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Experience in using a process language to define scientific workflow and generate dataset provenance

Leon J. Osterweil, Lori A. Clarke, Aaron M. Ellison, Rodion Podorozhny, Alexander Wise, Emery Boose, Julian Hadley
2008 Proceedings of the 16th ACM SIGSOFT International Symposium on Foundations of software engineering - SIGSOFT '08/FSE-16  
Specifically, this paper describes how process definition languages can be used to expedite production of scientific datasets as well as to generate documentation of their provenance.  ...  Our approach uses a process definition language that incorporates powerful semantics to encode scientific processes in the form of a Process Definition Graph (PDG).  ...  We are grateful to many colleagues who contributed ideas that led to the analytic web concept. We thank E. Riseman, A. Hanson, D. Jensen, P. Kuzeja, D. Foster, H. Schultz, G. Avrunin, and M.  ... 
doi:10.1145/1453101.1453147 dblp:conf/sigsoft/OsterweilCEPWBH08 fatcat:66flks7mjndi3g6ei2sdkd6k3q

UTPB: A Benchmark for Scientific Workflow Provenance Storage and Querying Systems

Artem Chebotko, Eugenio De Hoyos, Carlos Gomez, Andrey Kashlev, Xiang Lian, Christine Reilly
2012 2012 IEEE Eighth World Congress on Services  
A crucial challenge for scientific workflow management systems is to support the efficient and scalable storage and querying of large provenance datasets that record the history of in silico experiments  ...  In this paper, based on the requirements for scientific workflow provenance systems, we design an extensible benchmark that features a collection of techniques and tools for workload generation, query  ...  INTRODUCTION The provenance of data generated by scientific workflows plays a central role in enabling critical eScience functionalities, including experiment reproducibility, result interpretation, and  ... 
doi:10.1109/services.2012.29 dblp:conf/services/ChebotkoHGKLR12 fatcat:2olpocfj6rgtzku65j3gulfotq

A survey of data provenance in e-science

Yogesh L. Simmhan, Beth Plale, Dennis Gannon
2005 SIGMOD record  
In this paper we create a taxonomy of data provenance characteristics and apply it to current research efforts in e-science, focusing primarily on scientific workflow approaches.  ...  Metadata describing the data products used in and generated by these applications is essential to disambiguate the data and enable reuse.  ...  Four of the projects use workflows to perform scientific experiments and simulations.  ... 
doi:10.1145/1084805.1084812 fatcat:ldlsaejpmnclxi3rzz2mf2rk2q

A Logic Programming Approach to Scientific Workflow Provenance Querying [chapter]

Yong Zhao, Shiyong Lu
2008 Lecture Notes in Computer Science  
In order to support understanding, validation, and reproduction of scientific results, provenance querying and management has become a critical component in scientific workflows.  ...  for a scientific workflow provenance query language; ii) Based on these requirements, we propose FLOQ, a Frame Logic based query language for scientific workflow provenance, iii) We demonstrate that our  ...  Introduction Today, scientists use scientific workflows to integrate and structure various local and remote data and service resources to perform various in silico experiments to produce scientific discoveries  ... 
doi:10.1007/978-3-540-89965-5_5 fatcat:i5thodt4zzb6pcdo3pib7ha55e

OPQL: A First OPM-Level Query Language for Scientific Workflow Provenance

Chunhyeok Lim, Shiyong Lu, Artem Chebotko, Farshad Fotouhi
2011 2011 IEEE International Conference on Services Computing  
it, has become increasingly important in services computing and scientific workflows to validate, interpret, and analyze the result of scientific computing.  ...  To our best knowledge, OPQL is the first OPM-level query language for scientific workflow provenance.  ...  OPM graph, we used four OPM-compliant datasets generated via the simulation over four synthetic workflows, which are a sequential type of workflows (i.e., a workflow step is connected to only one workflow  ... 
doi:10.1109/scc.2011.60 dblp:conf/IEEEscc/LimLCF11 fatcat:qentemz4azchtactq4ml4nv4tu

Collaborative Scientific Workflows

Shiyong Lu, Jia Zhang
2009 2009 IEEE International Conference on Web Services  
In recent years, a number of scientific workflow management systems (SWFMSs) have been developed to help domain scientists synergistically integrate distributed computations, datasets, and analysis tools  ...  As more scientific research projects become collaborative in nature, there is a compelling need of dedicated services to support collaborative scientific workflows on the Internet.  ...  We define a collaborative scientific workflow as the computerized facilitation or automation of a scientific process, in whole or part, which streamlines and integrates people, datasets, and scientific  ... 
doi:10.1109/icws.2009.150 dblp:conf/icws/LuZ09 fatcat:uixs7xfwond7ncnairul5yheje

Collaborative scientific workflows supporting collaborative science

Shiyong Lu, Jia Zhang
2011 International Journal of Business Process Integration and Management  
Recently, scientific workflows have emerged for scientists to integrate distributed computations, datasets, and analysis tools to enable and accelerate scientific discovery.  ...  This paper presents a disciplinary definition of this term, discusses the opportunities, requirements, and challenges of collaborative scientific workflows for the enablement of scientific collaboration  ...  We define a collaborative scientific workflow as the computerized facilitation or automation of a scientific process, in whole or part, which streamlines and integrates people, datasets, and scientific  ... 
doi:10.1504/ijbpim.2011.040209 fatcat:5op5on2xgffhjabh7wgjrfuhai

Indexing Execution Patterns in Workflow Provenance Graphs through Generalized Trie Structures [article]

