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	Provedor de dados Nature Precedings (7) Autor Frank Bergmann (7) Nicolas Le Novère (3) Akira Funahashi (2) Alice C. Villéger (2) Anatoly Sorokin (2) Augustin Luna (2) Emek Demir (2) Falk Schreiber (2) Hiroaki Kitano (2) Huaiyu Mi (2) Martijn P. van Iersel (2) Michael Hucka (2) Michael L. Blinov (2) Mirit I. Aladjem (2) Sarah E. Boyd (2) Stefan Hoops (2) Stuart Moodie (2) Tobias Czauderna (2) Ugur Dogrusoz (2) Yukiko Matsuoka (2) Mais... Palavra-chave Bioinformatics (7) Data Standards (7) Tipo do documento Manuscript (5) Poster (2) Ano 2011 (3) 2010 (4) País United Kingdom (7)		Ordenar por:  Relevância Autor Título Ano Registros recuperados: 7 Primeira ... 1 ... Última SED-ML Script Language Nature Precedings Frank Bergmann. The Simulation Experiment Description Markup Language (SED-ML) is a XML format describing simulation experiments, so that they can be easily exchanged independent of software tools that created them. This document describes the SED-ML Script, a Python based shorthand that makes it easy to create / edit SED-ML documents. Tipo: Manuscript Palavras-chave: Bioinformatics; Data Standards. Ano: 2011 URL: http://precedings.nature.com/documents/6105/version/1 The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core (Release 1 Candidate) Nature Precedings 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 SBML Level 3 Package Proposal: Flux Nature Precedings Frank Bergmann; Brett G. Olivier. This document describes an easy to implement package for storing information related 
to flux balance analysis of SBML Level 3 models (the FBA package). In addition, 
we provide an example of how this package may be implemented and used as a SBML
Level 2 annotation. Tipo: Manuscript Palavras-chave: Bioinformatics; Data Standards. Ano: 2010 URL: http://precedings.nature.com/documents/4236/version/1 SBML Level 3 Package Proposal: Annotation Nature Precedings Dagmar Waltemath; Neil Swainston; Allyson L. Lister; Frank Bergmann; Ron Henkel; Stefan Hoops; Michael Hucka; Nick Juty; Sarah Keating; Christian Knuepfer; Falko Krause; Camille Laibe; Wolfram Liebermeister; Catherine Lloyd; Goksel Misirli; Marvin Schulz; Morgan Taschuk; Nicolas Le Novère. The annotation of Systems Biology Markup Language (SBML) models with semantic terms has been supported for a number of years. The prevalence of such annotated models is growing, with repositories such as Biomodels.net and an increasing number of software tools supporting and encouraging their use and development.

With the increasing use of semantic annotations in the context of systems biology modeling has come the realization that the current Core SBML specification defining their use contains limitations that reduce the scope of metadata that can be captured in such models.

SBML Level 3 provides the facility to propose and develop optional extensions to the Core specification. One such... Tipo: Manuscript Palavras-chave: Bioinformatics; Data Standards. Ano: 2011 URL: http://precedings.nature.com/documents/5610/version/1 LibSBGN: Electronic Processing of SBGN maps Nature Precedings Martijn P. van Iersel; Sarah E. Boyd; Frank Bergmann; Stuart Moodie; Falk Schreiber; Tobias Czauderna; Emek Demir; Nicolas Le Novère; Anatoly Sorokin; Huaiyu Mi; Augustin Luna; Ugur Dogrusoz; Yukiko Matsuoka; Akira Funahashi; Hiroaki Kitano; Mirit I. Aladjem; Michael L. Blinov; Alice C. Villéger. Introduction

Graphical representations of participants and their relationships are essential for exchanging knowledge about complex biological processes. To convey this information clearly and unambiguously, it is necessary to assign standard meanings to symbols and their connectivity. For this purpose, the System Biology Graphical Notation (SBGN) has been developed.

As SBGN is becoming more widely adopted, and used in various software tools, there is an increasing need for a standard file format able to capture the SBGN maps. Exchange using graphics-only file formats (such as SVG) is insufficient, because the biological meaning of elements is lost. There is a need for a toolset that... Tipo: Poster Palavras-chave: Bioinformatics; Data Standards. Ano: 2010 URL: http://precedings.nature.com/documents/4967/version/1 Managing Multiple Parameter Sets in SBML Nature Precedings Frank Bergmann. This document describes the elements of a SBML annotation, for storing multiple parameter sets in an SBML model. A user might wish to store different parameter sets that exhibit interesting behavior of computational models. One common example would be to store parameter values for steady states, or even oscillating regimes. Tipo: Manuscript Palavras-chave: Bioinformatics; Data Standards. Ano: 2010 URL: http://precedings.nature.com/documents/4233/version/1 LibSBGN: Electronic Processing of SBGN maps Nature Precedings Martijn P. van Iersel; Sarah E. Boyd; Frank Bergmann; Stuart Moodie; Falk Schreiber; Tobias Czauderna; Emek Demir; Nicolas Le Novère; Anatoly Sorokin; Huaiyu Mi; Augustin Luna; Ugur Dogrusoz; Yukiko Matsuoka; Akira Funahashi; Hiroaki Kitano; Mirit I. Aladjem; Michael L. Blinov; Alice C. Villéger. Introduction

Graphical representations of participants and their relationships are essential for exchanging knowledge about complex biological processes. To convey this information clearly and unambiguously, it is necessary to assign standard meanings to symbols and their connectivity. For this purpose, the System Biology Graphical Notation (SBGN) has been developed.

As SBGN is becoming more widely adopted, and used in various software tools, there is an increasing need for a standard file format able to capture the SBGN maps. Exchange using graphics-only file formats (such as SVG) is insufficient, because the biological meaning of elements is lost. There is a need for a toolset that... Tipo: Poster Palavras-chave: Bioinformatics; Data Standards. Ano: 2011 URL: http://precedings.nature.com/documents/4967/version/2 Registros recuperados: 7 Primeira ... 1 ... Última

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