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Robust Cross-Platform Workflows: How Technical and Scientific Communities Collaborate to Develop, Test and Share Best Practices for Data Analysis

Steffen Möller, Stuart W. Prescott, Lars Wirzenius, Petter Reinholdtsen, Brad Chapman, Pjotr Prins, Stian Soiland-Reyes, Fabian Klötzl, Andrea Bagnacani, Matúš Kalaš, Andreas Tille, Michael R. Crusoe
<span title="">2017</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/4pfqfq76vvcxljfl7mvdl37n5q" style="color: black;">Data Science and Engineering</a> </i> &nbsp;
It is contended that, alleviated from technical differences for the execution on local machines, clusters or the cloud, communities also gain the technical means to test workflow-driven interaction across  ...  Information integration and workflow technologies for data analysis have always been major fields of investigation in bioinformatics.  ...  Acknowledgements The authors thank Fabien Pichon, Stephan Struckmann and Georg Fuellen for their review and comments to the manuscript.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/s41019-017-0050-4">doi:10.1007/s41019-017-0050-4</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ch2si66rgbd7fnkfz2fgx5joqq">fatcat:ch2si66rgbd7fnkfz2fgx5joqq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190426171716/https://www.duo.uio.no/bitstream/handle/10852/64669/10.1007_s41019-017-0050-4.pdf?sequence=2" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/85/91/8591a2b098c2c2932de6dd8b40752e0ed163b41e.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/s41019-017-0050-4"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a>

Scientific Workflows

Chee Sun Liew, Malcolm P. Atkinson, Michelle Galea, Tan Fong Ang, Paul Martin, Jano I. Van Hemert
<span title="2016-12-12">2016</span> <i title="Association for Computing Machinery (ACM)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/eiea26iqqjcatatlgxdpzt637y" style="color: black;">ACM Computing Surveys</a> </i> &nbsp;
This article looks at the overall challenge posed by a new order of scientific experiments and the systems they need to be run on, and examines how this challenge can be addressed by workflows and workflow  ...  Execution poses a challenge however due to a) the complexity and diversity of applications, b) the diversity of analysis goals, c) the heterogeneity of computing platforms, and d) the volume and distribution  ...  ACKNOWLEDGMENTS We thank James Cheney, University of Edinburgh (UoE) and Alessandro Spinuso of KNMI for alerting us to work on provenance and its standardisation, Murray Cole, UoE for encouraging our architectural  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1145/3012429">doi:10.1145/3012429</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/23z6g32jfvgeto5zrigk4ysmx4">fatcat:23z6g32jfvgeto5zrigk4ysmx4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180723054827/https://www.pure.ed.ac.uk/ws/files/28564153/FinalCRCwf_survey_3.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/78/b3/78b3bb02a8184bf743d98092ff148be5180ed2ff.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1145/3012429"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> acm.org </button> </a>

D5.4: Integrated Data Management Workflows

Ari Lukkarinen, Anne Fouilloux, Hamish Struthers, Tommi Bergmann, Risto Makkonen, Jean Iaquinta, Helmut Neukirchen, Ernir Erlingsson, Adil Hasan
<span title="2021-11-10">2021</span> <i title="Zenodo"> Zenodo </i> &nbsp;
This deliverable aims to investigate relevant EOSC and national services that can be leveraged to support cross-border data management, data-driven distributed computing and research workflows for two  ...  Emphasis is placed on data aggregation and interlinking of sharing and active data storage.  ...  We tested several candidates for the computational platform that could be suitable for collaborative data processing workflows.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5281/zenodo.5713744">doi:10.5281/zenodo.5713744</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/z6w6fnyya5hrpljcxcz5f4mo6e">fatcat:z6w6fnyya5hrpljcxcz5f4mo6e</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20211123041512/https://zenodo.org/record/5713745/files/EOSC-Nordic%20D5.4.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/1a/7e/1a7e32b19a033b421a6fd323c634fcb5a1936a6d.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5281/zenodo.5713744"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> zenodo.org </button> </a>

