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The Eclipse Integrated Computational Environment [article]

Jay Jay Billings, Andrew R. Bennett, Jordan Deyton, Kasper Gammeltoft, Jonah Graham, Dasha Gorin, Hari Krishnan, Menghan Li, Alexander J. McCaskey, Taylor Patterson, Robert Smith, Gregory R. Watson, Anna Wojtowicz
2017 arXiv   pre-print
Examples of the Environment's applicability to problems in energy science, general multiphysics simulations, quantum computing and other areas are presented as well as its impact on the community.  ...  It presents the Eclipse Integrated Computational Environment as a workflow management system and development environment for the modeling and simulation community.  ...  This includes many people who directly contributed to the project, either in its early days as "NiCE" or once it moved to Eclipse, including: Ronald Allen, Andrew Belt, Tim Bohn, David E.  ... 
arXiv:1704.01398v3 fatcat:7piadzhzmnbe7ivbdp5spmvsby

Virtual laboratory for planetary materials (VLab)

Pedro R. C. da Silveira, M. Núñez Valdez, Renata M. Wenzcovitch, Marlon Pierce, Cesar R. S. da Silva, David A. Yuen
2011 Proceedings of the 2011 TeraGrid Conference on Extreme Digital Discovery - TG '11  
In this paper we review the main features and illustrate the use of VLab, a Science Gateway that provides Cyberinfrastructure (CI) for distributed first principles computations in materials science.  ...  The VLab CI includes Web Services running in different computers, controlled from a Web Portal running predefined, distributed, and interactive workflows by multiple users.  ...  VLab's BoT executions are similar to "glide-in" or "pilot" job submissions used in many-task computing on the TeraGrid, Open Science Grid, and elsewhere.  ... 
doi:10.1145/2016741.2016777 fatcat:ykswhygbwzgpxi3jt2bvfetro4

A Taxonomy of Workflow Management Systems for Grid Computing

Jia Yu, Rajkumar Buyya
2005 Journal of Grid Computing  
Therefore, many efforts have been made towards the development of workflow management systems for Grid computing.  ...  We also survey several representative Grid workflow systems developed by various projects world-wide to demonstrate the comprehensiveness of the taxonomy.  ...  ACKNOWLEDGEMENTS We would like to acknowledge all developers of the workflow management systems described in the paper.  ... 
doi:10.1007/s10723-005-9010-8 fatcat:b2ptnwxnhbeltlybivpxl6m654

Read Mapping and Transcript Assembly: A Scalable and High-Throughput Workflow for the Processing and Analysis of Ribonucleic Acid Sequencing Data

Sateesh Peri, Sarah Roberts, Isabella R. Kreko, Lauren B. McHan, Alexandra Naron, Archana Ram, Rebecca L. Murphy, Eric Lyons, Brian D. Gregory, Upendra K. Devisetty, Andrew D. L. Nelson
2020 Frontiers in Genetics  
For extremely large datasets (tens of thousands of FASTq files) we developed a high-throughput, scalable, and parallelized version of RMTA optimized for launching on the Open Science Grid (OSG) from within  ...  RMTA is containerized using Docker for easy deployment within any compute environment [cloud, local, or high-performance computing (HPC)] and is available as two apps in CyVerse's Discovery Environment  ...  FUNDING This work has been supported by the National Science Foundation grants IOS-1758532 (to ADN, RM, and UD), IOS-1743442 (to CyVerse), IOS-1444490 (to EL and BG), NSF Research Experience for Undergraduates  ... 
doi:10.3389/fgene.2019.01361 pmid:32038716 pmcid:PMC6993073 fatcat:eouw5cuoazgpnopug542qu2muq

Pegasus, a workflow management system for science automation

Ewa Deelman, Karan Vahi, Gideon Juve, Mats Rynge, Scott Callaghan, Philip J. Maechling, Rajiv Mayani, Weiwei Chen, Rafael Ferreira da Silva, Miron Livny, Kent Wenger
2015 Future generations computer systems  
This paper describes the design, development and evolution of the Pegasus Workflow Management System, which maps abstract workflow descriptions onto distributed computing infrastructures.  ...  The paper describes how Pegasus achieves reliable, scalable workflow execution across a wide variety of computing infrastructures.  ...  This research was done using resources provided by the Open Science Grid, which is supported by the National Science Foundation and the U.S. Department of Energy's Office of Science.  ... 
doi:10.1016/j.future.2014.10.008 fatcat:u5lbouuekvduhfdvdi7phfyn7i

