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From the Desktop to the Grid: conversion of KNIME Workflows to gUSE

Luis de la Garza, Jens Krüger, Charlotta Schärfe, Marc Röttig, Stephan Aiche, Knut Reinert, Oliver Kohlbacher
2013 International Workshop on Science Gateways  
We present a solution permitting the conversion of workflows between the two platforms. This enables a convenient development, debugging, and maintenance of scientific workflows on the desktop.  ...  The grid and cloud User Support Environment is a free and open source project created for parallelized and distributed systems, but the creation of workflows with the included components has a steeper  ...  Stephan Aiche gratefully acknowledges funding by the European Commissions's seventh Framework Program (GA263215).  ... 
dblp:conf/iwsg/Garza0SRARK13 fatcat:3lbof7hn5rc5jnycs6q23bmcc4

From the desktop to the grid: scalable bioinformatics via workflow conversion

Luis de la Garza, Johannes Veit, Andras Szolek, Marc Röttig, Stephan Aiche, Sandra Gesing, Knut Reinert, Oliver Kohlbacher
2016 BMC Bioinformatics  
workflow editor, and the Grid and User Support Environment, a web-based framework able to interact with several high-performance computing resources.  ...  Results: We have developed a set of tools that enables the scientific community to benefit from workflow interoperability.  ...  Acknowledgements The authors would like to thank Bernd Wiswedel, Thorsten Meinl, Patrick Winter and Michael Berthold for their support, patience and help in developing the KNIME2gUSE extension.  ... 
doi:10.1186/s12859-016-0978-9 pmid:26968893 pmcid:PMC4788856 fatcat:2peb7eek2baynnkplbnh42xyrm

Scientific Workflows

Chee Sun Liew, Malcolm P. Atkinson, Michelle Galea, Tan Fong Ang, Paul Martin, Jano I. Van Hemert
2016 ACM Computing Surveys  
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  ... 
doi:10.1145/3012429 fatcat:23z6g32jfvgeto5zrigk4ysmx4

Fine-Grained Workflow Interoperability in Life Sciences [article]

Luis De La Garza, Universitaet Tuebingen, Universitaet Tuebingen, Kohlbacher, Oliver (Prof. Dr.)
2020
for a workflow), allows easy development of new tasks and is able to integrate external command line tools.  ...  Recognizing the importance of early and robust workflow design, we also extended a well–established, desktop–based analytics platform that contains more than two thousand tasks (each being a building block  ...  From the Desktop to the Grid and Cloud: Conversion of KNIME Workflows to WS-PGRADE.In 8th International Workshop of Science Gateways, PeerJ Preprints, 5:e2849v1.de la Garza, L., Veit, J., Szolek, A., Röttig  ... 
doi:10.15496/publikation-42827 fatcat:inv6hxbezbe3ladyt7lkeyjvii