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Provenance for Visualizations: Reproducibility and Beyond

Claudio T. Silva, Juliana Freire, Steven P. Callahan
2007 Computing in science & engineering (Print)  
The authors present VisTrails, an open source provenance-management system that provides infrastructure for data exploration and visualization.  ...  The US Department of Energy, an IBM Faculty Award, and a University of Utah Seed Grant also partially supported this work.  ...  Scheidegger, and Huy T. Vo. The data used in this article is available courtesy of the National Library of Medicine's Visible Human Project.  ... 
doi:10.1109/mcse.2007.106 fatcat:hqkcl2jllzemtdj2pl73tapc5e

SWIRRL. Managing Provenance-aware and Reproducible Workspaces

Alessandro Spinuso, Mats Veldhuizen, Daniele Bailo, Valerio Vinciarelli, Tor Langeland
2022 Data Intelligence  
The system keeps track of updates and changes affecting the data and the tools by adopting versioning and standard provenance technologies.  ...  SWIRRL is built in cooperation with two research infrastructures in the field of solid earth science and climate data modeling. We report on the particular adoptions and use cases.  ...  ACKNOWLEDGEMENTS The core development of SWIRRL has been conducted by the Observations and Data Technology Department of KNMI, with special contributions by Ian van Der Neut and Friedrich Striewski.  ... 
doi:10.1162/dint_a_00129 fatcat:wia4rml4lrg57iw4jl5mnwzwhy

Intermediate Notation for Provenance and Workflow Reproducibility [chapter]

Danius T. Michaelides, Richard Parker, Chris Charlton, William J. Browne, Luc Moreau
2016 Lecture Notes in Computer Science  
Our goal is to facilitate portability of processes between the tools to enhance usability and to support reproducibility.  ...  We describe an intermediate notation to aid runtime capture of provenance and demonstrate conversion to an executable and editable workflow.  ...  Acknowledgments This research was supported by the UK's Economic and Social Research Council (grant reference ES/K007246/1).  ... 
doi:10.1007/978-3-319-40593-3_7 fatcat:fzji6rz3ojf5rgsxpcyybrzno4

Provenance and Reproducibility: A Look into Jupyter Notebooks [article]

Sheeba Samuel
2021 figshare.com  
and re-run REPRODUCE-ME P-Plan PROV-O An ontology is a formal, explicit specification of a shared conceptualization - [Studer et al., 1998] ➢ Jupyter Notebook and its provenance described using the  ...  to differentiate between two executions ➢ Extends the nbdime library from the Project Jupyter ➢ Help repository users and owners to reproduce, directly analyze and assess the reproducibility of notebooks  ... 
doi:10.6084/m9.figshare.14818578.v1 fatcat:beiftczaknekpd7cjgmy4bog3a

Reproducibility and Provenance in Earth and Environmental Science

Matthew B. Jones
2021 Zenodo  
Issues surrounding reproducibility and transparency have grown in importance across these allied disciplines.  ...  reproducibility in the environmental sciences.  ...  RStudio, Jupyter) • "Reproducible Run" • https://wholetale.org 11 Code/Narrative Compute environment Data www. .org Provenance in DataONE  ... 
doi:10.5281/zenodo.4707709 fatcat:y33iyz2ox5gavba53b6sxcqrqu

Provenance and data differencing for workflow reproducibility analysis

Paolo Missier, Simon Woodman, Hugo Hiden, Paul Watson
2013 Concurrency and Computation  
As well as automatically generating a provenance trace for consumption by \PDIFF, the platform supports the storage and re-use of old versions of workflows, data and services; the paper shows how this  ...  Secondly, it describes a new algorithm, \PDIFF, that uses a comparison of workflow provenance traces to determine whether an experiment has been reproduced; the main innovation is that if this is not the  ...  In particular, after discussing general techniques for supporting repeatability and reproducibility, we focus on the last problem, namely the role of provenance traces in diagnosing divergence in non-reproducible  ... 
doi:10.1002/cpe.3035 fatcat:bsbkrlpll5fw7d57ekvlchxzyy

DEX: Digital evidence provenance supporting reproducibility and comparison

Brian Neil Levine, Marc Liberatore
2009 Digital Investigation. The International Journal of Digital Forensics and Incident Response  
Using a DEX description and the raw image file, evidence can be reproduced by other tools with the same functionality.  ...  Provenance Forensic tools a b s t r a c t The current standard and open formats for forensic data describe whole disk and memory image properties, but do not describe the products of detailed investigations  ...  The opinions, findings, and conclusions or recommendations expressed in this publication are those of the authors and do not necessarily reflect those of the NSF or the Dept. of Justice.  ... 
doi:10.1016/j.diin.2009.06.011 fatcat:25q7sq6pr5g67g6awfihmsb2lu

Machine Learning Pipelines: Provenance, Reproducibility and FAIR Data Principles [article]