Principles for data analysis workflows [article]

Sara Stoudt, Valeri N. Vasquez, Ciera C. Martinez
<span title="2020-07-17">2020</span> <i > arXiv </i> &nbsp; <span class="release-stage" >pre-print</span>
Where relevant, we draw analogies between principles for data-intensive research workflows and established practice in software development.  ...  The guidance provided here is not intended to be a strict rulebook; rather, the suggestions for practices and tools to advance reproducible, sound data-intensive analysis may furnish support for both students  ...  We thank the Berkeley Institute for Data Science for hosting meetings that brought together data scientists, biologists, statisticians, computer scientists, and software engineers to discuss how data-intensive  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/2007.08708v1">arXiv:2007.08708v1</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/voyn755cmffvdlwiloqdm36n3u">fatcat:voyn755cmffvdlwiloqdm36n3u</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200723020230/https://arxiv.org/ftp/arxiv/papers/2007/2007.08708.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] </button> </a> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/2007.08708v1" title="arxiv.org access"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> arxiv.org </button> </a>

Principles for data analysis workflows

Sara Stoudt, Váleri N. Vásquez, Ciera C. Martinez, Patricia M. Palagi
<span title="2021-03-18">2021</span> <i title="Public Library of Science (PLoS)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/ch57atmlprauhhbqdf7x4ytejm" style="color: black;">PLoS Computational Biology</a> </i> &nbsp;
The guidance provided here is not intended to be a strict rulebook; rather, the suggestions for practices and tools to advance reproducible, sound data-intensive analysis may furnish support for both students  ...  A systematic and reproducible "workflow"—the process that moves a scientific investigation from raw data to coherent research question to insightful contribution—should be a fundamental part of academic  ...  We thank the Berkeley Institute for Data Science for hosting meetings that brought together data scientists, biologists, statisticians, computer scientists, and software engineers to discuss how data-intensive  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pcbi.1008770">doi:10.1371/journal.pcbi.1008770</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/33735208">pmid:33735208</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/a6lovq3zffdg5c4p3papcx6ydi">fatcat:a6lovq3zffdg5c4p3papcx6ydi</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210329025755/https://storage.googleapis.com/plos-corpus-prod/10.1371/journal.pcbi.1008770/1/pcbi.1008770.pdf?X-Goog-Algorithm=GOOG4-RSA-SHA256&amp;X-Goog-Credential=wombat-sa%40plos-prod.iam.gserviceaccount.com%2F20210329%2Fauto%2Fstorage%2Fgoog4_request&amp;X-Goog-Date=20210329T025755Z&amp;X-Goog-Expires=3600&amp;X-Goog-SignedHeaders=host&amp;X-Goog-Signature=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" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/eb/cd/ebcd30a6db184a6ba86eeb314b5774c6f19ac59e.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pcbi.1008770"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> plos.org </button> </a>

Scientific workflows: Past, present and future

Malcolm Atkinson, Sandra Gesing, Johan Montagnat, Ian Taylor
<span title="">2017</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/idqeix2ukbd5fbgjjdkjmaj3ka" style="color: black;">Future generations computer systems</a> </i> &nbsp;
This special issue and our editorial celebrate 10 years of progress with data-intensive or scientific workflows.  ...  Improved abstraction supports cross-fertilisation between different workflow communities and consistent interpretation as WMS evolve.  ...  Acknowledgements We thank Supercomputing for hosting WORKS -now extended to SC17.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.future.2017.05.041">doi:10.1016/j.future.2017.05.041</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/j6ofz4kjjbdgdjmnsnj3fe63ju">fatcat:j6ofz4kjjbdgdjmnsnj3fe63ju</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190430221903/https://hal.archives-ouvertes.fr/hal-01544818/file/Editorial_Special_Issue_WORKS.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/e7/4e/e74e50416cc1487b56857df36693b99944b9ce6f.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.future.2017.05.041"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> elsevier.com </button> </a>