Esteban García-Cuesta (Data Science Laboratory, School of Arquitecture, Engineering and Design, Universidad Europea de Madrid, Spain), José M. Gómez-Pérez
2018 arXiv   pre-print
Over the last years, scientific workflows have become mature enough to be used in a production style.  ...  In this paper we address such limitations by applying statistically enriched generalized trie structures to exploit workflow execution provenance information in order to assist the analysis, indexing and  ...  Special thanks also to our University colleague Javier Martinez for his helpful discussions and insights.  ... 
arXiv:1807.07346v1 fatcat:atc4gsqqhzckjnxu5mayfjayre

Describing Configurations of Software Experiments as Linked Data

Joachim Van Herwegen, Ruben Taelman, Sarven Capadisli, Ruben Verborgh
2017 International Semantic Web Conference  
This article discusses the ontology and its application, and demonstrates with a use case how to publish experiments and their software configurations on the Web.  ...  This brings us faster to accurate reproductions of experiments, and facilitates the evaluation of new research contributions with different software configurations.  ...  In four-level provenance [4] , the authors show that infrastructural, environmental, workflow and data provenance, are needed to achieve reproducibility of scientific workflows.  ... 
dblp:conf/semweb/HerwegenTCV17 fatcat:sypm2rfapvew7n4f5vtbnovbf4

Provenance management in Swift

Luiz M.R. Gadelha Jr., Ben Clifford, Marta Mattoso, Michael Wilde, Ian Foster
2011 Future generations computer systems  
We also describe and evaluate activities performed within the Third Provenance Challenge, which consisted of implementing a specific scientific workflow, capturing and recording provenance information  ...  In this article we describe these capabilities and evaluate interoperability with other systems through the use of the Open Provenance Model.  ...  Vistrails [14] , for instance, has a specialized provenance query language and uses both XML and relational databases to store provenance about data, processes and workflow evolution.  ... 
doi:10.1016/j.future.2010.05.003 fatcat:7nbxrnrbbrcnlfoc7y7b7rkwpe

OPQL: Querying scientific workflow provenance at the graph level

Chunhyeok Lim, Shiyong Lu, Artem Chebotko, Farshad Fotouhi, Andrey Kashlev
2013 Data & Knowledge Engineering  
Provenance has become increasingly important in scientific workflows to understand, verify, and reproduce the result of scientific data analysis.  ...  Most existing systems store provenance data in provenance stores with proprietary provenance data models and conduct query processing over the physical provenance storages using query languages, such as  ...  Acknowledgments The authors would like to thank Dr. Murali Mani [27, 34] for providing valuable advices regarding OPMPROV and for sharing his expertise in the area of provenance management.  ... 
doi:10.1016/j.datak.2013.08.008 fatcat:jhxpmfqtefcalh3prsqyrmuuvu

Enhancing workflow with a semantic description of scientific intent

Edoardo Pignotti, Peter Edwards, Nick Gotts, Gary Polhill
2011 Journal of Web Semantics  
This paper investigates the use of workflow tools enhanced with semantics to facilitate the design, execution, analysis and interpretation of workflow experiments and exploratory studies.  ...  Through the use of social simulation case studies the paper illustrates the benefits of using this framework in terms of workflow monitoring, workflow provenance and annotation of experimental results.  ...  Capturing the Provenance of an Experiment Using workflow technologies to perform scientific experiments has a significant advantage in terms of annotating, discovering and reasoning about processes and  ... 
doi:10.1016/j.websem.2011.05.001 fatcat:jbo4xgu6rjhotgazjpxkst4t34

A semantic workflow mechanism to realise experimental goals and constraints

Edoardo Pignotti, Peter Edwards, Gary Polhill, Nick Gotts, Alun Preece
2008 2008 Third Workshop on Workflows in Support of Large-Scale Science  
Through the use of a social simulation case study we illustrate the benefits of using this framework in terms of workflow monitoring, workflow provenance and enrichment of experimental results.  ...  In this paper we argue that in order to better characterise such experiments we need to go beyond low-level service composition and execution details by capturing higher-level descriptions of the scientific  ...  Within our ontology we define the concept of Work-flowExperiment as a specific type of process which represents an instance of a workflow used to conduct a scientific experiment.  ... 
doi:10.1109/works.2008.4723962 fatcat:qxcj36q5y5h5zgpbczt6ihjdgi

Geoweaver: Advanced Cyberinfrastructure for Managing Hybrid Geoscientific AI Workflows

Ziheng Sun, Liping Di, Annie Burgess, Jason A. Tullis, Andrew B. Magill
2020 ISPRS International Journal of Geo-Information  
To demonstrate its utility, we present a use case in which Geoweaver manages end-to-end deep learning for in-time crop mapping using Landsat data.  ...  It supports linking all the preprocessing, AI training and testing, and post-processing steps into a single automated workflow.  ...  Acknowledgments: Thanks to the authors of all the open source libraries and software we used in developing Geoweaver.  ... 
doi:10.3390/ijgi9020119 fatcat:foijkptf6bfdtlmhjpptsa2ywe

Storing, reasoning, and querying OPM-compliant scientific workflow provenance using relational databases

Chunhyeok Lim, Shiyong Lu, Artem Chebotko, Farshad Fotouhi
2011 Future generations computer systems  
Provenance, the metadata that records the derivation history of scientific results, is essential in scientific workflows to support the reproducibility of scientific discovery, result interpretation, and  ...  Experiments are conducted to evaluate the performance of OPMProv in data mapping and provenance querying.  ...  Acknowledgments The authors would like to thank Girish Subramanian from Indiana University for helping us set up the provenance database of Karma.  ... 
doi:10.1016/j.future.2010.10.013 fatcat:mdzm4lhc7fcmpir6xxvvnb4nvm
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