpenAIRE

    Alper, Pinar

    2014-01-01

    This report is the first installment of a two-part knowledge transfer. In this first part we introduce the status quo and issues, (with underlying reasons and remedies) in exploiting provenance information. The second report will provide details on approaches and techniques that can help towards increased use of provenance information.We start by revisiting the workflow provenance capabilities of the Taverna system, and the provenance-related information needs during stages of workflow- based...

  14. Automatic personnel contamination monitor

    International Nuclear Information System (INIS)

    United Nuclear Industries, Inc. (UNI) has developed an automatic personnel contamination monitor (APCM), which uniquely combines the design features of both portal and hand and shoe monitors. In addition, this prototype system also has a number of new features, including: micro computer control and readout, nineteen large area gas flow detectors, real-time background compensation, self-checking for system failures, and card reader identification and control. UNI's experience in operating the Hanford N Reactor, located in Richland, Washington, has shown the necessity of automatically monitoring plant personnel for contamination after they have passed through the procedurally controlled radiation zones. This final check ensures that each radiation zone worker has been properly checked before leaving company controlled boundaries. Investigation of the commercially available portal and hand and shoe monitors indicated that they did not have the sensitivity or sophistication required for UNI's application, therefore, a development program was initiated, resulting in the subject monitor. Field testing shows good sensitivity to personnel contamination with the majority of alarms showing contaminants on clothing, face and head areas. In general, the APCM has sensitivity comparable to portal survey instrumentation. The inherit stand-in, walk-on feature of the APCM not only makes it easy to use, but makes it difficult to bypass. (author)

  15. Data Processing Workflows to Support Reproducible Data-driven Research in Hydrology

    Science.gov (United States)

    Goodall, J. L.; Essawy, B.; Xu, H.; Rajasekar, A.; Moore, R. W.

    2015-12-01

    Geoscience analyses often require the use of existing data sets that are large, heterogeneous, and maintained by different organizations. A particular challenge in creating reproducible analyses using these data sets is automating the workflows required to transform raw datasets into model specific input files and finally into publication ready visualizations. Data grids, such as the Integrated Rule-Oriented Data System (iRODS), are architectures that allow scientists to access and share large data sets that are geographically distributed on the Internet, but appear to the scientist as a single file management system. The DataNet Federation Consortium (DFC) project is built on iRODS and aims to demonstrate data and computational interoperability across scientific communities. This paper leverages iRODS and the DFC to demonstrate how hydrological modeling workflows can be encapsulated as workflows using the iRODS concept of Workflow Structured Objects (WSO). An example use case is presented for automating hydrologic model post-processing routines that demonstrates how WSOs can be created and used within the DFC to automate the creation of data visualizations from large model output collections. By co-locating the workflow used to create the visualization with the data collection, the use case demonstrates how data grid technology aids in reuse, reproducibility, and sharing of workflows within scientific communities.

  16. An iterative expanding and shrinking process for processor allocation in mixed-parallel workflow scheduling.

    Science.gov (United States)

    Huang, Kuo-Chan; Wu, Wei-Ya; Wang, Feng-Jian; Liu, Hsiao-Ching; Hung, Chun-Hao

    2016-01-01

    Parallel computation has been widely applied in a variety of large-scale scientific and engineering applications. Many studies indicate that exploiting both task and data parallelisms, i.e. mixed-parallel workflows, to solve large computational problems can get better efficacy compared with either pure task parallelism or pure data parallelism. Scheduling traditional workflows of pure task parallelism on parallel systems has long been known to be an NP-complete problem. Mixed-parallel workflow scheduling has to deal with an additional challenging issue of processor allocation. In this paper, we explore the processor allocation issue in scheduling mixed-parallel workflows of moldable tasks, called M-task, and propose an Iterative Allocation Expanding and Shrinking (IAES) approach. Compared to previous approaches, our IAES has two distinguishing features. The first is allocating more processors to the tasks on allocated critical paths for effectively reducing the makespan of workflow execution. The second is allowing the processor allocation of an M-task to shrink during the iterative procedure, resulting in a more flexible and effective process for finding better allocation. The proposed IAES approach has been evaluated with a series of simulation experiments and compared to several well-known previous methods, including CPR, CPA, MCPA, and MCPA2. The experimental results indicate that our IAES approach outperforms those previous methods significantly in most situations, especially when nodes of the same layer in a workflow might have unequal workloads. PMID:27504236

