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Supporting Scientists' Everyday Work: Automating Scientific Workflows

Mark Vigder, Norman G. Vinson, Janice Singer, Darlene Stewart, Keith Mews
2008 IEEE Software  
In Section 2, we describe scientific workflows, and relate this to the Sweet Framework we developed. Section 3 provides an overview of the Sweet Framework.  ...  We refer to these sequences as scientific workflows. Working with the scientists, we developed a scientific workflow management software system.  ... 
doi:10.1109/ms.2008.97 fatcat:obzkduubzvaahfejcpvcy33ejm

Scientific Workflow Composition in Heterogeneous Environments

Jamal Alhiyafi, Shiyong Lu, Jeffrey L. Ram
2012 International Journal of Intelligent Information Processing  
However, scientific workflows are emerging as an important technology for solving complex scientific problems and thereby contributing to scientific development.  ...  The main contributions of this paper are: 1) to propose a scientific workflow system to design, develop, and execute scientific workflows from heterogeneous scientific workflows; 2) to propose a scheduling  ...  Scientific workflow management systems (SWFMSs) provide an environment to model, develop and run scientific workflows efficiently.  ... 
doi:10.4156/ijiip.vol3.issue1.3 fatcat:qikhy7bk3nhafobwbxph2m3fmi

Middleware Building Blocks for Workflow Systems [article]

Matteo Turilli, Vivek Balasubramanian, Andre Merzky, Ioannis Paraskevakos, Shantenu Jha
2019 arXiv   pre-print
This paper describes a building blocks approach to the design of scientific workflow systems.  ...  Four case studies are presented, discussing how RADICAL-Cybertools are integrated with existing workflow, workload, and general purpose computing systems to support the execution of scientific workflows  ...  We acknowledge access to computational facilities: XSEDE resources (TG-MCB090174) and Blue Waters (NSF-1713749).  ... 
arXiv:1903.10057v1 fatcat:vvlkcxkuebhdxcp5bcqrcwu4tu

Introduction to Science Gateways and Science Gateway Frameworks [chapter]

Péter Kacsuk
2014 Science Gateways for Distributed Computing Infrastructures  
It contains the major functionalities to develop and run work- flows by the workflow developers and to run workflows by the end-user scientists.  ...  Similar activities are supported among workflow developers and end-users belonging to different gateway communities via the SHIWA Workflow Repository.  ... 
doi:10.1007/978-3-319-11268-8_1 fatcat:ver23izz6vfa7kcpni2mexmpqe

A collaborative scheduling approach for service-driven scientific workflow execution

Wanchun Dou, J. Leon Zhao, Shaokun Fan
2010 Journal of computer and system sciences (Print)  
Further, an evaluation is also presented to demonstrate the proposed approach for coordinating multiple scientific workflow executions in a concurrent environment.  ...  Scientific workflow execution often spans multiple self-managing administrative domains to obtain specific processing capabilities.  ...  First, as a typical application environment, grid is an efficient infrastructure for scientific workflow development and execution.  ... 
doi:10.1016/j.jcss.2009.11.004 fatcat:cjk6s7pljbawxdwk45o6s3pize

Interoperability and automation in searches for Hard X-ray counterparts of multi-messenger transients with INTEGRAL

Volodymyr Savchenko
2019 Zenodo  
The core of the platform is built around the mechanisms of workflow introspection and flexible interface-first modular development, allowing the researches to efficiently contribute to the constant improvement  ...  I will review the follow-up and dissemination strategy we have developed in these searches, which have in particular allowed to maximize scientific benefit of the first confident detection of the multi-messenger  ...  planning tools (remote ESAC service) experts 17 "Standard" INTEGRAL transient analysis: end to end Research, development environment lets experts develop standardized, test, and integrate:  ... 
doi:10.5281/zenodo.3560566 fatcat:6fseop7jajga7n2dngyp6lqkja

Agile parallel bioinformatics workflow management using Pwrake

Hiroyuki Mishima, Kensaku Sasaki, Masahiro Tanaka, Osamu Tatebe, Koh-ichiro Yoshiura
2011 BMC Research Notes  
Here, we show the application of a scientific workflow system Pwrake to bioinformatics workflows.  ...  In bioinformatics projects, scientific workflow systems are widely used to manage computational procedures.  ...  Acknowledgements The authors would like to thank members of the BioRuby mailing list for their informative discussions.  ... 
doi:10.1186/1756-0500-4-331 pmid:21899774 pmcid:PMC3180464 fatcat:6drb333wlfh5lg5ukrtx3eapde

Service-Oriented Architecture for VIEW: A Visual Scientific Workflow Management System

Cui Lin, Shiyong Lu, Zhaoqiang Lai, Artem Chebotko, Xubo Fei, Jing Hua, Farshad Fotouhi
2008 2008 IEEE International Conference on Services Computing  
In contrast to business workflows, which are typically controlflow oriented, scientific workflows tend to be dataflow oriented, introducing a new set of requirements for system development.  ...  Scientific workflows have recently emerged as a new paradigm for scientists to formalize and structure complex and distributed scientific processes to enable and accelerate many scientific discoveries.  ...  In scientific workflows, scientists are often the end users to design, modify, run, re-run, and monitor scientific workflows.  ... 
doi:10.1109/scc.2008.118 dblp:conf/IEEEscc/LinLLCFHF08 fatcat:drwsybovbrgqfczphkwj7latem

