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1. MIRIAM Identifiers and Resources / 2. Existing Identifier Schemes Nature Precedings
Nick Juty; Camille Laibe; Nicolas Le Novere.
(1) An overview of the MIRIAM identifier scheme is presented, together with a description of the supporting tools and resources which allow its use as a robust cross-referencing framework.
(2) An overview of existing identifier schemes within the life sciences is presented, describing the status of each scheme, the prerequisites that a user must meet to use them, and their limitations.
Tipo: Presentation Palavras-chave: Data Standards.
Ano: 2011 URL: http://precedings.nature.com/documents/6154/version/1
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COMBINE - a vision Nature Precedings
Nicolas Le Novere.
A decade ago, the creation of the Systems Biology Markup Language (SBML) changed the way people exchanged, verified and re-used models in systems biology. The robustness and versatility of this format, coupled to a wide software support, fostered the emergence of an entire area of research centered on model processing such as encoding, annotation, merging, comparison and integration with other datasets. Recently, new languages appeared that complement the model description, such as SED-ML to describe the simulation experiments or SBRML to encode the numerical results. In neuroscience, other fledgling efforts cover for instance multi-compartment neurons with NeuroML, and neuronal networks with NineML. More are needed to cover the wide spectrum of...
Tipo: Presentation Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011 URL: http://precedings.nature.com/documents/5992/version/1
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COMBINE and MIRIAM Registry Nature Precedings
Nicolas Le Novere.
N/A
Tipo: Presentation Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011 URL: http://precedings.nature.com/documents/6152/version/1
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COMBINE - What it is, what it could be Nature Precedings
Nicolas Le Novere.
The 'COmputational Modeling in BIology' NEtwork (COMBINE) is an initiative to coordinate the development of the various community standards and formats for computational models, initially in Systems Biology and related fields. By doing so, it is expected that the federated projects will develop a set of interoperable and non-overlapping standards covering all the aspects of modeling in biology.

Building on the experience of mature projects, which already have stable specifications, software support, user-base and community governance, COMBINE will help foster or support fledging efforts aimed at filling gaps or new needs. As those efforts mature, they may become part of the core set of COMBINE...
Tipo: Presentation Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011 URL: http://precedings.nature.com/documents/6332/version/1
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DARPP-32 is a robust integrator of dopamine and glutamate signals Nature Precedings
Nicolas Le Novere; Eric Fernandez; Renaud Schiappa; Jean-Antoine Girault.
Integration of neurotransmitter and neuromodulator signals in the striatum plays a central role in the functions and dysfunctions of the basal ganglia. DARPP-32 is a key actor of this integration in the GABAergic medium-size spiny neurons, in particular in response to dopamine and glutamate. When phosphorylated by cAMP-dependent protein kinase (PKA) DARPP-32 inhibits protein phosphatase-1 (PP1), whereas when phosphorylated by cyclin-dependent kinase 5 (CDK5) it inhibits PKA. DARPP-32 is also regulated by casein kinases and by several protein phosphatases. These complex and intricate regulations make simple predictions of DARPP-32 dynamic behaviour virtually impossible. We used detailed quantitative modelling of the regulation of DARPP-32 phosphorylation to...
Tipo: Poster Palavras-chave: Neuroscience.
Ano: 2006 URL: http://precedings.nature.com/documents/9/version/1
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Identifiers.org/MIRIAM Registry annotation and cross-referencing framework Nature Precedings
Nick Juty; Camille Laibe; Nicolas Le Novere.
We describe the MIRIAM Registry, which forms a foundation layer database upon which persistent, unambiguous and perennial identifiers of data can be built. We describe the existing MIRIAM URI identifiers, and the newly minted resolvable, parallel forms of these identifiers which use Identifiers.org URLs.
Tipo: Poster Palavras-chave: Data Standards.
Ano: 2011 URL: http://precedings.nature.com/documents/6396/version/1
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Open Standards and Resources in Systems Biology: collaborative scale-up toward virtual life Nature Precedings
Nicolas Le Novere.
The practise of Systems Biology relies on interfaces. Interfaces
between the entities we study: the paradigm moved from a physical
object centric view toward a relationship-centric one; interfaces
between tools: From the retrieval of the primary data to the fine
analysis of a model's behaviour, one uses many tools, more or less
well connected; interfaces between individuals: To build any
non-trivial mechanistic model requires to merge existing work and
gather external expertise.

If we want these interfaces to be generic enough to allow for anybody
to leverage on existing...