Perspectives on automated composition of workflows in the life sciences

Anna-Lena Lamprecht, Magnus Palmblad, Jon Ison, Veit Schwämmle, Mohammad Sadnan Al Manir, Ilkay Altintas, Christopher J. O. Baker, Ammar Ben Hadj Amor, Salvador Capella-Gutierrez, Paulos Charonyktakis, Michael R. Crusoe, Yolanda Gil (+20 others)
<span title="2021-09-07">2021</span> <i title="F1000 Research Ltd"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/lz7xw3k77zcg5f66jhfurufu64" style="color: black;">F1000Research</a> </i> &nbsp;
We start by drawing the "big picture" of the scientific workflow development life cycle, before surveying and discussing current methods, technologies and practices for semantic domain modelling, automation  ...  We believe that this can lead to more robust, reusable, and sustainable workflows in the future.  ...  Create infrastructure for (automated) workflow integration testing (in silico generated data and community-maintained test data). Support open-source community health checks (e.g.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.12688/f1000research.54159.1">doi:10.12688/f1000research.54159.1</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/34804501">pmid:34804501</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC8573700/">pmcid:PMC8573700</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ht57fgnzwbbmdmkazs7wi7r5s4">fatcat:ht57fgnzwbbmdmkazs7wi7r5s4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210908195624/https://f1000researchdata.s3.amazonaws.com/manuscripts/57615/5081daa9-34e0-466f-a807-2d5ddba1df4b_54159_-_anna-lena_anna-lena.pdf?doi=10.12688/f1000research.54159.1&amp;numberOfBrowsableCollections=26&amp;numberOfBrowsableInstitutionalCollections=4&amp;numberOfBrowsableGateways=29" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/ae/79/ae795a158489c5a42ff282ec26433b09aff6629d.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.12688/f1000research.54159.1"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8573700" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

A Reproducible Data Analysis Workflow

Aaron Peikert, Andreas M. Brandmaier
<span title="2021-05-11">2021</span> <i title="Leibniz Institute for Psychology (ZPID)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/temuitievvg35evam4buyjx57q" style="color: black;">Quantitative and Computational Methods in Behavioral Sciences</a> </i> &nbsp;
conforming to various journal styles, and full cross-platform and long-term computational reproducibility.  ...  In this tutorial, we describe a workflow to ensure long-term reproducibility of R-based data analyses. The workflow leverages established tools and practices from software engineering.  ...  A reproducible data analysis workflow with R Markdown, Git, Make, and Docker [Materials for reproducing the journal paper]. GitHub. https://github.com/aaronpeikert/reproducible-research/  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5964/qcmb.3763">doi:10.5964/qcmb.3763</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/iyxbwlyl6fh4dl2kemycl25izy">fatcat:iyxbwlyl6fh4dl2kemycl25izy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210512022528/https://qcmb.psychopen.eu/index.php/qcmb/article/download/3763/3763.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/a1/43/a143860735ea495b9dcd525d8ca1e4c04c1c1253.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5964/qcmb.3763"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

D5.5 - A workflow and checklist of key information needed from modelling tool owners to facilitate integration into KB

Anastasios Papadiamantis, Thomas Exner, Haralambos Sarimveis, Vladimir Lobaskin
<span title="2020-01-09">2020</span> <i title="Zenodo"> Zenodo </i> &nbsp;
For this process to be successful, a clearly defined modelling tools integration workflow needs to be developed and implemented.  ...  This deliverable is part of Work Package 5 (WP5), which aims to integrate state-of-the-art data mining, analysis and modelling tools into the NanoCommons Knowledge Base (KB).  ...  The workflows presented below constitute the recommended best-practice workflows and are these that the NanoCommons project will pursue implementing.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5281/zenodo.3603087">doi:10.5281/zenodo.3603087</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/hqha7hguwze5zm635tnffhjnri">fatcat:hqha7hguwze5zm635tnffhjnri</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200210135105/https://zenodo.org/record/3603088/files/D5.5%20-%20A%20workflow%20and%20checklist%20of%20key%20information%20needed%20from%20modelling%20tool%20owners%20to%20facilitate%20integration%20into%20KB.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/1e/93/1e9386190dabea84bab94f14720bf9027789105d.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5281/zenodo.3603087"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> zenodo.org </button> </a>

