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VLAB: Web services, portlets, and workflows for enabling cyber-infrastructure in computational mineral physics

Evan F. Bollig, Paul A. Jensen, Martin D. Lyness, Mehmet A. Nacar, Pedro R.C. da Silveira, Dan Kigelman, Gordon Erlebacher, Marlon Pierce, David A. Yuen, Cesar R.S. da Silva
2007 Physics of the Earth and Planetary Interiors  
VLab provides a front-end portal, accessible from a browser, for scientists to submit large-scale simulations and interactively analyze their results.  ...  The cyber-infrastructure of VLab concentrates on scientific workflows, portal development, responsive user-interfaces and automatic generation of web services, all necessary to ensure a maximum degree  ...  Changing trends in technology have also led to a high demand for service-oriented applications such as the portals and workflows described above.  ... 
doi:10.1016/j.pepi.2007.03.005 fatcat:tvvipjuolfabfocr7rsq22uoju

A Need-Oriented Assessment of Technological Trends in Web Engineering [chapter]

Damith C. Rajapakse, Stan Jarzabek
2005 Lecture Notes in Computer Science  
We identify important technological needs in relation to a reference architecture for Web Applications, and show how different technological trends address each need.  ...  We believe a need-oriented organization of Web technologies, as presented in this paper, is a useful starting point for comprehending the multitude of existing and emerging Web technologies from an essential  ...  Framework applications written in a variety of languages, including C, C++, C#, and Visual Basic. The NET Framework class library includes ASP.NET, ADO.NET, and support for Web services.  ... 
doi:10.1007/11531371_7 fatcat:bgjcn7kqlbedvaqi5chb7mjyxq

A Service-oriented Framework for Integration of Domain-specific Data Models in Scientific Workflows

Andreas Bender, Angela Poschlad, Stefan Bozic, Ivan Kondov
2013 Procedia Computer Science  
Managing data exchange in scientific workflow simulations is a challenge for which existing solutions have only limited success.  ...  After implementing a working prototype of the framework we demonstrated its benefits for a complex workflow application from the domain of multiscale materials modeling.  ...  Acknowledgements This work has been partially funded by the 7th Framework Programme of the European Commission within the Research Infrastructures with grant agreement number RI-261594, project MMM@HPC  ... 
doi:10.1016/j.procs.2013.05.274 fatcat:rbclfo6t6fh2dkmko2uva33o54

COMP Superscalar, an interoperable programming framework

Rosa M. Badia, Javier Conejero, Carlos Diaz, Jorge Ejarque, Daniele Lezzi, Francesc Lordan, Cristian Ramon-Cortes, Raul Sirvent
2015 SoftwareX  
COMPSs is a programming framework that aims to facilitate the parallelization of existing applications written in Java, C/C++ and Python scripts.  ...  For that purpose, it offers a simple programming model based on sequential development in which the user is mainly responsible for (i) identifying the functions to be executed as asynchronous parallel  ...  Fig. 1 . 1 Sample application code written in Java. Fig. 2 . 2 Example of a sequential Python script parallelized with PyCOMPSs: (a) main program of the script, (b) task definition.  ... 
doi:10.1016/j.softx.2015.10.004 fatcat:wdihysbvvzgythxojl4uu7fbg4

SUSHI: an exquisite recipe for fully documented, reproducible and reusable NGS data analysis

Masaomi Hatakeyama, Lennart Opitz, Giancarlo Russo, Weihong Qi, Ralph Schlapbach, Hubert Rehrauer
2016 BMC Bioinformatics  
SUSHI lets users build reproducible data analysis workflows from individual applications and manages the input data, the parameters, meta-information with user-driven semantics, and the job scripts.  ...  Our SUSHI instance is in productive use and has served as data analysis interface for more than 1000 data analysis projects. SUSHI source code as well as a demo server are freely available.  ...  Additionally we would like to thank all users for their valuable feedback. Funding No funding was obtained for this study.  ... 
doi:10.1186/s12859-016-1104-8 pmid:27255077 pmcid:PMC4890512 fatcat:nneymzltsbdjxefvnjqf2qgtmy

Domain-specific languages for composing signature discovery workflows

Ferosh Jacob, Jeff Gray, Adam Wynne, Yan Liu, Nathan Baker
2012 Proceedings of the 2012 workshop on Domain-specific modeling - DSM '12  
The breadth and cross-disciplinary nature of this work requires that existing executable applications be integrated with new capabilities into workflows, representing a wide range of user tasks.  ...  An algorithm may be written in multiple programming languages for various hardware platforms, and so workflow composition requires integrating executables from any number of remote hosts.  ...  For example, in our system, manually wrapping a simple script that has a single input and output file requires 121 lines of Java code (in five Java classes) and 35 lines of XML code (in two files).  ... 
doi:10.1145/2420918.2420934 fatcat:nxiu4z4itzg6jnxahspdujqrta

AIBench: A rapid application development framework for translational research in biomedicine

D. Glez-Peña, M. Reboiro-Jato, P. Maia, M. Rocha, F. Díaz, F. Fdez-Riverola
2010 Computer Methods and Programs in Biomedicine  
AIBench incorporates a powerful plug-in engine, a flexible scripting platform and takes advantage of Java annotations, reflection and various design principles in order to make it easy to use, lightweight  ...  In this context this paper presents AIBench, an open-source Java desktop application framework for scientific software development with the goal of providing support to both fundamental and applied research  ...  Acknowledgements This work was partially supported by the Integrated Action Development of computational tools for cancer diagnosis using gene expression data (HP2006-0125) between Portugal (University  ... 
doi:10.1016/j.cmpb.2009.12.003 pmid:20047774 fatcat:ktx3i7xqsvflrgb3lzsb3zdvau