  17. An iterative expanding and shrinking process for processor allocation in mixed-parallel workflow scheduling.

    Science.gov (United States)

    Huang, Kuo-Chan; Wu, Wei-Ya; Wang, Feng-Jian; Liu, Hsiao-Ching; Hung, Chun-Hao

    2016-01-01

    Parallel computation has been widely applied in a variety of large-scale scientific and engineering applications. Many studies indicate that exploiting both task and data parallelisms, i.e. mixed-parallel workflows, to solve large computational problems can get better efficacy compared with either pure task parallelism or pure data parallelism. Scheduling traditional workflows of pure task parallelism on parallel systems has long been known to be an NP-complete problem. Mixed-parallel workflow scheduling has to deal with an additional challenging issue of processor allocation. In this paper, we explore the processor allocation issue in scheduling mixed-parallel workflows of moldable tasks, called M-task, and propose an Iterative Allocation Expanding and Shrinking (IAES) approach. Compared to previous approaches, our IAES has two distinguishing features. The first is allocating more processors to the tasks on allocated critical paths for effectively reducing the makespan of workflow execution. The second is allowing the processor allocation of an M-task to shrink during the iterative procedure, resulting in a more flexible and effective process for finding better allocation. The proposed IAES approach has been evaluated with a series of simulation experiments and compared to several well-known previous methods, including CPR, CPA, MCPA, and MCPA2. The experimental results indicate that our IAES approach outperforms those previous methods significantly in most situations, especially when nodes of the same layer in a workflow might have unequal workloads.

  18. Re-engineering Workflows: Changing the Life Cycle of an Electronic Health Record System

    Directory of Open Access Journals (Sweden)

    Jane M. Brokel

    2011-01-01

    Full Text Available An existing electronic health record (EHR system was re-engineered with cross-functional workflows to enhance the efficiency and clinical utility of health information technology. The new designs were guided by a systematic review of clinicians' requests, which were garnered by direct interviews. To design cross-functional, patient-centered workflows, several multi-disciplinary teams from the health system of hospitals, clinics, and other services participated. We identified gaps and inconsistencies with current care processes and implemented changes that improved workflow for patients and clinicians. Our findings emphasize that, to coordinate care between many providers, process workflow must be standardized within and across settings and focus on patient care processes, not the technology. These new, comprehensive, admission-to-discharge workflows replaced the older, functional- and departmental-process flow charts that had fallen short. Our experience led to integrated redesign of the workflows, review prior to implementation and ongoing maintenance of this process knowledge across 37 hospital facilities.

  19. CO2 storage feasibility: A work-flow for site characterisation

    International Nuclear Information System (INIS)

    In this paper, we present an overview of the SiteChar work-flow model for site characterisation and assessment for CO2 storage. Site characterisation and assessment is required when permits are requested from the legal authorities in the process of starting a CO2 storage process at a given site. The goal is to assess whether a proposed CO2 storage site can indeed be used for permanent storage while meeting the safety requirements demanded by the European Commission (EC) Storage Directive (EU, 2009, Storage Directive 2009/31/EC). Many issues have to be scrutinised, and the work-flow presented here is put forward to help efficiently organise this complex task. Three issues are highlighted: communication within the working team and with the authorities; interdependencies in the work-flow and feedback loops; and the risk-based character of the work-flow. A general overview (helicopter view) of the work-flow is given; the issues involved in communication and the risk assessment process are described in more detail. The work-flow as described has been tested within the SiteChar project on five potential storage sites throughout Europe. This resulted in a list of key aspects of site characterisation which can help prepare and focus new site characterisation studies. (authors)

  20. Quality Metadata Management for Geospatial Scientific Workflows: from Retrieving to Assessing with Online Tools

    Science.gov (United States)

    Leibovici, D. G.; Pourabdollah, A.; Jackson, M.

