Scientific Workflow Management -- For Whom?

2014 ◽  
Author(s):  
Silvia Olabarriaga ◽  
Gabrielle Pierantoni ◽  
Giuliano Taffoni ◽  
Eva Sciacca ◽  
Mahdi Jaghoori ◽  
...  
Keyword(s):  
Workflow Management ◽  
Scientific Workflow

A new optimization phase for scientific workflow management systems

2014 ◽  
Vol 36 ◽  
pp. 352-362 ◽  
Author(s):  
Sonja Holl ◽  
Olav Zimmermann ◽  
Magnus Palmblad ◽  
Yassene Mohammed ◽  
Martin Hofmann-Apitius
Keyword(s):  
Workflow Management ◽  
Scientific Workflow ◽  
Management Systems ◽  
Workflow Management Systems

scholarly journals Tripal and Galaxy: supporting reproducible scientific workflows for community biological databases

Database ◽  
2020 ◽  
Vol 2020 ◽  
Author(s):  
Shawna Spoor ◽  
Connor Wytko ◽  
Brian Soto ◽  
Ming Chen ◽  
Abdullah Almsaeed ◽  
...  
Keyword(s):  
Workflow Management ◽  
Application Programming Interface ◽  
Scientific Workflow ◽  
Biological Databases ◽  
Web Based ◽  
Job Management ◽  
The Galaxy ◽  
Application Programming ◽  
Computational Resources ◽  
Programming Interface

Abstract Online biological databases housing genomics, genetic and breeding data can be constructed using the Tripal toolkit. Tripal is an open-source, internationally developed framework that implements FAIR data principles and is meant to ease the burden of constructing such websites for research communities. Use of a common, open framework improves the sustainability and manageability of such as site. Site developers can create extensions for their site and in turn share those extensions with others. One challenge that community databases often face is the need to provide tools for their users that analyze increasingly larger datasets using multiple software tools strung together in a scientific workflow on complicated computational resources. The Tripal Galaxy module, a ‘plug-in’ for Tripal, meets this need through integration of Tripal with the Galaxy Project workflow management system. Site developers can create workflows appropriate to the needs of their community using Galaxy and then share those for execution on their Tripal sites via automatically constructed, but configurable, web forms or using an application programming interface to power web-based analytical applications. The Tripal Galaxy module helps reduce duplication of effort by allowing site developers to spend time constructing workflows and building their applications rather than rebuilding infrastructure for job management of multi-step applications.

scholarly journals Scientific Workflow Management in Proteomics

2012 ◽  
Vol 11 (7) ◽  
pp. M111.010595 ◽  
Author(s):  
Jeroen S. de Bruin ◽  
André M. Deelder ◽  
Magnus Palmblad
Keyword(s):  
Workflow Management ◽  
Scientific Workflow

Integrating Scientific Workflows with Scientific Gateways: A Bioinformatics Experiment in the Brazilian National High-Performance Computing Network

2020 ◽  
Author(s):  
Maria Luiza Mondelli ◽  
Marcelo Monteiro Galheigo ◽  
Vivivan Medeiros ◽  
Bruno F. Bastos ◽  
Antônio Tadeu Azevedo Gomes ◽  
...  
Keyword(s):  
High Performance ◽  
Workflow Management ◽  
Scientific Workflow ◽  
Scientific Workflows ◽  
Management Systems ◽  
Workflow Management Systems ◽  
Sequencing Technologies ◽  
Geographically Distributed ◽  
Performance Computing ◽  
High Performance Computation

Bioinformatics experiments are rapidly and constantly evolving due improvements in sequencing technologies. These experiments usually demand high performance computation and produce huge quantities of data. They also require different programs to be executed in a certain order, allowing the experiments to be modeled as workflows. However, users do not always have the infrastructure needed to perform these experiments. Our contribution is the integration of scientific workflow management systems and grid-enabled scientific gateways, providing the user with a transparent way to run these workflows in geographically distributed computing resources. The availability of the workflow through the gateway allows for a better usability of these experiments.

scholarly journals A Survey of Data-Intensive Scientific Workflow Management

2015 ◽  
Vol 13 (4) ◽  
pp. 457-493 ◽  
Author(s):  
Ji Liu ◽  
Esther Pacitti ◽  
Patrick Valduriez ◽  
Marta Mattoso
Keyword(s):  
Workflow Management ◽  
Scientific Workflow ◽  
Data Intensive
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