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Component Technology for High-Performance Scientific Simulation Software [chapter]

Tom Epperly, Scott Kohn, Gary Kumfert
2001 IFIP Advances in Information and Communication Technology  
In this paper, we describe a language interoperability tool named Babel that enables the creation and distribution of language-independent software libraries using interface definition language (IDL) techniques  ...  Preliminary results indicate that in addition to language interoperability, this approach provides useful tools for the design of modern object-oriented scientific software libraries.  ...  Acknowledgments We would like to thank Andrew Cleary, Jeff Painter, and Cal rubbens for integrating the Babel language interoperability technology into the hypre library and for their many useful suggestions  ... 
doi:10.1007/978-0-387-35407-1_5 fatcat:rpkjlieabnadngq2q2kvuzv3yu

BioUML: plugin for population-based modeling

Ilya Kiselev, Fedor Kolpakov
2014 Virtual Biology  
library written in R language implementing log-likelihood approach for NLME models creation and analysis.  ...  Motivation and Aim: Non-linear mixed effects (NLME) model is an efficient tool for analyzing of population data and estimating of model parameters.  ...  There are also libraries for R language such as nlme [3] , nlmeODE [4] , seamix. In past year, new language for NLME models description, PharmML [5] has appeared.  ... 
doi:10.12704/vb/e15 fatcat:f52jyhvuhrbjtjvy57xf444cda

Unambiguous power system dynamic modeling and simulation using modelica tools

L. Vanfretti, W. Li, T. Bogodorova, P. Panciatici
2013 2013 IEEE Power & Energy Society General Meeting  
The nature of the Modelica modeling language supports model exchange at the "equation-level", this allows for unambiguous model exchange between different Modelica-based simulation tools without loss of  ...  Therefore, there is a clear need for unambiguous dynamic model exchange. In this article, a possible solution is proposed by using open modeling equation-based Modelica tools.  ...  They allow for straightforward implementation of new elements and libraries in order to simulate the behavior of each component and a system as a whole.  ... 
doi:10.1109/pesmg.2013.6672476 fatcat:qb73ghjgg5ggpcp7c42d4tm254

Reducing and manipulating complex trace data

Hervé Touati, Alan Jay Smith
1991 Software, Practice & Experience  
This paper presents TRAMP, a tool for the data reduction and data analysis phases of trace-driven simulation studies.  ...  This paper presents the design principles and implementation techniques of TRAMP and provides a few concrete examples of the use of this tool.  ...  ACKNOWLEDGEMENTS The authors would like to thank Fred Douglis, Bruce Holmer, Rafael Saavedra-Barrera, Dain Samples, Margo Seltzer, Barbara Tockey, Peter Van Roy and the referees for their helpful comments  ... 
doi:10.1002/spe.4380210607 fatcat:zndfugujlvajzbwukwh63sqbye

Reproducible computational biology experiments with SED-ML - The Simulation Experiment Description Markup Language

Dagmar Waltemath, Richard Adams, Frank T Bergmann, Michael Hucka, Fedor Kolpakov, Andrew K Miller, Ion I Moraru, David Nickerson, Sven Sahle, Jacky L Snoep, Nicolas Le Novère
2011 BMC Systems Biology  
SED-ML is a software-independent format for encoding the description of simulation experiments; it is not specific to particular simulation tools.  ...  users and software tools.  ...  AKM was funded partly by the VPH-Share Project and partly by the Maurice Wilkins Centre For Molecular Biodiscovery. RA is grateful for funding by the BBSRC grant BB/D019621/1.  ... 
doi:10.1186/1752-0509-5-198 pmid:22172142 pmcid:PMC3292844 fatcat:lct3n2evrzdpvftrhiajn4isdq

OpenAlea: a visual programming and component-based software platform for plant modelling

Christophe Pradal, Samuel Dufour-Kowalski, Frédéric Boudon, Christian Fournier, Christophe Godin
2008 Functional Plant Biology  
The system architecture is based on the use of a general purpose, high-level, object-oriented script language, Python, widely used in other scientific areas.  ...  OpenAlea allows researchers to build models using a visual programming interface and provides a set of tools and models dedicated to plant modelling.  ...  However, the user had to re-use 363 and adapt the existing models developed using different kinds of tools (R scripts for pre 364 and post processing, Unix scripts and open-L-system scripts for simulation  ... 
doi:10.1071/fp08084 pmid:32688829 fatcat:ura6jrenqbdhjlcypvfclxf3fm

Python as a Federation Tool for GENESIS 3.0

Hugo Cornelis, Armando L. Rodriguez, Allan D. Coop, James M. Bower, Kelvin E. Jones
2012 PLoS ONE  
to define bindings for the Python scripting language.  ...  Python is a scripting language that provides rich sets of freely available open source libraries.  ...  Acknowledgments We thank the Computational Biology Initiative at UTSA (http://www.cbi. utsa.edu) for their support when installing, using, and updating G-3 on their computers.  ... 
doi:10.1371/journal.pone.0029018 pmid:22276101 pmcid:PMC3262781 fatcat:mqcysdbsnvculf3e2pojyu6jba

