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The Promise and Shortcomings of XML as an Interchange Format for Computational Models of Biology

The Promise and Shortcomings of XML as an Interchange Format for Computational Models of Biology Neuroinform (2012) 10:1–3 DOI 10.1007/s12021-011-9136-8 EDITORIAL The Promise and Shortcomings of XML as an Interchange Format for Computational Models of Biology Ivan Raikov & Erik De Schutter Published online: 7 December 2011 Springer Science+Business Media, LLC 2011 A number of XML-based (Extensible Markup Language ) XML, a data exchange language closely related to model description languages have been developed for rep- HTML, is a widely accepted standard for describing resenting models of dynamic biological processes indepen- structured textual data. Its often advertised advantage is dently of simulator platforms. NineML is an effort that that XML documents with different structure can be read aims to provide an unambiguous description of large-scale by the same generic reusable parser. However, XML by neuronal network models. NeuroML is a language for itself does not enable information interchange. Human defining and exchanging descriptions of neuronal cell and readers of XML may be able to guess the meaning of a network models. The Systems Biology Markup Language statement such as (SBML) can represent cell signaling pathways, regulatory <neuron> g ¼ 0:1 <=neuron> networks, and other kinds of biochemical network models. CellML aims for a wider scope of model description and is but to a computer http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Neuroinformatics Springer Journals

The Promise and Shortcomings of XML as an Interchange Format for Computational Models of Biology

Raikov, Ivan; Schutter, Erik
Neuroinformatics , Volume 10 (1) – Dec 7, 2011
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References (10)

Publisher
Springer Journals
Copyright
Copyright © 2011 by Springer Science+Business Media, LLC
Subject
Biomedicine; Neurology; Computational Biology/Bioinformatics; Neurosciences; Computer Appl. in Life Sciences; Bioinformatics
ISSN
1539-2791
eISSN
1559-0089
DOI
10.1007/s12021-011-9136-8
pmid
22147428
Publisher site
See Article on Publisher Site

Abstract

Neuroinform (2012) 10:1–3 DOI 10.1007/s12021-011-9136-8 EDITORIAL The Promise and Shortcomings of XML as an Interchange Format for Computational Models of Biology Ivan Raikov & Erik De Schutter Published online: 7 December 2011 Springer Science+Business Media, LLC 2011 A number of XML-based (Extensible Markup Language ) XML, a data exchange language closely related to model description languages have been developed for rep- HTML, is a widely accepted standard for describing resenting models of dynamic biological processes indepen- structured textual data. Its often advertised advantage is dently of simulator platforms. NineML is an effort that that XML documents with different structure can be read aims to provide an unambiguous description of large-scale by the same generic reusable parser. However, XML by neuronal network models. NeuroML is a language for itself does not enable information interchange. Human defining and exchanging descriptions of neuronal cell and readers of XML may be able to guess the meaning of a network models. The Systems Biology Markup Language statement such as (SBML) can represent cell signaling pathways, regulatory <neuron> g ¼ 0:1 <=neuron> networks, and other kinds of biochemical network models. CellML aims for a wider scope of model description and is but to a computer

Journal

Neuroinformatics – Springer Journals

Published: Dec 7, 2011

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