Scalable Workflow-Driven Hydrologic Analysis in HydroFrame [chapter]

Shweta Purawat, Cathie Olschanowsky, Laura E. Condon, Reed Maxwell, Ilkay Altintas
2020 Lecture Notes in Computer Science  
This workflow performs end-to-end hydrology simulations involving data ingestion, preprocessing, analysis, modeling, and visualization.  ...  We present the initial progress on the HydroFrame community platform using an automated Kepler workflow.  ...  In contrast to isolated and partially focused development efforts, this paper presents an end-to-end solution that couples the Kepler System and the Smart Flows toolset to provide Hydrology researchers  ... 
doi:10.1007/978-3-030-50371-0_20 fatcat:c6632vj24nd25dcdq73i6bxhyu

Vision and Requirements of Scenario-Driven Environmental Decision Support Systems Supporting Automation for End Users [chapter]

Sascha Schlobinski, Ralf Denzer, Steven Frysinger, Reiner Güttler, Thorsten Hell
2011 IFIP Advances in Information and Communication Technology  
& Customizing Modell Development Scientific Workflows Scenario Management Vision and Requirements of Scenario-driven Environmental DSS Supporting Automation for End Users develop, integrate  ...  Scientific Workflows Scenario Management User Categories Analyst System Manager Modeller Reporting & Decision Making Service Provision & Customizing Modell Development Scientific  ... 
doi:10.1007/978-3-642-22285-6_6 fatcat:p3nt65g4afhf5ox2g426kjofie

A Data Science environment for climate change research at CMCC

Donatello Elia, Paola Nassisi, Cosimo Palazzo, Fabrizio Antonio, Bernardo Sbarro, Alessandro D'Anca, Sandro Fiore, Giovanni Aloisio
2019 Zenodo  
It will enable climate scientists to address key challenges, such as: • managing large scientific end-to-end climate experiments (aka workflows); • performing interactive data exploration; • analyzing  ...  The CMCC Data Science environment aims to provide a data science and learning based end-to-end scientific environment to support climate change research at scale, seamlessly integrated into a single high  ... 
doi:10.5281/zenodo.3941838 fatcat:3zbvvm4p6bfhjkyo6ojcmgjioy

Kepler for 'Omics Bioinformatics

Mark Bieda
2012 Procedia Computer Science  
We suggest concrete steps to enable further use of this flexible workflow system in 'omics analyses.  ...  analysis, and the growing complexity of analyses as important factors in considering workflow design criteria in this field and also future development of Kepler.  ...  Acknowledgements We thank Thomas Stropp and Timothy McPhillips for discussions relevant to this topic.  ... 
doi:10.1016/j.procs.2012.04.180 fatcat:mw5qso7bl5b4dlg7dfavl627qa

Complex Workflow Management and Integration of Distributed Computing Resources by Science Gateway Portal for Molecular Dynamics Simulations in Materials Science [article]

Yuri Gordienko, Lev Bekenov, Olexandr Gatsenko, Elena Zasimchuk, Valentin Tatarenko
2014 arXiv   pre-print
The typical scientific workflow with possible scenarios of its preparation and usage is considered.  ...  Several typical science applications (scientific workflows) are considered for molecular dynamics (MD) simulations of complex behavior of various nanostructures (nanoindentation of graphene layers, defect  ...  and related simulation workflows (referenced as "developers" or "power users") need to build and to fit the application to be as comfortable as possible for the end users.  ... 
arXiv:1404.5458v1 fatcat:atd6eak7lrdsvcghex5eorauie

A semantic Web services enabled Web portal architecture

Xiaorong Xiang, G. Madey
2004 Proceedings. IEEE International Conference on Web Services, 2004.  
In this paper, we present a web portal architecture that enables end users to access the distributed application through the web interface and to compose new tasks by integrating a set of high level web  ...  Web services technologies are emerging as a new approach for supporting e-Science and e-Engineering by providing access to heterogeneous computation resources and integration of distributed scientific  ...  If the end user is satisfied with the generated workflow, the composer sends a query to the database and gets a session number as an identifier for the task.  ... 
doi:10.1109/icws.2004.1314964 dblp:conf/icws/XiangM04 fatcat:atzc544ewbfhxlxjiyvgpuqo34

Automatic Transformation from Geospatial Conceptual Workflow to Executable Workflow Using GRASS GIS Command Line Modules in Kepler [chapter]

Jianting Zhang, Deana D. Pennington, William K. Michener
2006 Lecture Notes in Computer Science  
To utilize scientific workflow technology in geospatial modeling, it is important to support command line GIS modules in scientific workflow systems.  ...  We describe the preliminary implementation of the proposed approach in the Kepler scientific workflow system and demonstrate its feasibility using an example.  ...  We are in the process of developing more sophisticated algorithms to handle complex conceptual workflows.  ... 
doi:10.1007/11758532_122 fatcat:i4npyt5vmbd6fkmso4znbhjbgq
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