Workflows in a Dashboard: A New Generation of Usability

Sandra Gesing, Malcolm Atkinson, Rosa Filgueira, Ian Taylor, Andrew Jones, Vlado Stankovski, Chee Sun Liew, Alessandro Spinuso, Gabor Terstyanszky, Peter Kacsuk
<span title="">2014</span> <i title="IEEE"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/zigbcra6rjdivda6lkzknwuo5q" style="color: black;">2014 9th Workshop on Workflows in Support of Large-Scale Science</a> </i> &nbsp;
In the last 20 years quite a few mature workflow engines and workflow editors have been developed to support communities in managing workflows.  ...  of data.  ...  The dashboard monitoring Web GUI and RPC backend implementation has been developed by the Information Technology Division at the Naval Research Laboratory, led by Joseph P. Macker.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1109/works.2014.6">doi:10.1109/works.2014.6</a> <a target="_blank" rel="external noopener" href="https://dblp.org/rec/conf/sc/GesingAFTJSLSTK14.html">dblp:conf/sc/GesingAFTJSLSTK14</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/5rilrknh7vckjfavqi4tzbz32m">fatcat:5rilrknh7vckjfavqi4tzbz32m</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170808204958/http://conferences.computer.org/works/2014/papers/7067a082.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/ed/00/ed00bdffff99af5836890ef6273c5284a575d195.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1109/works.2014.6"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> ieee.com </button> </a>

Sharing interoperable workflow provenance: A review of best practices and their practical application in CWLProv

Farah Zaib Khan, Stian Soiland-Reyes, Richard O. Sinnott, Andrew Lonie, Carole Goble, Michael R. Crusoe
<span title="2019-07-15">2019</span> <i title="Zenodo"> Zenodo </i> &nbsp;
The automation of data analysis in the form of scientific workflows has become a widely adopted practice in many fields of research.  ...  that any platform supporting CWL will be able to understand the analysis, re-use the methods for partial [...]  ...  We would like to thank the Common Work ow Language community, and in particular Peter Amstutz, Pau Ruiz Safont and Pjotr Prins, for their continuing support, review and feedback.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5281/zenodo.3336124">doi:10.5281/zenodo.3336124</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/faagbj7brndqxlhhejaqhlun7m">fatcat:faagbj7brndqxlhhejaqhlun7m</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20201226071445/https://zenodo.org/record/3336124/files/CWLProv.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/a6/39/a639c79a02ce36b6eff9fdc5be424b28c5a436ff.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5281/zenodo.3336124"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> zenodo.org </button> </a>

Sharing interoperable workflow provenance: A review of best practices and their practical application in CWLProv

Farah Zaib Khan, Stian Soiland-Reyes, Richard O. Sinnott, Andrew Lonie, Carole Goble, Michael R. Crusoe
<span title="2019-05-23">2019</span> <i title="Zenodo"> Zenodo </i> &nbsp;
The automation of data analysis in the form of scientific workflows has become a widely adopted practice in many fields of research.  ...  that any platform supporting CWL will be able to understand the analysis, re-use the methods for partia [...]  ...  We would like to thank the Common Work ow Language community, and in particular Peter Amstutz, Pau Ruiz Safont and Pjotr Prins, for their continuing support, review and feedback.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5281/zenodo.3196309">doi:10.5281/zenodo.3196309</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/b6cfgirat5gszboaahoypk4yyu">fatcat:b6cfgirat5gszboaahoypk4yyu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20220127113930/https://zenodo.org/record/3196309/files/CWLProv.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/42/ae/42ae11ef4ec642ea4810467d4de292c1ca7e2f65.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5281/zenodo.3196309"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> zenodo.org </button> </a>

Sharing interoperable workflow provenance: A review of best practices and their practical application in CWLProv

