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Generating Scientific Documentation for Computational Experiments Using Provenance [chapter]

Adianto Wibisono, Peter Bloem, Gerben K. D. de Vries, Paul Groth, Adam Belloum, Marian Bubak
2015 Lecture Notes in Computer Science  
In this work, we look at generating notebook documentation from multi-environment workflows by using provenance represented in the W3C PROV model.  ...  entirely in silico (i.e. as a computer program) a computational experiment.  ...  We thank the reviewers and Rinke Hoekstra for their useful feedbacks and discussion. This publication was supported by the Dutch national program COMMIT.  ... 
doi:10.1007/978-3-319-16462-5_13 fatcat:uq42b7fsh5fzdbtmfviqm5j6u4

The W3C PROV family of specifications for modelling provenance metadata

Paolo Missier, Khalid Belhajjame, James Cheney
2013 Proceedings of the 16th International Conference on Extending Database Technology - EDBT '13  
of provenance documents, and concludes with example applications that show the extension points in use.  ...  The PROV provenance model is deliberately generic and domain-agnostic, but extension mechanisms are available and can be exploited for modelling specific domains.  ...  In bioinformatics, for example, they are used for rapid implementation of in-silico experiments.  ... 
doi:10.1145/2452376.2452478 dblp:conf/edbt/MissierBC13 fatcat:dcwytsvrqrdudizwskazrfbmoy

End-to-End provenance representation for the understandability and reproducibility of scientific experiments using a semantic approach

Sheeba Samuel, Birgitta König-Ries
2022 Journal of Biomedical Semantics  
However, there is a lack of interoperable representation of end-to-end provenance of scientific experiments that interlinks data, processing steps, and results from an experiment's computational and non-computational  ...  The ontology brings together different aspects of the provenance of scientific studies by interlinking non-computational data and steps with computational data and steps to achieve understandability and  ...  and our colleagues Martin Bücker, Frank Taubert und Daniel Walther for their feedback.  ... 
doi:10.1186/s13326-021-00253-1 pmid:34991705 pmcid:PMC8734275 fatcat:lwc57qbra5bcxiadcrimbufezi

Towards Complete Tracking of Provenance in Experimental Distributed Systems Research [chapter]

Tomasz Buchert, Lucas Nussbaum, Jens Gustedt
2015 Lecture Notes in Computer Science  
It is difficult to re-run an experiment or understand its results even with technical background on the technology and methods used.  ...  In this paper, we (1) survey provenance collection in various domains of computer science, (2) introduce a new classification of provenance types, and (3) sketch a design of a provenance system inspired  ...  Provenance in general computing In this section, we explore how provenance is provided in a general context (programming languages, scientific computing, data analysis, etc.).  ... 
doi:10.1007/978-3-319-27308-2_49 fatcat:ajzcc6pu2nbhvcagaf67waas44

Semantic web applications to e-science in silico experiments

Jun Zhao, Carole Goble, Robert Stevens
2004 Alternate track papers & posters of the 13th international conference on World Wide Web - WWW Alt. '04  
Compared to annotating general Web documents, annotations for scientific data require more sophisticated professional knowledge to recognize concepts from documents, and more complex text extraction and  ...  This paper explains our research and implementations of manual, automatic and deep annotations of provenance logs for e-Science in silico experiments.  ...  INTRODUCTION e-Science in silico experiments complement traditional lab work by using computer-based information repositories and computational analysis to test a hypothesis, search for patterns, or demonstrate  ... 
doi:10.1145/1010432.1010502 fatcat:kkwbup3adbemtjz5rppd7mclw4

Semantic web applications to e-science in silico experiments

Jun Zhao, Carole Goble, Robert Stevens
2004 Proceedings of the 13th international World Wide Web conference on Alternate track papers & posters - WWW Alt. '04  
Compared to annotating general Web documents, annotations for scientific data require more sophisticated professional knowledge to recognize concepts from documents, and more complex text extraction and  ...  This paper explains our research and implementations of manual, automatic and deep annotations of provenance logs for e-Science in silico experiments.  ...  INTRODUCTION e-Science in silico experiments complement traditional lab work by using computer-based information repositories and computational analysis to test a hypothesis, search for patterns, or demonstrate  ... 
doi:10.1145/1013367.1013437 dblp:conf/www/ZhaoGS04 fatcat:x4et7bng65gopnprzjojywpv7m

Connecting Scientific Data to Scientific Experiments with Provenance

Simon Miles, Ewa Deelman, Paul Groth, Karan Vahi, Gaurang Mehta, Luc Moreau
2007 Third IEEE International Conference on e-Science and Grid Computing (e-Science 2007)  
To reconnect the scientific data with the original experiment, we argue that scientists should have access to the full provenance of their data, including not only parameters, inputs and intermediary data  ...  As scientific workflows and the data they operate on, grow in size and complexity, the task of defining how those workflows should execute (which resources to use, where the resources must be in readiness  ...  • What computations where conducted to generate these data items? • Where did the computations occur? • Which version of the software was used?  ... 
doi:10.1109/e-science.2007.22 dblp:conf/eScience/MilesDGVMM07 fatcat:dn7i4mxwoffzlpa65ks4dykis4