    2011-12-01

    Experts and decision-makers use or develop models to monitor global and local changes of the environment. Their activities require the combination of data and processing services in a flow of operations and spatial data computations: a geospatial scientific workflow. The seamless ability to generate, re-use and modify a geospatial scientific workflow is an important requirement but the quality of outcomes is equally much important [1]. Metadata information attached to the data and processes, and particularly their quality, is essential to assess the reliability of the scientific model that represents a workflow [2]. Managing tools, dealing with qualitative and quantitative metadata measures of the quality associated with a workflow, are, therefore, required for the modellers. To ensure interoperability, ISO and OGC standards [3] are to be adopted, allowing for example one to define metadata profiles and to retrieve them via web service interfaces. However these standards need a few extensions when looking at workflows, particularly in the context of geoprocesses metadata. We propose to fill this gap (i) at first through the provision of a metadata profile for the quality of processes, and (ii) through providing a framework, based on XPDL [4], to manage the quality information. Web Processing Services are used to implement a range of metadata analyses on the workflow in order to evaluate and present quality information at different levels of the workflow. This generates the metadata quality, stored in the XPDL file. The focus is (a) on the visual representations of the quality, summarizing the retrieved quality information either from the standardized metadata profiles of the components or from non-standard quality information e.g., Web 2.0 information, and (b) on the estimated qualities of the outputs derived from meta-propagation of uncertainties (a principle that we have introduced [5]). An a priori validation of the future decision-making supported by the

  1. Molecular simulation workflows as parallel algorithms: the execution engine of Copernicus, a distributed high-performance computing platform.

    Science.gov (United States)

    Pronk, Sander; Pouya, Iman; Lundborg, Magnus; Rotskoff, Grant; Wesén, Björn; Kasson, Peter M; Lindahl, Erik

    2015-06-01

    Computational chemistry and other simulation fields are critically dependent on computing resources, but few problems scale efficiently to the hundreds of thousands of processors available in current supercomputers-particularly for molecular dynamics. This has turned into a bottleneck as new hardware generations primarily provide more processing units rather than making individual units much faster, which simulation applications are addressing by increasingly focusing on sampling with algorithms such as free-energy perturbation, Markov state modeling, metadynamics, or milestoning. All these rely on combining results from multiple simulations into a single observation. They are potentially powerful approaches that aim to predict experimental observables directly, but this comes at the expense of added complexity in selecting sampling strategies and keeping track of dozens to thousands of simulations and their dependencies. Here, we describe how the distributed execution framework Copernicus allows the expression of such algorithms in generic workflows: dataflow programs. Because dataflow algorithms explicitly state dependencies of each constituent part, algorithms only need to be described on conceptual level, after which the execution is maximally parallel. The fully automated execution facilitates the optimization of these algorithms with adaptive sampling, where undersampled regions are automatically detected and targeted without user intervention. We show how several such algorithms can be formulated for computational chemistry problems, and how they are executed efficiently with many loosely coupled simulations using either distributed or parallel resources with Copernicus.

  2. Integrated exploration workflow in the south Middle Magdalena Valley (Colombia)

    Science.gov (United States)

    Moretti, Isabelle; Charry, German Rodriguez; Morales, Marcela Mayorga; Mondragon, Juan Carlos

    2010-03-01

    The HC exploration is presently active in the southern part of the Middle Magdalena Valley but only moderate size discoveries have been made up to date. The majority of these discoveries are at shallow depth in the Tertiary section. The structures located in the Valley are faulted anticlines charged by lateral migration from the Cretaceous source rocks that are assumed to be present and mature eastward below the main thrusts and the Guaduas Syncline. Upper Cretaceous reservoirs have also been positively tested. To reduce the risks linked to the exploration of deeper structures below the western thrusts of the Eastern Cordillera, an integrated study was carried out. It includes the acquisition of new seismic data, the integration of all surface and subsurface data within a 3D-geomodel, a quality control of the structural model by restoration and a modeling of the petroleum system (presence and maturity of the Cretaceous source rocks, potential migration pathways). The various steps of this workflow will be presented as well as the main conclusions in term of source rock, deformation phases and timing of the thrust emplacement versus oil maturation and migration. Our data suggest (or confirm) The good potential of the Umir Fm as a source rock. The early (Paleogene) deformation of the Bituima Trigo fault area. The maturity gap within the Cretaceous source rock between the hangingwall and footwall of the Bituima fault that proves an initial offset of Cretaceous burial in the range of 4.5 km between the Upper Cretaceous series westward and the Lower Cretaceous ones eastward of this fault zone. The post Miocene weak reactivation as dextral strike slip of Cretaceous faults such as the San Juan de Rio Seco fault that corresponds to change in the Cretaceous thickness and therefore in the depth of the thrust decollement.