Tipo: Presentation Palavras-chave: Biotechnology; Data Standards.
Ano: 2006 URL: http://precedings.nature.com/documents/10/version/1
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Report on the status of SBGN ER and proposed extensions Nature Precedings
Nicolas Le Novere.
The Systems Biology Graphical Notation (SBGN) is an effort to standardize the graphical notation used in maps of biochemical and cellular processes studied in systems biology. SBGN is made up of three orthogonal languages, representing different visions of biological systems. Each language defines a comprehensive set of symbols with precise semantics, together with detailed syntactic rules how maps are to be interpreted. In this presentation I recapitulated why SBGN was developed, and discuss the current state of the Entity Relationships language. I then describe the coming evolutions and the pending issues.
Tipo: Presentation Palavras-chave: Bioinformatics.
Ano: 2010 URL: http://precedings.nature.com/documents/4963/version/1
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Simulation Experiment Description Markup Language (SED-ML) : Level 1 Version 1 Nature Precedings
Dagmar Waltemath; Frank T. Bergmann; Richard Adams; Nicolas Le Novere.
The Simulation Experiment Description Markup Language (SED-ML) is an XML-based format for encoding simulation experiments, following the requirements defined in the MIASE guidelines. SED-ML allows one to define the model to use, the experimental task to run, and which result to produce.
Tipo: Manuscript Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011 URL: http://precedings.nature.com/documents/5846/version/1
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Some thoughts about the future of SBML Nature Precedings
Nicolas Le Novere.
SBML was designed in 2000, merely 2 years after the first official specification of XML. 11 years afterward, the current structure of the language is largely unchanged. Since then, its user base evolved much, as did the whole field of modeling in biology. 
If one wants SBML to evolve in the next decade, it is time to start discussing the basics now. The presentation covers a series of fundamental issues such as SBML coverage, unity of the language, use of elements and attributes etc.
Tipo: Presentation Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011 URL: http://precedings.nature.com/documents/6387/version/1
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Systems Biology Graphical Notation: Entity Relationship language Level 1 (Version 1.2) Nature Precedings
Nicolas Le Novere; Emek Demir; Huaiyu Mi; Stuart Moodie; Alice Villeger.
Standard graphical representations have played a crucial role in science and engineering throughout the last century. Without electrical symbolism, it is very likely that our industrial society would not have evolved at the same pace. Similarly, specialised notations such as the Feynmann notation or the process flow diagrams did a lot for the adoption of concepts in their own fields. With the advent of Systems Biology, and more recently of Synthetic Biology, the need for precise and unambiguous descriptions of biochemical interactions has become more pressing. While some ideas have been advanced over the last decade, with a few detailed proposals, no actual community standard has emerged. The Systems Biology Graphical Notation (SBGN) is a graphical...
Tipo: Manuscript Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011 URL: http://precedings.nature.com/documents/5902/version/1
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Systems Biology Graphical Notation: Process Diagram Level 1 Nature Precedings
Nicolas Le Novere; Stuart Moodie; Anatoly Sorokin; Michael Hucka; Falk Schreiber; Emek Demir; Huaiyu Mi; Yukiko Matsuoka; Katja Wegner; Hiroaki Kitano.
Standard graphical representations have played a crucial role in science and engineering throughout the last century. Without electrical symbolism, it is very likely that our industrial society would not have evolved at the same pace. Similarly, specialised notations such as the Feynmann notation or the process flow diagrams did a lot for the adoption of concepts in their own fields. With the advent of Systems Biology, and more recently of Synthetic Biology, the need for precise and unambiguous descriptions of biochemical interactions has become more pressing. While some ideas have been advanced over the last decade, with a few detailed proposals, no actual community standard has emerged. The Systems Biology Graphical Notation (SBGN) is a graphical...
Tipo: Manuscript Palavras-chave: Biotechnology; Bioinformatics.
Ano: 2008 URL: http://precedings.nature.com/documents/2320/version/1
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Systems Biology Markup Language (SBML) Level 2: Structures and Facilities for Model Definitions Nature Precedings
Michael Hucka; Andrew M. Finney; Stefan Hoops; Sarah M. Keating; Nicolas Le Novere.
Not applicable
Tipo: Manuscript Palavras-chave: Bioinformatics.
Ano: 2007 URL: http://precedings.nature.com/documents/58/version/1
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Systems Biology Markup Language (SBML) Level 2: Structures and Facilities for Model Definitions Nature Precedings
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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