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| Michael Hucka; Frank Bergmann; Stefan Hoops; Sarah M. Keating; Sven Sahle; Darren J. Wilkinson. |
| This is the specification for _Release 1 Candidate_ of *SBML Level 3 Version 1 Core*, an electronic model representation format for systems biology.

SBML is oriented towards describing biological processes of the sort common in research on a number of topics, including metabolic pathways, cell signaling pathways, and many others. SBML is defined neutrally with respect to programming languages and software encoding; however, it is oriented primarily towards allowing models to be encoded using XML. This document contains many examples of SBML models written in XML.

 More information about SBML and this specification is available online at "http://sbml.org/Documents/Specifications/... |
| Tipo: Manuscript |
Palavras-chave: Bioinformatics; Data Standards. |
| Ano: 2010 |
URL: http://precedings.nature.com/documents/4123/version/1 |
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| Michael Hucka. |
| SBML is a machine-readable model representation language for software tools in computational systems biology. By supporting SBML as an input/output format, different tools can all operate on an identical representation of a model, removing opportunities for translation errors and assuring a common starting point for analyses and simulations.

The evolution of SBML continues. The latest iteration is SBML Level 3, a modular language consisting of a Core and optional "packages" that add topic-specific features to the Core to support more specialized models and application areas. In this presentation, I provide a very brief overview of SBML Level 3 activity areas. |
| Tipo: Presentation |
Palavras-chave: Bioinformatics; Data Standards. |
| Ano: 2010 |
URL: http://precedings.nature.com/documents/5011/version/2 |
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| Michael Hucka. |
| SBML is a machine-readable model representation language for software tools in computational systems biology. By supporting SBML as an input/output format, different tools can all operate on an identical representation of a model, removing opportunities for translation errors and assuring a common starting point for analyses and simulations.

The evolution of SBML continues. The latest iteration is SBML Level 3, a modular language consisting of a Core and optional "packages" that add topic-specific features to the Core to support more specialized models and application areas. In this presentation, I provide a very brief overview of SBML Level 3 activity areas. |
| Tipo: Presentation |
Palavras-chave: Bioinformatics. |
| Ano: 2010 |
URL: http://precedings.nature.com/documents/5011/version/1 |
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| Michael Hucka; Andrew M. Finney; Stefan Hoops; Sarah M. Keating; Nicolas Le Novere. |
| With the rise of Systems Biology as a new paradigm for understanding biological processes, the development of quantitative models is no longer restricted to a small circle of theoreticians. The dramatic increase in the number of these models precipitates the need to exchange and reuse both existing and newly created models. The Systems Biology Markup Language (SBML) is a free, open, XML-based format for representing quantitative models of biological interest that advocates the consistent specification of such models and thus facilitates both software development and model exchange.

Principally oriented towards describing systems of biochemical reactions, such as cell signalling pathways, metabolic networks and gene... |
| Tipo: Manuscript |
Palavras-chave: Bioinformatics; Data Standards. |
| Ano: 2007 |
URL: http://precedings.nature.com/documents/58/version/2 |
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| Michael Hucka; Stefan Hoops; Sarah M. Keating; Nicolas Le Novère; Sven Sahle; Darren Wilkinson. |
| With the rise of Systems Biology as a new paradigm for understanding biological processes, the development of quantitative models is no longer restricted to a small circle of theoreticians. The dramatic increase in the number of these models precipitates the need to exchange and reuse both existing and newly created models. The Systems Biology Markup Language (SBML) is a free, open, XML-based format for representing quantitative models of biological interest that advocates the consistent specification of such models and thus facilitates both software development and model exchange.

Principally oriented towards describing systems of biochemical reactions, such as cell signalling pathways, metabolic networks and gene... |
| Tipo: Manuscript |
Palavras-chave: Bioinformatics; Data Standards. |
| Ano: 2008 |
URL: http://precedings.nature.com/documents/2715/version/1 |
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| Michael Hucka. |
| Systems biology has arisen through the convergence of theoretical, computational, and mathematical modeling of systems and the need to understand the wealth of information being rapidly generated in biology. Systems biology by its nature requires collaborations between scientists with expertise in biology, chemistry, computer sciences, engineering, mathematics, and physics. Successful integration of these disciplines depends on bringing to bear both social and technological tools: namely, consortia that help forge collaborations and common understanding, software tools that permit analysis of vast and complex data, and agreed-upon standards that enable researchers to communicate and reuse each other's results in practical and unambiguous ways.... |
| Tipo: Presentation |
Palavras-chave: Biotechnology; Bioinformatics; Data Standards. |
| Ano: 2007 |
URL: http://precedings.nature.com/documents/20/version/1 |
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| Michael Hucka; Sarah M. Keating. |
| The Systems Biology Markup Language (SBML) is a machine-readable model representation language for software tools in computational systems biology. By supporting SBML as an input/output format, different tools can all operate on an identical representation of a model, removing opportunities for translation errors and assuring a common starting point for analyses and simulations. SBML is by no means a perfect format, but it has achieved widespread acceptance as a de facto standard. It is supported worldwide by over 100 software systems (both open-source and commercial). The broad acceptance of a common, open format for exchanging models between software tools is a crucial step towards wider use of quantitative modeling in biology, because it allows... |
| Tipo: Presentation |
Palavras-chave: Biotechnology; Bioinformatics. |
| Ano: 2007 |
URL: http://precedings.nature.com/documents/19/version/1 |
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| Michael Hucka. |
| A cornerstone of systems biology is the use of computational modeling, by which hypotheses can be cast into a quantitative form that can be tested systematically. The use of computational modeling by biologists promises to pave the way for more rigorous analyses of biological functions, and ultimately will lead to new and better treatments for disease.

A crucial enabler for more widespread use of computational modeling in biology is reaching agreement on how to represent, store, and communicate models between software tools. The Systems Biology Markup Language (SBML) project is an effort to create a machine-readable format for representing computational models in biology. By supporting SBML as an input and output... |
| Tipo: Presentation |
Palavras-chave: Biotechnology; Bioinformatics. |
| Ano: 2007 |
URL: http://precedings.nature.com/documents/21/version/1 |
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| Registros recuperados: 16 | |
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