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A Binary XML for Scientific Applications

K. Chiu, T. Devadithya, W. Lu, A. Slominski
First International Conference on e-Science and Grid Computing (e-Science'05)  
In this paper we present a binary XML format and implementation for scientific data called Binary XML for Scientific Applications (BXSA).  ...  These results challenge the prevailing practice of handling control and data separately in scientific applications, with web services for control and specialized binary formats for data.  ...  Therefore, we have developed a specific binary XML format called Binary XML for Scientific Applications (BXSA) (pronounced "bix-sah").  ... 
doi:10.1109/e-science.2005.1 dblp:conf/eScience/ChiuDLS05 fatcat:ljxuaaytvvfp3ncmsqpex6jlpq

Python and XML for Agile Scientific Computing

Michele Vallisneri, Stanislav Babak
2008 Computing in science & engineering (Print)  
Here, they describe how Python and XML came to the rescue.  ...  to string together a lot of existing and new code.  ...  impression is that the situation is still very fluid, and it might be too early to embrace binary XmL in mainstream scientific applications.  ... 
doi:10.1109/mcse.2008.20 fatcat:vtt5g4z7njbzxlul7jzewqznnq

Rapid Real-Time Interdisciplinary Ocean Forecasting Using Adaptive Sampling and Adaptive Modeling and Legacy Codes: Component Encapsulation Using XML [chapter]

Constantinos Evangelinos, Robert Chang, Pierre F. J. Lermusiaux, Nicholas M. Patrikalakis
2003 Lecture Notes in Computer Science  
Legacy applications of this form are encapsulated using XML. We present a method that uses XML documents to describe the parameters for executing a binary.  ...  Such binaries, that are most common in scientific applications, expect a standard input stream, maybe some command line options, a set of input files and generate a set of output files as well as standard  ...  By providing a detailed XML description for a binary, this binary is treated as a black-box.  ... 
doi:10.1007/3-540-44864-0_39 fatcat:yi4acglphrde3axhqe2dgl63su

SOAP-binQ: high-performance SOAP with continuous quality management

Balasubramanian Seshasayee, K. Schwan, P. Widener
2004 24th International Conference on Distributed Computing Systems, 2004. Proceedings.  
This paper aims to make SOAP useful for high end or resource-constrained applications. The basic idea is to replace SOAP's XML/Ascii-based parameter representations with binary ones.  ...  Such client-and network-aware data filtering has been shown useful for a variety of applications and platforms, including to control the data volumes required for remote 3D visualizations across the Internet  ...  SOAP-binQ: Sample Applications We present three applications -a scientific application, an image application, and a commerical application , and describe a fourth, a visualization application, that are  ... 
doi:10.1109/icdcs.2004.1281579 dblp:conf/icdcs/SeshasayeeSW04 fatcat:kexz4xc7kjc3pnf7r5xazeouh4

GPML: an XML-based standard for the interchange of genetic programming trees

Tiantian Dou, Yuri Kaszubowski Lopes, Peter Rockett, Elizabeth A. Hathway, Esmail Saber
2019 Genetic Programming and Evolvable Machines  
We propose a Genetic Programming Markup Language (GPML), an XML-based standard for the interchange of genetic programming trees, and outline the benefits such a format would bring.  ...  The coupling of the end-application and the GP training/test software is a major inconvenience, especially in embedded systems.  ...  In a given application, an XML file has to conform to a specified structure.  ... 
doi:10.1007/s10710-019-09370-4 fatcat:qwotg3oxxvbntbeseuq53bwfe4

An ontology driven architecture for derived representations of macromolecular structure

D. S. Greer, J. D. Westbrook, P. E. Bourne
2002 Bioinformatics  
An object metamodel based on a standard scientific ontology has been developed and used to generate a CORBA interface, an SQL schema and an XML representation for macromolecular structure (MMS) data.  ...  In addition to the interface and schema definitions, the metamodel was also used to generate the core elements of a CORBA reference server and a JDBC database loader.  ...  Support for this effort was provided through the Protein Data Bank (Grant DBI-9814284) and the National Partnership for Advanced Computational Infrastructure (Grant ACI-9619020).  ... 
doi:10.1093/bioinformatics/18.9.1280 pmid:12217927 fatcat:zyj2opr6t5ex3giuu7hrr6ztny

Mapping Physical Formats to Logical Models to Extract Data and Metadata: The Defuddle Parsing Engine [chapter]

Tara D. Talbott, Karen L. Schuchardt, Eric G. Stephan, James D. Myers
2006 Lecture Notes in Computer Science  
In this paper, we describe a complementary approach -a general capability for articulating the format of arbitrary textual and binary data using a logical data model, expressed in XML-Schema, which can  ...  This work is based on the draft specification for the Data Format Description Language and our open source "Defuddle" parser.  ...  However, extending XML technology to handle arbitrary un-tagged, binary and textual files would make the extensive XML tools applicable to scientific data and provide analogous benefits.  ... 
doi:10.1007/11890850_9 fatcat:uddrdxg6tnfebjvptk4yg5vuqq

XCEDE: An Extensible Schema for Biomedical Data

Syam Gadde, Nicole Aucoin, Jeffrey S. Grethe, David B. Keator, Daniel S. Marcus, Steve Pieper
2011 Neuroinformatics  
Currently at version 2.0, the XCEDE schema serves as a specification for the exchange of scientific data between databases, analysis tools, and web services.  ...  The XCEDE (XML-based Clinical and Experimental Data Exchange) XML schema, developed by members of the BIRN (Biomedical Informatics Research Network), provides an extensive metadata hierarchy for storing  ...  Many thanks to NITRC for hosting development sandboxes for XCEDE and supporting tools.  ... 
doi:10.1007/s12021-011-9119-9 pmid:21479735 pmcid:PMC3836560 fatcat:unuoxb4rcfgxdk3ph4ymd7krxe