Build-and-Test Workloads for Grid Middleware: Problem, Analysis, and Applications

Alexandru Iosup, Dick Epema
2007 Seventh IEEE International Symposium on Cluster Computing and the Grid (CCGrid '07)  
However, it is unclear what good build-and-test environments for grid middleware should look like, and how to use them efficiently. In this work we address both these problems.  ...  First, we study the characteristics of the NMI build-and-test environment, which handles millions of testing tasks annually, for major Grid middleware such as Condor, Globus, VDT, and gLite.  ...  Acknowledgements This work was carried out in the context of the Virtual Laboratory for e-Science project (www.vl-e.nl), which is supported by a BSIK grant from the Dutch Ministry of Education, Culture  ... 
doi:10.1109/ccgrid.2007.29 dblp:conf/ccgrid/IosupE07 fatcat:uh4tu66h2rbunjcp6umyzgcfgy

An Intelligent Recommender System for Web Resource Discovery and Selection [chapter]

Liming Chen, Feng Tao
2008 Studies in Computational Intelligence  
A number of technologies and tools are developed, and further applied to a real world application -the UK e-Science GEODISE project, to demonstrate the system's applicability and benefits. 6  ...  The Web is now evolving from information sharing to resource provisioning as the emerging Web services and Grid technologies are widely accepted and practiced.  ...  Acknowledgement This work is supported by the UK EPSRC Geodise e-Science pilot (GR/R67705/01). The authors gratefully acknowledge the contributions from the project team.  ... 
doi:10.1007/978-3-540-78308-4_7 fatcat:6gltjqgkhzd3bln7jisycxhopa

Dealing with Software Complexity in Individual‐Based Models

Daniel Vedder, Markus Ankenbrand, Juliano Sarmento Cabral
2021 Methods in Ecology and Evolution  
TA B L E 2 Examples of open-source individual-based models and other ecological software that are referred to in the text.  ...  As another example, the RangeShifter model separates organisms from their environment: there is a Landscape object that holds the environment's grid cells, and a Community object that contains all individual  ...  PE E R R E V I E W The peer review history for this article is available at https://publo ns.com/publo n/10.1111/2041-210X.13716.  ... 
doi:10.1111/2041-210x.13716 fatcat:a2fnfvhuijbp5m664liffrxnvy

The iPlant Collaborative: Cyberinfrastructure for Plant Biology

Stephen A. Goff, Matthew Vaughn, Sheldon McKay, Eric Lyons, Ann E. Stapleton, Damian Gessler, Naim Matasci, Liya Wang, Matthew Hanlon, Andrew Lenards, Andy Muir, Nirav Merchant (+53 others)
2011 Frontiers in Plant Science  
the physical sciences. iPlant is an open-source project with application programming interfaces that allow the community to extend the infrastructure to meet its needs. iPlant is sponsoring community-driven  ...  The iPlant cyberinfrastructure design is based on an unprecedented period of research community input, and leverages developments in high-performance computing, data storage, and cyberinfrastructure for  ...  -NSF Plant Science Cyberinfrastructure Collaborative HPC -high-performance computing HTC -high-throughput computing TeraGrid -NSF's open scientific grid computing project that includes 11 partners  ... 
doi:10.3389/fpls.2011.00034 pmid:22645531 pmcid:PMC3355756 fatcat:nwkuqfhsorddrppjjzs6oz76ci

