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Provenance for Scientific Workflows Towards Reproducible Research

Roger S. Barga, Yogesh L. Simmhan, Eran Chinthaka, Satya Sanket Sahoo, Jared Jackson, Nelson Araujo
2010 IEEE Data Engineering Bulletin  
Trident is implemented on top of Windows Workflow Foundation [6] , a workflow enactment engine included in the Windows operating system. Windows Workflow Foundation is highly extensible.  ...  The different sources of dynamic information include the execution service that submits and triggers workflow job execution, the Windows WF engine that orchestrates the workflow instance by invoking activities  ... 
dblp:journals/debu/BargaSCSJA10 fatcat:vau5nyssgvc7xlkry2xylwr3qe

Leveraging Windows Workflow Foundation for Scientific Workflows in Wind Tunnel Applications

A. Paventhan, K. Takeda, S.J. Cox, D.A. Nicole
2006 22nd International Conference on Data Engineering Workshops (ICDEW'06)  
In this paper we explore two approaches based on Windows Workflow Foundation, a component of Microsoft WinFX.  ...  In our first approach, we present a framework for users to compose sequential workflows and access Globus grid services seamlessly using a . NET-based Commodity Grid Toolkit (MyCoG.NET).  ...  Acknowledgment The authors would like to thank Microsoft for its ongoing support.  ... 
doi:10.1109/icdew.2006.71 dblp:conf/icde/PaventhanTCN06 fatcat:ae27oyvp55csjls4rxv7yvloba

e-Science Project and Experiment Management with Microsoft Project

Gregor von Laszewski, Leor E. Dilmanian
2008 2008 Grid Computing Environments Workshop  
The motivation for this choice is that many scientists are already familiar with Microsoft Project.  ...  Our framework also allows integration with other resources, including Microsoft Windows HPC Server 2008 (HPC) clusters.  ...  There are many features found in Windows Workflow Foundation which are suitable for the interactive and long running workflows.  ... 
doi:10.1109/gce.2008.4738449 fatcat:w5vb7ukrufgazfcs5gugeemjma

Realization of Dynamically Adaptive Weather Analysis and Forecasting in LEAD: Four Years Down the Road [chapter]

Lavanya Ramakrishnan, Yogesh Simmhan, Beth Plale
2007 Lecture Notes in Computer Science  
One of the primary goals of the infrastructure is support for real-time dynamic, adaptive response to severe weather.  ...  Linked Environments for Atmospheric Discovery (LEAD) is a large-scale cyberinfrastructure effort in support of mesoscale meteorology.  ...  LEAD uses the Karma provenance system for workflow instrumentation and services to generate real-time monitoring events and for storing them for future mining.  ... 
doi:10.1007/978-3-540-72584-8_147 fatcat:y33cpour4zgorbuq7malcmdbm4

A non-targeted data processing workflow for volatile organic compound data acquired using comprehensive two-dimensional gas chromatography with dual channel detection

Julianne M. Byrne, Lena M. Dubois, Jonathan D. Baker, Jean-François Focant, Katelynn A. Perrault
2020 MethodsX  
There has been an influx of technology for comprehensive two-dimensional gas chromatography analyses in recent years, calling for development of guided workflows and rigorous reporting of processes.  ...  •Stencils were transformed onto FID data and sequenced for quantitative information.This dataset can be used as a training tool, as all details, methods and results for the workflow have been provided  ...  This material is based upon work supported by the National Science Foundation under Grant Number 1752607 .  ... 
doi:10.1016/j.mex.2020.101009 pmid:32775230 pmcid:PMC7397399 fatcat:vvhu7ztwafdsvbpdezsmbgd7ui

Monitoring of Grid Scientific Workflows

Bartosz Balis, Marian Bubak, Bartłomiej Łabno
2008 Scientific Programming  
We propose a Grid monitoring architecture for scientific workflows.  ...  We demonstrate a prototype implementation of the proposed workflow monitoring architecture, the GEMINI monitoring system, and its use for monitoring of a real-life scientific workflow.  ...  Acknowledgements The work described in this paper is supported by the European Union through the projects IST-2002-511385 K-WfGrid and IST-034364 Gredia, and by the Foundation for Polish Science within  ... 
doi:10.1155/2008/849354 fatcat:7syumxpg6vd6vdjicatxivafqq

Client + Cloud: Evaluating Seamless Architectures for Visual Data Analytics in the Ocean Sciences [chapter]

Keith Grochow, Bill Howe, Mark Stoermer, Roger Barga, Ed Lazowska
2010 Lecture Notes in Computer Science  
Science is becoming data-intensive, requiring new software architectures that can exploit resources at all scales: local GPUs for interactive visualization, server-side multi-core machines with fast processors  ...  Informed by a long-term collaboration with ocean scientists, we articulate a suite of representative visual data analytics workflows and use them to design and implement a multi-tier immersive visualization  ...  The authors wish to thank Microsoft's Technical Computing Initiative, University of Washington School of Oceanography, and Monterey Bay Aquarium Research Institute for data and technical advice.  ... 
doi:10.1007/978-3-642-13818-8_10 fatcat:yzav53caw5g6pmbqvvaws7hwju

Trapped Ion Mobility Spectrometry Reduces Spectral Complexity in Mass Spectrometry Based Workflow [article]