  3. Management of natural resources through automatic cartographic inventory

    Science.gov (United States)

    Rey, P. A.; Gourinard, Y.; Cambou, F. (Principal Investigator)

    1974-01-01

    The author has identified the following significant results. Significant correspondence codes relating ERTS imagery to ground truth from vegetation and geology maps have been established. The use of color equidensity and color composite methods for selecting zones of equal densitometric value on ERTS imagery was perfected. Primary interest of temporal color composite is stressed. A chain of transfer operations from ERTS imagery to the automatic mapping of natural resources was developed.

  4. Implementation of the CUAHSI information system for regional hydrological research and workflow

    Science.gov (United States)

    Bugaets, Andrey; Gartsman, Boris; Bugaets, Nadezhda; Krasnopeyev, Sergey; Krasnopeyeva, Tatyana; Sokolov, Oleg; Gonchukov, Leonid

    2013-04-01

    stations) for the period beginning 1930 through 1990. Both of the data resources are maintained in a test mode at the project site http://gis.dvo.ru:81/, which is permanently updated. After first success, the decision was made to use the CUAHSI technology as a basis for development of hydrological information system to support data publishing and workflow of Primgidromet, the regional office of Federal State Hydrometeorological Agency. At the moment, Primgidromet observation network is equipped with 34 automatic SEBA hydrological pressure sensor pneumatic gauges PS-Light-2 and 36 automatic SEBA weather stations. Large datasets generated by sensor networks are organized and stored within a central ODM database which allows to unambiguously interpret the data with sufficient metadata and provides traceable heritage from raw measurements to useable information. Organization of the data within a central CUAHSI ODM database was the most critical step, with several important implications. This technology is widespread and well documented, and it ensures that all datasets are publicly available and readily used by other investigators and developers to support additional analyses and hydrological modeling. Implementation of ODM within a Relational Database Management System eliminates the potential data manipulation errors and intermediate the data processing steps. Wrapping CUAHSI WaterOneFlow web-service into OpenMI 2.0 linkable component (www.openmi.org) allows a seamless integration with well-known hydrological modeling systems.

  5. Coupled Workflow Approach to Scalable Multi-Scale Subsurface Simulations

    Science.gov (United States)

    Schuchardt, K.; Agarwal, K.; Chase, J.; Scheibe, T. D.; Palmer, B. J.; Tartakovsky, A. M.

    2012-12-01

    Continuum scale models have been used to study subsurface flow, transport, and reactions for many years but lack the capability to resolve fine-grained processes. Recently, pore scale models, which operate at scales of individual soil grains, have been developed to more accurately model pore scale phenomena, such as mineral precipitation and dissolution reactions. Pore-scale methods to study microbially-mediated surface reactions are also under development. However, these finer-grained models are prohibitively expensive for modeling realistic domains. To apply these new techniques to realistic systems, we are developing a hybrid, multi-scale model which initially simulates the full domain at continuum scale and applies the pore scale model only to areas of high reactivity. Since the location and number of pore regions in the model varies as the reactions proceed, an adaptive Pore Generator code defines the number and location of pore regions at each continuum iteration. A fourth code provides data transformation from the pore scale back to the continuum scale. These components are loosely coupled into a single multi-scale model using the Swift workflow system for two reasons: we have several choices of simulators for the continuum and pore codes, and the mathematical model integration methods, data transformations, and adaptive behavior are all highly problem dependent at this time. Our approach provides a framework to solve new problems by replacing individual components. Our initial experiment simulates the parallel transport of two solutes with an irreversible mixing-controlled kinetic bimolecular reaction occurring at the interface between the two solutes. The system is filled with porous medium like sand. The sand is saturated with water, and two solutes (denoted A and B) are injected at the bottom and flow to the top at a specified rate. As the solutions flow upward through the flow cell, they mix along the centerline, leading to reaction and formation of a

  6. A workflow for the 3D visualization of meteorological data

    Science.gov (United States)