Optimized communication using the SOAP infoset for mobile multimedia collaboration applications

S. Oh, H. Bulut, A. Uyar, W. Wu, G. Fox
2005 Proceedings of the 2005 International Symposium on Collaborative Technologies and Systems, 2005.  
We provide a flexible representation of binary encoding with a description file for message format and include a QoS framework in the architecture, such as reliability and security.  ...  However, there are performance limitations if we use the current SOAP approaches to integrate mobile applications with Web Services based collaboration systems, especially for multimedia applications.  ...  Lab at Indiana University researched SOAP negotiation and binary data transfers [2] , [3] for the scientific computing field.  ... 
doi:10.1109/iscst.2005.1553291 dblp:conf/cts/OhBUWF05 fatcat:ad3eocxmsbbahlgu7xddb4jor4

XDTM: The XML Data Type and Mapping for Specifying Datasets [chapter]

Luc Moreau, Yong Zhao, Ian Foster, Jens Voeckler, Michael Wilde
2005 Lecture Notes in Computer Science  
We use XML Schema as a type system for expressing the logical structure of datasets and define a separate notion of a mapping that combines declarative and procedural elements to describe physical representations  ...  We present the XDTM design and also the results of application experiments with an XDTM prototype.  ...  XSIL (XSIL: Java/XML for Scientific Data) comprises an XML format for scientific data objects and a corresponding Java object model, so that XML files can be read, transformed, and visualized [14] .  ... 
doi:10.1007/11508380_51 fatcat:plko4guv3bbm5fxpx2omtjmydu

Extending LabVIEW Aptitude for Distributed Controls and Data Acquisition [chapter]

Luciano Catani
2011 Practical Applications and Solutions Using LabVIEW™ Software  
, or they are proprietary so that, for instance, integration with the control system of a nearby experiment or with a bigger apparatus, that could have been 400 Practical Applications and Solutions Using  ...  Fig.2 shows an example of messages passed between a client and a server in the XML-RPC protocol. They include header with declarations and methodCall or method Response fields.  ...  Binary data, for instance, can be enclosed with the XML CDATA tag, a special tag for processing data that isn't going to be parsed during XML processing.  ... 
doi:10.5772/20416 fatcat:nbcfleo23rdxvpvy64aho7znqu

Standardization of the MSA/MAS/AMAS Hyper-Dimensional File Format

Aaron Torpy, Mike Kundmann, Nick Wilson, Colin MacRae, Nestor J. Zaluzec
2017 Microscopy and Microanalysis  
The XML file is used to define the layout of the binary data in the HMSA file in a human-readable format, which would not be possible if this information was stored within the binary file itself.  ...  The XML file is divided into three sections. The first section is the 'header', which may be used to record non-scientific metadata such as the creation date and owner.  ... 
doi:10.1017/s1431927617006122 fatcat:7sfxzl4zqzdinmizrwh3s7xjxu

Bootstrapping to a semantic grid

J. Schwidder, T. Talbott, J. Myers
2005 CCGrid 2005. IEEE International Symposium on Cluster Computing and the Grid, 2005.  
The Scientific Annotation Middleware (SAM) is a set of components and services that enable researchers, applications, problem solving environments (PSE) and software agents to create metadata and annotations  ...  Developed starting in 2001, SAM allows applications to encode metadata within files or to manage metadata at the level of individual relationships as desired.  ...  Acknowledgements This work was supported as part of the Scientific Annotation Middleware (SAM) project.  ... 
doi:10.1109/ccgrid.2005.1558551 dblp:conf/ccgrid/SchwidderTM05 fatcat:xsa5jijblje5xe6gtui46q42t4

Migration to Intermediate XML for Electronic Data (MIXED): Repository of Durable File Format Conversions

René Van Horik, Dirk Roorda
2011 International Journal of Digital Curation  
It can be used, for example, for the binary DataPerfect format, that was used on a large scale about twenty years ago, and for which no existing XML schema could be found.  ...  Data Archiving and Networked Services (DANS), the Dutch scientific data archive for the social sciences and humanities, is engaged in the Migration to Intermediate XML for Electronic Data (MIXED) project  ...  But we expect that, over time, the SDFP format will change at a much slower rate than the individual binary application formats, which makes the application of the MIXED framework an appropriate option  ... 
doi:10.2218/ijdc.v6i2.200 fatcat:ivwuovc3yzfqvkxtyubkhiij7u

An evaluation of binary xml encoding optimizations for fast stream based xml processing

R. J. Bayardo, D. Gruhl, V. Josifovski, J. Myllymaki
2004 Proceedings of the 13th conference on World Wide Web - WWW '04  
This paper provides an objective evaluation of the performance impacts of binary XML encodings, using a fast stream-based XQuery processor as our representative application.  ...  Our goal is to provide a deeper understanding of the performance impacts of binary XML encodings in order to clarify the ongoing and often contentious debate over their merits, particularly in the domain  ...  We have attempted to remain impartial regarding the debate over the need for a standard binary encoding format for XML.  ... 
doi:10.1145/988672.988719 dblp:conf/www/BayardoGJM04 fatcat:hyzjr2xr6ndzpokfnbl75weh7q
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