Sheeba Samuel, Frank Löffler, Birgitta König-Ries
2020 arXiv   pre-print
We present our preliminary results on the role of our tool, ProvBook, in capturing and comparing provenance of ML experiments and their reproducibility using Jupyter Notebooks.  ...  Rather, ML, similar to many other disciplines, faces a reproducibility crisis. In this paper, we describe our goals and initial steps in supporting the end-to-end reproducibility of ML pipelines.  ...  Along with the provenance, the version for each provenance item needs to be maintained for the end-to-end reproducibility of an ML pipeline.  ... 
arXiv:2006.12117v1 fatcat:fldgjlz2o5gpfj52stkbhwvene

Cloud infrastructure provenance collection and management to reproduce scientific workflows execution

Khawar Hasham, Kamran Munir, Richard McClatchey
2018 Future generations computer systems  
Provenance has been thought of a mechanism to verify a workflow and to provide workflow reproducibility.  ...  One of the obstacles in reproducing an experiment execution is the lack of information about the execution infrastructure in the collected provenance.  ...  Provenance has been thought of a mechanism to verify a workflow and to provide workflow reproducibility.  ... 
doi:10.1016/j.future.2017.07.015 fatcat:mmzzhovmqbhhtovcvq2ztp2c6i

ProvenanceWeek 2020: Machine Learning Pipelines: Provenance, Reproducibility and FAIR Data Principles [article]

Sheeba Samuel, Frank Loeffler, Birgitta König-Ries
2020 Figshare  
We present our preliminary results on the role of our tool, ProvBook, in capturing and comparing provenance of ML experiments and their reproducibility using Jupyter Notebooks.Paper: https://fusion.cs.uni-jena.de  ...  This presentation is given in ProvenanceWeek2020.In this presentation, we describe our goals and initial steps in supporting the end-to-end reproducibility of ML pipelines.  ...  ➢ Repeating and reproducing results and reusing pipelines is difficult. 11 ProvBook: Provenance of the Notebook [Samuel and König-Ries 2018b] 12 Achieving Reproducibility in ML using ProvBook  ... 
doi:10.6084/m9.figshare.12529634.v1 fatcat:6ls7f7hlqbcuzo27zkzfsdsuhi

Overview of reproducibility and replicability in economics, with a side trip to provenance

Lars Vilhuber
2021 Zenodo  
Presentation at the Banco de Portugal Workshop on Reproducibility of Scientific Results.  ...  on computational reproducibility Report on provenance and data citations Can we access all the data?  ...  Request for evaluation Report on provenance and data citations Data citation and provenance analysis Do we know how/ somebody who can?  ... 
doi:10.5281/zenodo.5786463 fatcat:x7v6uo52nrhctc7uiccrqtctn4

Using Cloud-Aware Provenance to Reproduce Scientific Workflow Execution on Cloud

Khawar Hasham, Kamran Munir, Richard McClatchey
2015 Proceedings of the 5th International Conference on Cloud Computing and Services Science  
Provenance has been thought of a mechanism to verify a workflow and to provide workflow reproducibility.  ...  This approach can collect Cloud infrastructure information from an outside Cloud client along with workflow provenance and can establish a mapping between them.  ...  This project aims to assist the neuro-scientific community in analysing brain scans using workflows and distributed infrastructure (Grid and Cloud) to identify biomarkers that can help in diagnosing the  ... 
doi:10.5220/0005452800490059 dblp:conf/closer/HashamMM15 fatcat:mx7k3dqbdzdabeuwwdpnh2x35a

Preserving Reproducibility: Provenance And Executable Containers In Dataone Data Packages

Bryce Mecum, Matthew B. Jones, Dave Vieglais, Craig Willis
2018 Zenodo  
Additional support was provided by the National Center for Ecological Analysis and Synthesis, a Center funded by the University of California, Santa Barbara, and the State of California.  ...  Acknowledgements 7 Funding support for the work described in this paper was provided by National Science Foundation awards 1430508, 1541450, and 1262458.  ...  Incorporating Provenance in Packages Archiving the input and output objects of research for later access is a key piece of a reproducible scientific process.  ... 
doi:10.5281/zenodo.1313218 fatcat:gey5myxzgfcynmmgjowiimobiy

Preserving Reproducibility: Provenance And Executable Containers In Dataone Data Packages

Bryce Mecum, Matthew B. Jones, Dave Vieglais, Craig Willis
2018 Zenodo  
Provenance relationships link the objects within and across Data Packages into computational workflows for reproducible science.  ...  INCORPORATING PROVENANCE IN PACKAGES Archiving the input and output objects of research for later access is a key piece of a reproducible scientific process.  ... 
doi:10.5281/zenodo.1420531 fatcat:jpfnlb7mz5dcjiu5zmov6ttd54

Open Data Fabric: A Decentralized Data Exchange and Transformation Protocol With Complete Reproducibility and Provenance [article]

Sergii Mikhtoniuk, Ozge Nilay Yalcin
2021 arXiv   pre-print
, provenance, autonomy, and low latency.  ...  As a result, governments, institutions, and businesses remain largely impaired in their ability to make data-driven decisions. At the same time, data science is undergoing a reproducibility crisis.  ...  We think of metadata as a digital passport of data that is instrumental to reproducibility, verifiability, and data provenance.  ... 
arXiv:2111.06364v1 fatcat:r6p5d47atnh6ppp3mw45vndstm
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