    Helbig, Carolin; Rink, Karsten

    2014-05-01

    In the future, climate change will strongly influence our environment and living conditions. To predict possible changes, climate models that include basic and process conditions have been developed and big data sets are produced as a result of simulations. The combination of various variables of climate models with spatial data from different sources helps to identify correlations and to study key processes. For our case study we use results of the weather research and forecasting (WRF) model of two regions at different scales that include various landscapes in Northern Central Europe and Baden-Württemberg. We visualize these simulation results in combination with observation data and geographic data, such as river networks, to evaluate processes and analyze if the model represents the atmospheric system sufficiently. For this purpose, a continuous workflow that leads from the integration of heterogeneous raw data to visualization using open source software (e.g. OpenGeoSys Data Explorer, ParaView) is developed. These visualizations can be displayed on a desktop computer or in an interactive virtual reality environment. We established a concept that includes recommended 3D representations and a color scheme for the variables of the data based on existing guidelines and established traditions in the specific domain. To examine changes over time in observation and simulation data, we added the temporal dimension to the visualization. In a first step of the analysis, the visualizations are used to get an overview of the data and detect areas of interest such as regions of convection or wind turbulences. Then, subsets of data sets are extracted and the included variables can be examined in detail. An evaluation by experts from the domains of visualization and atmospheric sciences establish if they are self-explanatory and clearly arranged. These easy-to-understand visualizations of complex data sets are the basis for scientific communication. In addition, they have

  7. Seamless online science workflow development and collaboration using IDL and the ENVI Services Engine

    Science.gov (United States)

    Harris, A. T.; Ramachandran, R.; Maskey, M.

    2013-12-01

    The Exelis-developed IDL and ENVI software are ubiquitous tools in Earth science research environments. The IDL Workbench is used by the Earth science community for programming custom data analysis and visualization modules. ENVI is a software solution for processing and analyzing geospatial imagery that combines support for multiple Earth observation scientific data types (optical, thermal, multi-spectral, hyperspectral, SAR, LiDAR) with advanced image processing and analysis algorithms. The ENVI & IDL Services Engine (ESE) is an Earth science data processing engine that allows researchers to use open standards to rapidly create, publish and deploy advanced Earth science data analytics within any existing enterprise infrastructure. Although powerful in many ways, the tools lack collaborative features out-of-box. Thus, as part of the NASA funded project, Collaborative Workbench to Accelerate Science Algorithm Development, researchers at the University of Alabama in Huntsville and Exelis have developed plugins that allow seamless research collaboration from within IDL workbench. Such additional features within IDL workbench are possible because IDL workbench is built using the Eclipse Rich Client Platform (RCP). RCP applications allow custom plugins to be dropped in for extended functionalities. Specific functionalities of the plugins include creating complex workflows based on IDL application source code, submitting workflows to be executed by ESE in the cloud, and sharing and cloning of workflows among collaborators. All these functionalities are available to scientists without leaving their IDL workbench. Because ESE can interoperate with any middleware, scientific programmers can readily string together IDL processing tasks (or tasks written in other languages like C++, Java or Python) to create complex workflows for deployment within their current enterprise architecture (e.g. ArcGIS Server, GeoServer, Apache ODE or SciFlo from JPL). Using the collaborative IDL

  8. Potential of knowledge discovery using workflows implemented in the C3Grid

    Science.gov (United States)

    Engel, Thomas; Fink, Andreas; Ulbrich, Uwe; Schartner, Thomas; Dobler, Andreas; Fritzsch, Bernadette; Hiller, Wolfgang; Bräuer, Benny

    2013-04-01

    With the increasing number of climate simulations, reanalyses and observations, new infrastructures to search and analyse distributed data are necessary. In recent years, the Grid architecture became an important technology to fulfill these demands. For the German project "Collaborative Climate Community Data and Processing Grid" (C3Grid) computer scientists and meteorologists developed a system that offers its users a webinterface to search and download climate data and use implemented analysis tools (called workflows) to further investigate them. In this contribution, two workflows that are implemented in the C3Grid architecture are presented: the Cyclone Tracking (CT) and Stormtrack workflow. They shall serve as an example on how to perform numerous investigations on midlatitude winterstorms on a large amount of analysis and climate model data without having an insight into the data source, program code and a low-to-moderate understanding of the theortical background. CT is based on the work of Murray and Simmonds (1991) to identify and track local minima in the mean sea level pressure (MSLP) field of the selected dataset. Adjustable thresholds for the curvature of the isobars as well as the minimum lifetime of a cyclone allow the distinction of weak subtropical heat low systems and stronger midlatitude cyclones e.g. in the Northern Atlantic. The user gets the resulting track data including statistics about the track density, average central pressure, average central curvature, cyclogenesis and cyclolysis as well as pre-built visualizations of these results. Stormtrack calculates the 2.5-6 day bandpassfiltered standard deviation of the geopotential height on a selected pressure level. Although this workflow needs much less computational effort compared to CT it shows structures that are in good agreement with the track density of the CT workflow. To what extent changes in the mid-level tropospheric storm track are reflected in trough density and intensity

  9. Incorporating Semantics into Data Driven Workflows for Content Based Analysis

    Science.gov (United States)

    Argüello, M.; Fernandez-Prieto, M. J.