Bioinformatics Workflows With NoSQL Database in Cloud Computing

Polyane Wercelens, Waldeyr da Silva, Fernanda Hondo, Klayton Castro, Maria Emília Walter, Aletéia Araújo, Sergio Lifschitz, Maristela Holanda
2019 Evolutionary Bioinformatics  
We present here the results and a guide for the deployment of a cloud environment for Bioinformatics exploring the characteristics of various NoSQL database systems to persist provenance data.  ...  for researchers.  ...  possibility of easily creating, evaluating, or modifying the computational models or scientific experiments once the provenance expresses the accumulation of knowledge of what was done. 2 Studies in  ... 
doi:10.1177/1176934319889974 pmid:31839702 pmcid:PMC6896126 fatcat:sumlr4mluve7bfhodh2max45gi

Towards Reproducibility of Microscopy Experiments

Sheeba Samuel, Frank Taubert, Daniel Walther, Birgitta König-Ries, H. Martin Bücker
2017 D-Lib Magazine  
For reproducible experiments, these processing steps need to be documented as well.  ...  It can be used to create new classes and properties to model provenance information for different contexts.  ... 
doi:10.1045/january2017-samuel fatcat:nmbbqgzu25gqtlqzljszptbz6u

Making Computations and Publications Reproducible with VisTrails

Juliana Freire, Claudio T. Silva
2012 Computing in science & engineering (Print)  
experiments Provenance is a critical ingredient for reproducible experiments. 5, 6 If we know how a figure or table was generated (the computational processes and data used), we can incorporate them  ...  The availability of fully documented experiments enables scientific advances that combine previous tools as well as ideas.  ... 
doi:10.1109/mcse.2012.76 fatcat:fyc7kqgam5bwnc53ztkyr52iue

Provenance: The Bridge Between Experiments and Data

Simon Miles, Paul Groth, Ewa Deelman, Karan Vahi, Gaurang Mehta, Luc Moreau
2008 Computing in science & engineering (Print)  
We investigate how provenance helps scientists to connect their results with the actual execution that took place, their original experiment and its inputs and parameters.  ...  Current scientific applications are often structured as workflows and rely on workflow systems to compile abstract experiment designs into enactable workflows that utilise the best available resources.  ...  What computation were conducted to generate these data items? o mproject and mdiff were used. Where did the computations occur?  ... 
doi:10.1109/mcse.2008.82 fatcat:q2yrpgyi2je6xa3uv2baezj6om

SHARP: Harmonizing and Bridging Cross-Workflow Provenance [chapter]

Alban Gaignard, Khalid Belhajjame, Hala Skaf-Molli
2017 Lecture Notes in Computer Science  
We experimentally evaluate the effectiveness of SHARP using a real-world omic experiment involving workflow traces generated by the Taverna and Galaxy systems.  ...  The harmonization is performed by chasing tuple-generating and equalitygenerating dependencies defined for workflow provenance.  ...  Harmonization of heterogeneous PROV traces In this experiment, we used provenance document of ProvStore 17 .  ... 
doi:10.1007/978-3-319-70407-4_35 fatcat:jcdfy5x7a5dztltlxygutdrdva

Combining P-Plan and the REPRODUCE-ME Ontology to Achieve Semantic Enrichment of Scientific Experiments Using Interactive Notebooks [chapter]

Sheeba Samuel, Birgitta König-Ries
2018 Lecture Notes in Computer Science  
End-to-end reproducibility of scientific experiments requires scientists to share their experimental data along with the computational environment.  ...  In a multi-user environment where users can run and modify the shared notebooks, it becomes essential to capture the provenance of notebooks along with the experiments which used them.  ...  We thank Christoph Biskup, Kathrin Groeneveld and Tom Kache from University Hospital Jena, Germany, for providing the requirements to develop the proposed approach and evaluating the system.  ... 
doi:10.1007/978-3-319-98192-5_24 fatcat:osoplq6q7rgcpgft6o7snrei5y

The design and realisation of the Virtual Research Environment for social sharing of workflows

David De Roure, Carole Goble, Robert Stevens
2009 Future generations computer systems  
Treating workflows as science currency could change the practice, accelerate the pace, and broaden participation in scientific endeavors: Scientific discovery would advance at a faster pace if computational  ...  Workflows offer explicit representations of computational methods, and have long been recognized as a crucial element of scientific discourse [Gil et al 07].  ...  Workflows could also document how data is processed, so that published data is appropriately documented for others to use.  ... 
doi:10.1016/j.future.2008.06.010 fatcat:zpnpnz44vzhj7awqqkgiy3elje

Provenance Support for Grid-Enabled Scientific Workflows

Fakhri Alam Khan, Yuzhang Han, Sabri Pllana, Peter Brezany
2008 2008 Fourth International Conference on Semantics, Knowledge and Grid  
Computational scientists typically use workflows to describe and manage scientific discovery processes.  ...  However, the credibility of the obtained results in the scientific community is questionable if the computational experiment is not reproducible.  ...  The provenance recording technique and the PMML document structure used are described in Section IV. The provenance visualization application for scientific workflows is presented in Section V.  ... 
doi:10.1109/skg.2008.86 dblp:conf/skg/KhanHPB08 fatcat:5uunb2dskjchnonxqcgadt4q4e
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