Joshua Charkow, Hannes Rost
2021 bioRxiv   pre-print
In the context of a Data Independent Acquisition (DIA), the reduction in spectral complexity resulting from IM separation is estimated to be equivalent to a 4-fold decrease in isolation window width (from  ...  In a Data Dependent Acquisition (DDA) PASEF workflow, IM separation increased the number of spectra without cofragmentation by a factor of 4.1 and the number of high quality spectra 17-fold.  ...  H.L.R. is supported by the Canadian Foundation for Innovation and the John R. Evans Leaders Fund and is the Canada Research Chair in Mass Spectrometry-based Personalized Medicine.  ... 
doi:10.1101/2021.04.01.438072 fatcat:vtwaea4245htjk36q2neq7ytpq

Sensitivity Analysis for Time Dependent Problems: Optimal Checkpoint-Recompute HPC Workflows

Varis Carey, Hasan Abbasi, Ivan Rodero, Hemanth Kolla
2014 2014 9th Workshop on Workflows in Support of Large-Scale Science  
However, one of the challenges of the adjoint workflow for time-dependent applications is the storage and I/O requirements for the application state.  ...  During the time-reversal portion of the workflow, forward state is required in last-in-first-out order. The resulting requirements for storage at exascale are enormous.  ...  National Science Foundation (NSF) via grants numbers ACI 1339036, ACI 1310283, CNS 1305375.  ... 
doi:10.1109/works.2014.15 dblp:conf/sc/CareyARK14 fatcat:4yfpvys5fjb3hnasg5uu2bn3fa

A novel spectral library workflow to enhance protein identifications

Haomin Li, Nobel C. Zong, Xiangbo Liang, Allen K. Kim, Jeong Ho Choi, Ning Deng, Ivette Zelaya, Maggie Lam, Huilong Duan, Peipei Ping
2013 Journal of Proteomics  
A spectral library search engine makes use of previously annotated experimental spectra as references for subsequent spectral analyses.  ...  In this study, we created a spectral matching engine to address challenges commonly associated with a library search workflow.  ...  Taken together, this workflow mobilizes mass spectra accumulated by the proteomics community, which serves as a foundation for future investigations.  ... 
doi:10.1016/j.jprot.2013.01.026 pmid:23391412 pmcid:PMC3737079 fatcat:fhpvtfvevfe3nn2x3lzfbbeuqy

Science Platforms for Heliophysics Data Analysis [article]

Monica G. Bobra, Will T. Barnes, Mark C. M. Cheung, Laura A. Hayes, Jack Ireland, Miho Janvier, Michael S. F. Kirk, James P. Mason, Stuart J. Mumford, Paul J. Wright
2020 Zenodo  
details our recommendation that NASA maintain and fund science platforms that enable interactive and scalable data analysis in order to maximize the scientific return of data collected from space-based instruments  ...  NASA instruments designed to study the heliosphere take more data, at faster rates than ever before. For example, the Solar Dynamics Observatory (SDO) mission data set currently totals 19 petabytes.  ...  think about data science workflows.  ... 
doi:10.5281/zenodo.4025216 fatcat:jvfbzumkwjgkzemvfm6xvcbw5y

Workflows in Dynamic Development Processes [chapter]

Thomas Heer, Christoph Briem, René Wörzberger
2009 Lecture Notes in Business Information Processing  
In this paper we describe the integration of a specialized system for the management of dynamic development processes with a conventional workflow management system.  ...  On the one hand, they comprise highly dynamic process parts, which cannot be defined until project runtime.  ...  Integrating Static and Dynamic Process Parts In our research project we built a full-fledged WfMS as an extension of the CAEtool Comos by means of the Microsoft Windows Workflow Foundation (WF) [8] .  ... 
doi:10.1007/978-3-642-00328-8_26 fatcat:b7zwcbxcgvdvrdr6tsd4d55bnq

Organic Data Publishing: A Novel Approach to Scientific Data Sharing

Yolanda Gil, Varun Ratnakar, Paul C. Hanson
2012 International Semantic Web Conference  
semantic framework that 1) links dataset contributions directly to science questions, 2) reduces the burden of data sharing by enabling any scientist to contribute metadata, and 3) tracks and exposes credit for  ...  This research was supported in part by a grant from the National Science Foundation through award number IIS-1117281.  ...  In the figure, one window shows a wiki page for a dataset, including semantic metadata properties that describe the collection instrument, location, and time as well as the investigator who contributed  ... 
dblp:conf/semweb/GilRH12 fatcat:n2bsa7r4e5h3df256umiovvwsq

Managing and Documenting Legacy Scientific Workflows

Ruben Acuña, Jacques Chomilier, Zoé Lacroix
2015 Journal of Integrative Bioinformatics  
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  ...  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.  ...  Acknowledgements We thank Rida A Bazzi for contributing to the development of the WISE method and K. Selcuk Candan for his valuable input on workflow analysis. We also thank Matthew G.  ... 
doi:10.1515/jib-2015-277 fatcat:pz7jmwvfjjgcbm4q4zaqwdlitq

Managing and Documenting Legacy Scientific Workflows

Ruben Acuña, Jacques Chomilier, Zoé Lacroix
2015 Journal of Integrative Bioinformatics  
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  ...  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.  ...  Acknowledgements We thank Rida A Bazzi for contributing to the development of the WISE method and K. Selcuk Candan for his valuable input on workflow analysis. We also thank Matthew G.  ... 
doi:10.2390/biecoll-jib-2015-277 pmid:26673793 fatcat:slxvld23rfdmnlbo54b2zegwza
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