    Finding meaningful associations between text elements and knowledge structures within clinical narratives in a highly verbal domain, such as psychiatry, is a challenging goal. The research presented here uses a small corpus of case histories and brings into play pre-existing knowledge, and therefore, complements other approaches that use large corpus (millions of words) and no pre-existing knowledge. The paper describes a variety of experiments for content-based analysis: Linguistic Analysis using NLP-oriented approaches, Sentiment Analysis, and Semantically Meaningful Analysis. Although it is not standard practice, the paper advocates providing automatic support to annotate the functionality as well as the data for each experiment by performing semantic annotation that uses OWL and OWL-S. Lessons learnt can be transmitted to legacy clinical databases facing the conversion of clinical narratives according to prominent Electronic Health Records standards.

  10. Time-efficient CT colonography interpretation using an advanced image-gallery-based, computer-aided ''first-reader'' workflow for the detection of colorectal adenomas

    Energy Technology Data Exchange (ETDEWEB)

    Mang, Thomas; Ringl, Helmut; Weber, Michael; Mueller-Mang, Christina [Medical University of Vienna, Department of Radiology, Vienna (Austria); Hermosillo, Gerardo; Wolf, Matthias; Bogoni, Luca; Salganicoff, Marcos; Raykar, Vikas [Siemens Healthcare, Siemens Medical Solutions, H IM SY CAD R and D, Malvern, PA (United States); Graser, Anno [University of Munich - Grosshadern Campus, Department of Clinical Radiology, Munich (Germany)

    2012-12-15

    To assess the performance of an advanced ''first-reader'' workflow for computer-aided detection (CAD) of colorectal adenomas {>=} 6 mm at computed tomographic colonography (CTC) in a low-prevalence cohort. A total of 616 colonoscopy-validated CTC patient-datasets were retrospectively reviewed by a radiologist using a ''first-reader'' CAD workflow. CAD detections were presented as galleries of six automatically generated two-dimensional (2D) and three-dimensional (3D) images together with interactive 3D target views and 2D multiplanar views of the complete dataset. Each patient-dataset was interpreted by initially using CAD image-galleries followed by a fast 2D review to address unprompted colonic areas. Per-patient, per-polyp, and per-adenoma sensitivities were calculated for lesions {>=} 6 mm. Statistical testing employed Fisher's exact and McNemar tests. In 91/616 patients, 131 polyps (92 adenomas, 39 non-adenomas) {>=} 6 mm and two cancers were identified by reference standard. Using the CAD gallery-based first-reader workflow, the radiologist detected all adenomas {>=} 10 mm (34/34) and cancers. Per-patient and polyp sensitivities for lesions {>=} 6 mm were 84.3 % (75/89), and 83.2 % (109/131), respectively, with 89.1 % (57/64) and 85.9 % (79/92) for adenomas. Overall specificity was 95.6 % (504/527). Mean interpretation time was 3.1 min per patient. A CAD algorithm, applied in an image-gallery-based first-reader workflow, can substantially decrease reading times while enabling accurate detection of colorectal adenomas in a low-prevalence population. (orig.)

  11. Automatic Integration Testbeds validation on Open Science Grid

    International Nuclear Information System (INIS)

    A recurring challenge in deploying high quality production middleware is the extent to which realistic testing occurs before release of the software into the production environment. We describe here an automated system for validating releases of the Open Science Grid software stack that leverages the (pilot-based) PanDA job management system developed and used by the ATLAS experiment. The system was motivated by a desire to subject the OSG Integration Testbed to more realistic validation tests. In particular those which resemble to every extent possible actual job workflows used by the experiments thus utilizing job scheduling at the compute element (CE), use of the worker node execution environment, transfer of data to/from the local storage element (SE), etc. The context is that candidate releases of OSG compute and storage elements can be tested by injecting large numbers of synthetic jobs varying in complexity and coverage of services tested. The native capabilities of the PanDA system can thus be used to define jobs, monitor their execution, and archive the resulting run statistics including success and failure modes. A repository of generic workflows and job types to measure various metrics of interest has been created. A command-line toolset has been developed so that testbed managers can quickly submit 'VO-like' jobs into the system when newly deployed services are ready for testing. A system for automatic submission has been crafted to send jobs to integration testbed sites, collecting the results in a central service and generating regular reports for performance and reliability.