Farah Zaib Khan, Stian Soiland-Reyes, Richard O Sinnott, Andrew Lonie, Carole Goble, Michael R Crusoe
<span title="2019-11-01">2019</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/apde6vbe7vfoxkfibp7n4mzonm" style="color: black;">GigaScience</a> </i> &nbsp;
Background The automation of data analysis in the form of scientific workflows has become a widely adopted practice in many fields of research.  ...  that any platform supporting CWL will be able to understand the analysis, reuse the methods for partial reruns, or reproduce the analysis to validate the published findings.  ...  We would like to thank the Common Work ow Language community, and in particular Peter Amstutz, Pau Ruiz Safont and Pjotr Prins, for their continuing support, review and feedback.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/gigascience/giz095">doi:10.1093/gigascience/giz095</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/31675414">pmid:31675414</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6824458/">pmcid:PMC6824458</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/37kwf7emznba5ofmlozuqdhc74">fatcat:37kwf7emznba5ofmlozuqdhc74</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200319024422/https://www.research.manchester.ac.uk/portal/files/99565220/CWLProv.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/30/55/3055257a175c20d3b3682ed877c0ed42f9da9f27.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/gigascience/giz095"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6824458" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Sharing interoperable workflow provenance: A review of best practices and their practical application in CWLProv

Farah Zaib Khan, Stian Soiland-Reyes, Richard O. Sinnott, Andrew Lonie, Carole Goble, Michael R. Crusoe
<span title="2018-12-04">2018</span> <i title="Zenodo"> Zenodo </i> &nbsp;
The automation of data analysis in the form of scientific workflows has become a widely adopted practice in many fields of research.  ...  that any platform supporting CWL will be able to understand the analysis, re-use the methods for partia [...]  ...  We would like to thank the Common Work ow Language community, and in particular Peter Amstutz, Pau Ruiz Safont and Pjotr Prins, for their continuing support, review and feedback.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5281/zenodo.1966881">doi:10.5281/zenodo.1966881</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/gnpjnqu6pzdtfe7d4nzvi2r44a">fatcat:gnpjnqu6pzdtfe7d4nzvi2r44a</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20201223053603/https://zenodo.org/record/1966881/files/CWLProv.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/b7/c9/b7c99d5d785e3f5317500e6ff97c25da59efe4f8.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5281/zenodo.1966881"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> zenodo.org </button> </a>

Internal replication of computational workflows in scientific research

Jade Benjamin-Chung, John M. Colford, Jr., Andrew Mertens, Alan E. Hubbard, Benjamin F. Arnold
<span title="2020-06-17">2020</span> <i title="F1000 Research Ltd"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/kaotr3rrnbfr5jeruaniwd5taq" style="color: black;">Gates Open Research</a> </i> &nbsp;
Here we summarize the rationale and best practices for internal replication, a process in which multiple independent data analysts replicate an analysis and correct errors prior to publication.  ...  We explain how internal replication should reduce errors and bias that arise during data analyses and argue that it will be most effective when coupled with pre-specified hypotheses and analysis plans  ...  Acknowledgements The authors would like to thank Matthew Akamatsu for his helpful comments on this manuscript.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.12688/gatesopenres.13108.2">doi:10.12688/gatesopenres.13108.2</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/4mn3nl2fcvbc7ncyewwrmnsu2a">fatcat:4mn3nl2fcvbc7ncyewwrmnsu2a</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200618024357/https://dqo52087pnd5x.cloudfront.net/manuscripts/14341/d35fd5ce-d2c0-4d36-9623-2cc9e1252064_13108_-_jade_benjamin-chung_v2.pdf?doi=10.12688/gatesopenres.13108.2&amp;numberOfBrowsableCollections=2&amp;numberOfBrowsableInstitutionalCollections=0&amp;numberOfBrowsableGateways=5" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/bf/76/bf76d9630431c6eaceb2ba3f2e8436ff19994126.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.12688/gatesopenres.13108.2"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> Publisher / doi.org </button> </a>
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