A MARK-UP APPROACH TO SERVICE CREATION

Ivaylo Atanasov, Evelina Pencheva
2007 African Journal of Information & Communication Technology  
Based on ontology analysis of the application domain, language constructions are synthesized and formally defined. Language supporting tools are developed.  ...  The approach functionality is tested by simulation.  ...  These software tools include the following: a language interpreter that makes lexical and syntactical analysis of service logic description and interprets resulting abstract syntax tree; and a translator  ... 
doi:10.5130/ajict.v3i1.305 fatcat:se5i5gekfrgcldzybtq6qa5jgq

Architecture, design and source code comparison of ns-2 and ns-3 network simulators

Juan Luis Font, Pablo Iñigo, Manuel Domínguez, José Luis Sevillano, Claudio Amaya
2010 Proceedings of the 2010 Spring Simulation Multiconference on - SpringSim '10  
Ns-2 and its successor ns-3 are discrete-event simulators. Ns-3 is still under development, but offers some interesting characteristics for developers while ns-2 still has a big user base.  ...  Leaving performance and resources consumption aside, technical issues described in the present paper might help to choose one or another alternative depending of simulation and project management requirements  ...  is used as ns-2 scripting language for writing simulations.  ... 
doi:10.1145/1878537.1878651 fatcat:oxep3mokpvgc5jkpbwqno3pvhq

Collective Knowledge framework to automate, crowdsource, reproduce and share HPC experiments

Grigori Fursin
2019 Zenodo  
by volunteers similar to SETI@home, applying statistical analysis and machine learning, validating results and plotting them on a common scoreboard for open and fair comparison, automatically generating  ...  stacks for deep learning.  ...  Independent API: pull repository for Supercomputing18 paper • Go to scripts directory (ad-hoc *.sh or python scripts, and occasionally Jupyter notebooks) PI-API: find scripts for Supercomputing18 paper  ... 
doi:10.5281/zenodo.2554010 fatcat:moz2g4impjffhmqjghae37zct4

System modeling in SYsML and system analysis in Arena

Ola Batarseh, Leon F. McGinnis
2012 Proceedings Title: Proceedings of the 2012 Winter Simulation Conference (WSC)  
OMG's System Model Language, OMG SysML™, is used to define a platform independent model (PIM) and auto-translate it into an appropriate platform specific model (PSM).  ...  The proposed approach can be used for any analysis tool and application domain.  ...  ., first extend the language with a profile and then create library objects using the language extension.  ... 
doi:10.1109/wsc.2012.6465139 dblp:conf/wsc/BatarsehM12 fatcat:4auihcfpkbhodbop3brttmviaq

A software framework for efficient system-level performance evaluation of embedded systems

Joseph E. Coffland, Andy D. Pimentel
2003 Proceedings of the 2003 ACM symposium on Applied computing - SAC '03  
The Sesame environment provides modeling and simulation methods and tools for the efficient design space exploration of heterogeneous embedded multimedia systems.  ...  We show that Sesame significantly reduces model construction time through the use of modeling component libraries, hierarchy, and advanced model structure description features.  ...  We thank Frank Terpstra and Simon Polstra for their work on YML and PNRunner.  ... 
doi:10.1145/952660.952663 fatcat:vj3gm2yw3fbn5kxidgfsr2aa5a

A software framework for efficient system-level performance evaluation of embedded systems

Joseph E. Coffland, Andy D. Pimentel
2003 Proceedings of the 2003 ACM symposium on Applied computing - SAC '03  
The Sesame environment provides modeling and simulation methods and tools for the efficient design space exploration of heterogeneous embedded multimedia systems.  ...  We show that Sesame significantly reduces model construction time through the use of modeling component libraries, hierarchy, and advanced model structure description features.  ...  We thank Frank Terpstra and Simon Polstra for their work on YML and PNRunner.  ... 
doi:10.1145/952532.952663 dblp:conf/sac/CofflandP03 fatcat:4znqmkdtjjflvo6tyfbdhiulmy

LibKiSAO: a Java library for Querying KiSAO

Anna Zhukova, Richard Adams, Camille Laibe, Nicolas Le Novère
2012 BMC Research Notes  
LibKiSAO also enables simulation tools to handle a wider range of simulation descriptions by determining which of the available methods are similar and can be used instead of the one indicated in the simulation  ...  LibKiSAO can be used by simulation description editors and simulation tools to improve reproducibility of computational simulation tasks and facilitate model re-use.  ...  LibKiSAO can be used by simulation description language manipulating libraries, such as jlibSEDML [11] , and simulation tools, such as COPASI [12] .  ... 
doi:10.1186/1756-0500-5-520 pmid:23006857 pmcid:PMC3532180 fatcat:36flsimdlfaorhzfrz4532uifi

The review of heterogeneous design frameworks/Platforms for digital systems embedded in FPGAs and SoCs

Abdelhakim Alali, Hasna Elmaaradi, Mohammed Khaldoun, Mohamed Sadik
2021 Indonesian Journal of Electrical Engineering and Informatics (IJEEI)  
The objective of this article is to analyze each tool at several levels and to discuss the benefit of each in the scientific community.  ...  This paper illustrates some of them and presents a comparative study between them.  ...  the simulation kernel and C scripts or HLS enrich the simulation tools and the co-simulation for better performance  ... 
doi:10.52549/ijeei.v9i4.3243 fatcat:k76nmwodi5cfxk4c4hk3nojc7e
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