  12. Automatic Integration Testbeds validation on Open Science Grid

    Science.gov (United States)

    Caballero, J.; Thapa, S.; Gardner, R.; Potekhin, M.

    2011-12-01

    A recurring challenge in deploying high quality production middleware is the extent to which realistic testing occurs before release of the software into the production environment. We describe here an automated system for validating releases of the Open Science Grid software stack that leverages the (pilot-based) PanDA job management system developed and used by the ATLAS experiment. The system was motivated by a desire to subject the OSG Integration Testbed to more realistic validation tests. In particular those which resemble to every extent possible actual job workflows used by the experiments thus utilizing job scheduling at the compute element (CE), use of the worker node execution environment, transfer of data to/from the local storage element (SE), etc. The context is that candidate releases of OSG compute and storage elements can be tested by injecting large numbers of synthetic jobs varying in complexity and coverage of services tested. The native capabilities of the PanDA system can thus be used to define jobs, monitor their execution, and archive the resulting run statistics including success and failure modes. A repository of generic workflows and job types to measure various metrics of interest has been created. A command-line toolset has been developed so that testbed managers can quickly submit "VO-like" jobs into the system when newly deployed services are ready for testing. A system for automatic submission has been crafted to send jobs to integration testbed sites, collecting the results in a central service and generating regular reports for performance and reliability.

  13. Exploring Two Approaches for an End-to-End Scientific Analysis Workflow

    Science.gov (United States)

    Dodelson, Scott; Kent, Steve; Kowalkowski, Jim; Paterno, Marc; Sehrish, Saba

    2015-12-01

    The scientific discovery process can be advanced by the integration of independently-developed programs run on disparate computing facilities into coherent workflows usable by scientists who are not experts in computing. For such advancement, we need a system which scientists can use to formulate analysis workflows, to integrate new components to these workflows, and to execute different components on resources that are best suited to run those components. In addition, we need to monitor the status of the workflow as components get scheduled and executed, and to access the intermediate and final output for visual exploration and analysis. Finally, it is important for scientists to be able to share their workflows with collaborators. We have explored two approaches for such an analysis framework for the Large Synoptic Survey Telescope (LSST) Dark Energy Science Collaboration (DESC); the first one is based on the use and extension of Galaxy, a web-based portal for biomedical research, and the second one is based on a programming language, Python. In this paper, we present a brief description of the two approaches, describe the kinds of extensions to the Galaxy system we have found necessary in order to support the wide variety of scientific analysis in the cosmology community, and discuss how similar efforts might be of benefit to the HEP community.

  14. RECOMMENDATION FOR WEB SERVICE COMPOSITION BY MINING USAGE LOGS

    Directory of Open Access Journals (Sweden)

    Vivek R

    2016-03-01

    Full Text Available Web service composition has been one of the most researched topics of the past decade. Novel methods of web service composition are being proposed in the literature include Semantics-based composition, WSDLbased composition. Although these methods provide promising results for composition, search and discovery of web service based on QoS parameter of network and semantics or ontology associated with WSDL, they do not address composition based on usage of web service. Web Service usage logs capture time series data of web service invocation by business objects, which innately captures patterns or workflows associated with business operations. Web service composition based on such patterns and workflows can greatly streamline the business operations. In this research work, we try to explore and implement methods of mining web service usage logs. Main objectives include Identifying usage association of services. Linking one service invocation with other, Evaluation of the causal relationship between associations of services.

  15. Automatic Kurdish Dialects Identification

    Directory of Open Access Journals (Sweden)

    Hossein Hassani

    2016-02-01

    Full Text Available Automatic dialect identification is a necessary Lan guage Technology for processing multi- dialect languages in which the dialects are linguis tically far from each other. Particularly, this becomes crucial where the dialects are mutually uni ntelligible. Therefore, to perform computational activities on these languages, the sy stem needs to identify the dialect that is the subject of the process. Kurdish language encompasse s various dialects. It is written using several different scripts. The language lacks of a standard orthography. This situation makes the Kurdish dialectal identification more interesti ng and required, both form the research and from the application perspectives. In this research , we have applied a classification method, based on supervised machine learning, to identify t he dialects of the Kurdish texts. The research has focused on two widely spoken and most dominant Kurdish dialects, namely, Kurmanji and Sorani. The approach could be applied to the other Kurdish dialects as well. The method is also applicable to the languages which are similar to Ku rdish in their dialectal diversity and differences.