Exploring similarities among many species distributions

Scott Simmerman, Jingyuan Wang, James Osborne, Kimberly Shook, Jian Huang, William Godsoe, Theodore Simons
2012 Proceedings of the 1st Conference of the Extreme Science and Engineering Discovery Environment on Bridging from the eXtreme to the campus and beyond - XSEDE '12  
Our system can also compute and reveal uncertainties in the modeling results enabling domain experts to make informed judgments about the data.  ...  Due to limitations of computing power as well as limited means of using modeling software on HPC facilities, past species distribution studies have been unable to fully explore diverse data sets.  ...  Acknowledgment University of Tennessee computer science undergraduate students James White and Adam Haney worked on reliably running the MaxEnt model in parallel while maintaining system-wide stability  ... 
doi:10.1145/2335755.2335835 fatcat:i423ms5qeng7zls5mnksbwxxby

VM-Flow [chapter]

Ivo J. G. dos Santos, Edmundo R. M. Madeira
2004 IFIP International Federation for Information Processing  
The CONTRACT project is co-funded by the European Commission under the 6th Framework Programme for RTD with project number FP6-034418.  ...  For the avoidance of doubt, the content of this report reflects only the opinion of the project consortium members and its authors.  ...  Modeling Language EDI Electronic Data Interchange EGEE Enabling Grids for E-sciencE project EJBs Enterprise JavaBeans EPL Eclipse Public License EPR agreement endpoint reference ESB  ... 
doi:10.1007/1-4020-8155-3_15 fatcat:tdnlcms72rbznjvwphoztdx37y

Performance Analysis of Cloud Computing Services for Many-Tasks Scientific Computing

A Iosup, S Ostermann, M N Yigitbasi, R Prodan, T Fahringer, D H J Epema
2011 IEEE Transactions on Parallel and Distributed Systems  
In this work, we analyze the performance of cloud computing services for scientific computing workloads.  ...  Thus, clouds have the potential to provide to their owners the benefits of an economy of scale and, at the same time, become an alternative for scientists to clusters, grids, and parallel production environments  ...  ACKNOWLEDGMENTS This work is partially funded by the European Union under grant agreement number 261585/SHIWA Project.  ... 
doi:10.1109/tpds.2011.66 fatcat:wpiqxk75rzclfgwo25vpgvfotu

Eighth Workshop and Tutorial on Practical Use of Coloured Petri Nets and the CPN Tools, Aarhus, Denmark, October 22-24, 2007

Kurt Jensen
2007 DAIMI Report Series  
The workshop is organised by the CPN group at the Department of Computer Science, University of Aarhus, Denmark.  ...  Acknowledgment This paper is partially supported by CAPES/Brazil under grant 4635/06-0, CNPq WebMaps II Project, and FAPESP.  ...  Kjeldsen who are significantly contributing to the development of ASAP via their employment as student programmers in the ASCoVeCo project.  ... 
doi:10.7146/dpb.v36i584.7197 fatcat:fmzu5qetpnd6dpflqsuggbt7mm

Metamodelling for Design of Mechatronic and Cyber-Physical Systems

Krzysztof Pietrusewicz
2019 Applied Sciences  
It enables for fully-featured automatic code generation which is one of the main pillars of the agile management within mechatronic system design projects.  ...  Computer Numerically Controlled machine (CNC), loading crane, forestry crane) often depends on a proper communication between team members.  ...  The SGAM (Smart Grid Architecture Model) project, realized under the auspices of Smart Grid Coordination Group, resulted in the creation of a domain specific language that is accessible on the webpages  ... 
doi:10.3390/app9030376 fatcat:wzd4lmkzhbgypiyk2hla5qilne

USID and Pycroscopy -- Open frameworks for storing and analyzing spectroscopic and imaging data [article]

Suhas Somnath, Chris R. Smith, Nouamane Laanait, Rama K. Vasudevan, Anton Ievlev, Alex Belianinov, Andrew R. Lupini, Mallikarjun Shankar, Sergei V. Kalinin, Stephen Jesse
2019 arXiv   pre-print
Harnessing these data for scientific research requires an evolution of the associated computing and data infrastructure, bridging scientific instrumentation with super- and cloud- computing.  ...  We discuss a family of community-driven, open-source, and free python software packages for storing, processing and visualizing data.  ...  Jupyter notebooks using Pycroscopy are now regularly submitted as supplementary documents along with the conventional manuscript to academic journals to improve transparency in the push for open science  ... 
arXiv:1903.09515v2 fatcat:gfyrm4n3fza5nabnfgn4ie3aqy
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