TY - JOUR
T1 - YesWorkflow
T2 - A User-Oriented, Language-Independent Tool for Recovering Workflow Information from Scripts
AU - McPhillips, Timothy
AU - Song, Tianhong
AU - Kolisnik, Tyler
AU - Aulenbach, Steve
AU - Belhajjame, Khalid
AU - Bocinsky, Kyle
AU - Cao, Yang
AU - Chirigati, Fernando
AU - Dey, Saumen
AU - Freire, Juliana
AU - Huntzinger, Deborah
AU - Jones, Christopher
AU - Koop, David
AU - Missier, Paolo
AU - Schildhauer, Mark
AU - Schwalm, Christopher
AU - Wei, Yaxing
AU - Cheney, James
AU - Bieda, Mark
AU - Ludaescher, Bertram
PY - 2015
Y1 - 2015
N2 - Scientific workflow management systems offer features for composing complex computational pipelines from modular building blocks, for executing the resulting automated workflows, and for 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 versions of YesWorkflow also will 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.
AB - Scientific workflow management systems offer features for composing complex computational pipelines from modular building blocks, for executing the resulting automated workflows, and for 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 versions of YesWorkflow also will 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.
KW - cs.SE
U2 - 10.2218/ijdc.v10i1.370
DO - 10.2218/ijdc.v10i1.370
M3 - Article
SN - 1746-8256
VL - 10
SP - 298
EP - 313
JO - International Journal of Digital Curation
JF - International Journal of Digital Curation
IS - 1
ER -