  16. Automatic categorization of diverse experimental information in the bioscience literature

    Directory of Open Access Journals (Sweden)

    Fang Ruihua

    2012-01-01

    the curation work flow at WormBase for automatic association of newly published papers with ten data types including RNAi, antibody, phenotype, gene regulation, mutant allele sequence, gene expression, gene product interaction, overexpression phenotype, gene interaction, and gene structure correction. Conclusions Our methods are applicable to a variety of data types with training set containing several hundreds to a few thousand documents. It is completely automatic and, thus can be readily incorporated to different workflow at different literature-based databases. We believe that the work presented here can contribute greatly to the tremendous task of automating the important yet labor-intensive biocuration effort.

  17. Linked-OWL : A new approach for dynamic linked data service workflow composition

    OpenAIRE

    Hussien Ahmad; Salah Dowaji

    2013-01-01

    The shift from Web of Document into Web of Data based on Linked Data principles defined by Tim Berners-Lee posed a big challenge to build and develop applications to work in Web of Data environment. There are several attempts to build service and application models for Linked Data Cloud. In this paper, we propose a new service model for linked data "Linked-OWL" which is based on RESTful services and OWL-S and copes with linked data principles. This new model shifts the service concept from fu...

  18. Electronic amplifiers for automatic compensators

    CERN Document Server

    Polonnikov, D Ye

    1965-01-01

    Electronic Amplifiers for Automatic Compensators presents the design and operation of electronic amplifiers for use in automatic control and measuring systems. This book is composed of eight chapters that consider the problems of constructing input and output circuits of amplifiers, suppression of interference and ensuring high sensitivity.This work begins with a survey of the operating principles of electronic amplifiers in automatic compensator systems. The succeeding chapters deal with circuit selection and the calculation and determination of the principal characteristics of amplifiers, as

  19. The Automatic Telescope Network (ATN)

    CERN Document Server

    Mattox, J R

    1999-01-01

    Because of the scheduled GLAST mission by NASA, there is strong scientific justification for preparation for very extensive blazar monitoring in the optical bands to exploit the opportunity to learn about blazars through the correlation of variability of the gamma-ray flux with flux at lower frequencies. Current optical facilities do not provide the required capability.Developments in technology have enabled astronomers to readily deploy automatic telescopes. The effort to create an Automatic Telescope Network (ATN) for blazar monitoring in the GLAST era is described. Other scientific applications of the networks of automatic telescopes are discussed. The potential of the ATN for science education is also discussed.

  20. Talkoot Portals: Discover, Tag, Share, and Reuse Collaborative Science Workflows (Invited)

    Science.gov (United States)

    Wilson, B. D.; Ramachandran, R.; Lynnes, C.

    2009-12-01

    A small but growing number of scientists are beginning to harness Web 2.0 technologies, such as wikis, blogs, and social tagging, as a transformative way of doing science. These technologies provide researchers easy mechanisms to critique, suggest and share ideas, data and algorithms. At the same time, large suites of algorithms for science analysis are being made available as remotely-invokable Web Services, which can be chained together to create analysis workflows. This provides the research community an unprecedented opportunity to collaborate by sharing their workflows with one another, reproducing and analyzing research results, and leveraging colleagues’ expertise to expedite the process of scientific discovery. However, wikis and similar technologies are limited to text, static images and hyperlinks, providing little support for collaborative data analysis. A team of information technology and Earth science researchers from multiple institutions have come together to improve community collaboration in science analysis by developing a customizable “software appliance” to build collaborative portals for Earth Science services and analysis workflows. The critical requirement is that researchers (not just information technologists) be able to build collaborative sites around service workflows within a few hours. We envision online communities coming together, much like Finnish “talkoot” (a barn raising), to build a shared research space. Talkoot extends a freely available, open source content management framework with a series of modules specific to Earth Science for registering, creating, managing, discovering, tagging and sharing Earth Science web services and workflows for science data processing, analysis and visualization. Users will be able to author a “science story” in shareable web notebooks, including plots or animations, backed up by an executable workflow that directly reproduces the science analysis. New services and workflows of