YesWorkflow: A User-Oriented, Language-Independent Tool for Recovering Workflow Information from Scripts. McPhillips, T.; Song, T.; Kolisnik, T.; Aulenbach, S.; Belhajjame, K.; Bocinsky, R. K.; Cao, Y.; Cheney, J.; Chirigati, F.; Dey, S.; Freire, J.; Jones, C.; Hanken, J.; Kintigh, K. W.; Kohler, T. A.; Koop, D.; Macklin, J. A.; Missier, P.; Schildhauer, M.; Schwalm, C.; Wei, Y.; Bieda, M.; and Ludäscher, B. International Journal of Digital Curation, 10(1):298-313, May, 2015.
YesWorkflow: A User-Oriented, Language-Independent Tool for Recovering Workflow Information from Scripts [link]Paper  doi  abstract   bibtex   
Scientific workflow management systems offer features for composing complex computational pipelines from modular building blocks, executing the resulting automated workflows, and recording the provenance of data products resulting from workflow runs. Despite the advantages such features provide, many automated workflows continue to be implemented and executed outside of scientific workflow systems due to the convenience and familiarity of scripting languages (such as Perl, Python, R, and MATLAB), and to the high productivity many scientists experience when using these languages. YesWorkflow is a set of software tools that aim to provide such users of scripting languages with many of the benefits of scientific workflow systems. YesWorkflow requires neither the use of a workflow engine nor the overhead of adapting code to run effectively in such a system. Instead, YesWorkflow enables scientists to annotate existing scripts with special comments that reveal the computational modules and dataflows otherwise implicit in these scripts. YesWorkflow tools extract and analyze these comments, represent the scripts in terms of entities based on the typical scientific workflow model, and provide graphical renderings of this workflow-like view of the scripts. Future version of YesWorkflow will also allow the prospective provenance of the data products of these scripts to be queried in ways similar to those available to users of scientific workflow systems.
@article{mcphillips2015yesworkflowa,
  title = {{{YesWorkflow}}: {{A User}}-{{Oriented}}, {{Language}}-{{Independent Tool}} for {{Recovering Workflow Information}} from {{Scripts}}},
  volume = {10},
  copyright = {Copyright (c)},
  issn = {1746-8256},
  shorttitle = {{{YesWorkflow}}},
  doi = {10.2218/ijdc.v10i1.370},
  abstract = {Scientific workflow management systems offer features for composing complex computational pipelines from modular building blocks, executing the resulting automated workflows, and recording the provenance of data products resulting from workflow runs. Despite the advantages such features provide, many automated workflows continue to be implemented and executed outside of scientific workflow systems due to the convenience and familiarity of scripting languages (such as Perl, Python, R, and MATLAB), and to the high productivity many scientists experience when using these languages. YesWorkflow is a set of software tools that aim to provide such users of scripting languages with many of the benefits of scientific workflow systems. YesWorkflow requires neither the use of a workflow engine nor the overhead of adapting code to run effectively in such a system. Instead, YesWorkflow enables scientists to annotate existing scripts with special comments that reveal the computational modules and dataflows otherwise implicit in these scripts. YesWorkflow tools extract and analyze these comments, represent the scripts in terms of entities based on the typical scientific workflow model, and provide graphical renderings of this workflow-like view of the scripts. Future version of YesWorkflow will also allow the prospective provenance of the data products of these scripts to be queried in ways similar to those available to users of scientific workflow systems.},
  language = {en},
  number = {1},
  urldate = {2017-05-22},
  url = {http://www.ijdc.net/index.php/ijdc/article/view/10.1.298},
  journal = {International Journal of Digital Curation},
  author = {McPhillips, Timothy and Song, Tianhong and Kolisnik, Tyler and Aulenbach, Steve and Belhajjame, Khalid and Bocinsky, R. Kyle and Cao, Yang and Cheney, James and Chirigati, Fernando and Dey, Saumen and Freire, Juliana and Jones, Christopher and Hanken, James and Kintigh, Keith W. and Kohler, Timothy A. and Koop, David and Macklin, James A. and Missier, Paolo and Schildhauer, Mark and Schwalm, Christopher and Wei, Yaxing and Bieda, Mark and Lud\"ascher, Bertram},
  month = may,
  year = {2015},
  pages = {298-313},
  file = {/Users/ludaesch/Dropbox/zotero/storage/M2HD2N7U/McPhillips et al. - 2015 - YesWorkflow A User-Oriented, Language-Independent.pdf;/Users/ludaesch/Dropbox/zotero/storage/N2UXNBW6/10.1.html}
}
Downloads: 0