Experiment and Workflow Management Using Cyberaide Shell

Gregor von Laszewski, Andrew Younge, Xi He, Kumar Mahinthakumar, Lizhe Wang
2009 2009 9th IEEE/ACM International Symposium on Cluster Computing and the Grid  
Through a service integration mechanism, the shell's functionality is exposed to a wide variety of frameworks and programming languages.  ...  In order for the scientists to focus on actual scientific tasks, specialized tools and services need to be developed to ease the integration of complex middleware.  ...  A system shell provides a scripting framework to automate tasks in a coordinated way.  ... 
doi:10.1109/ccgrid.2009.66 dblp:conf/ccgrid/LaszewskiYHMW09 fatcat:6eut5uktijbslmh5yyj3ike3y4

MapReduce Operations with WS-VLAM Workflow Management System

Mikolaj Baranowski, Adam Belloum, Marian Bubak
2013 Procedia Computer Science  
To extend the role that workflow systems play in data-intensive science, we propose a solution that integrates WMS and MapReduce model.  ...  In this paper, we discuss possible solution of combining MapReduce and workflow applications, we describe the implementation of chosen solution based on metaprogramming approach in Ruby programming language  ...  We would like to thank Reginald Cushing and Spiros Koulouzis from University of Amsterdam for discussions and suggestions.  ... 
doi:10.1016/j.procs.2013.05.449 fatcat:qasbig2mhzdlvhzev3wglkeg2i

WETSUIT

Stefan Endrullis, Andreas Thor, Erhard Rahm
2012 Proceedings of the VLDB Endowment  
The operator implementation supports a high degree of parallel processing, in particular a streaming of entities between all data transformation operations facilitating a fast presentation of intermediate  ...  Mashups can be composed using a set of high-level operators based on the Javacompatible language Scala.  ...  WETSUIT In our framework mashup workflows are specified in a domain specific language (DSL) embedded in Scala.  ... 
doi:10.14778/2367502.2367550 fatcat:brcrcv5r5jfgzmlejzyrbquh2e

GridAnt: a client-controllable grid workflow system

K. Amin, G. von Laszewski, M. Hategan, N.J. Zaluzec, S. Hampton, A. Rossi
2004 37th Annual Hawaii International Conference on System Sciences, 2004. Proceedings of the  
This paper discusses the design principles, functionality, and application of the proposed GridAnt workflow manager.  ...  In the Grid community it is essential that the Grid users have such a tool available enabling them to orchestrate complex workflows on the fly without substantial help from the service providers.  ...  into other Java applications. • Ant distribution contains a large number of core and contributed tasks that provide extensive functionality similar to those available in shell scripts. • Ant is a community  ... 
doi:10.1109/hicss.2004.1265491 dblp:conf/hicss/AminLHZHR04 fatcat:32524mcqjjapxoho2dnszsui4y

Decentralized orchestration of data-centric workflows in Cloud environments

Bahman Javadi, Martin Tomko, Richard O. Sinnott
2013 Future generations computer systems  
Although there are a plethora of orchestration frameworks to implement workflows, most of them are unsuitable for executing (enacting) data-centric workflows since they are based on a centralized orchestration  ...  In this paper, we propose a flexible and lightweight workflow framework based on the Object Modeling Systems (OMS).  ...  Acknowledgments We would like to thank the AURIN architecture group for their support. The AURIN project is funded through the Australian Education Investment Fund SuperScience initiative.  ... 
doi:10.1016/j.future.2013.01.008 fatcat:tpmgbwshajc6dfbhl7h73qlc5i

Apache airavata

Suresh Marru, Ross Gardler, Aleksander Slominski, Ate Douma, Srinath Perera, Sanjiva Weerawarana, Lahiru Gunathilake, Chathura Herath, Patanachai Tangchaisin, Marlon Pierce, Chris Mattmann, Raminder Singh (+2 others)
2011 Proceedings of the 2011 ACM workshop on Gateway computing environments - GCE '11  
In this paper, we introduce Apache Airavata, a software framework to compose, manage, execute, and monitor distributed applications and workflows on computational resources ranging from local resources  ...  and workflow management systems.  ...  Airavata GFac provides a generic framework to wrap an application as a service interface in Java.  ... 
doi:10.1145/2110486.2110490 dblp:conf/sc/MarruGHTPMSGCGSDPW11 fatcat:aumigogsh5gflc242vkm6fchni

Decentralized Orchestration of Data-centric Workflows Using the Object Modeling System

Bahman Javadi, Martin Tomko, Richard O. Sinnott
2012 2012 12th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing (ccgrid 2012)  
The main issue is transferring output of service invocations through a centralized orchestration engine to the next service in the workflow, which can be a bottleneck for the performance of a data-centric  ...  In this paper, we propose a flexible and lightweight workflow framework based on the Object Modeling Systems (OMS).  ...  ACKNOWLEDGMENTS We would like to thank the AURIN architecture group for their support. The AURIN project is funded through the Australian Education Investment Fund SuperScience initiative.  ... 
doi:10.1109/ccgrid.2012.110 dblp:conf/ccgrid/JavadiTS12 fatcat:p7tljt4umbfwnemq6js6iaczra

Invocation of operations from script-based Grid applications

Maciej Malawski, Tomasz Bartyński, Marian Bubak
2010 Future generations computer systems  
Such an application model, based on high-level scripting, is an interesting alternative to graphical workflow-based tools.  ...  As a solution we have proposed the Grid Operation Invoker (GOI) which offers an object-oriented method invocation semantics for interacting with diverse computational services.  ...  Piotr Nowakowski for their comments and contributions.  ... 
doi:10.1016/j.future.2009.05.012 fatcat:7ts6rxjpgfexdo5n5xa4qeuzuq
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