http://precedings.nature.com/tags/SBGN Recently posted documents tagged with 'SBGN' Nature Publishing Group en Nature Precedings http://precedings.nature.com/images/header_logo.gif http://precedings.nature.com http://dx.doi.org/10.1038/npre.2009.3724.1 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, specialized 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 representation crafted over several years by a community of biochemists, modellers and computer scientists. Three orthogonal and complementary languages have been created, the Process Descriptions, the Entity Relationships and the Activity Flows. Using these three idioms a scientist can represent any network of biochemical interactions, which can then be interpreted in an unambiguous way. The set of symbols used is limited, and the grammar quite simple, to allow its usage ranging from textbooks and teaching in high schools to peer reviewed articles in scientific journals. The first level of the SBGN Activity Flow language has been publicly released. Shared by the communities of biochemists, genomic scientists, theoreticians and computational biologists, SBGN languages will foster efficient storage, exchange and reuse of information on signaling pathways, metabolic networks and gene regulatory maps. http://dx.doi.org/10.1038/npre.2009.3724.1 Mon, 07 Sep 2009 19:43:48 UTC Systems Biology Graphical Notation: Activity Flow language Level 1 doi:10.1038/npre.2009.3724.1 2009-09-07 Huaiyu Mi Nature Precedings 2009-09-07T19:43:48Z Manuscript Bioinformatics http://creativecommons.org/licenses/by/3.0/ http://dx.doi.org/10.1038/npre.2009.3719.1 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 representation crafted over several years by a community of biochemists, modellers and computer scientists. Three orthogonal and complementary languages have been created, the Process Descriptions, the Entity Relationships and the Activity Flows. Using these three idioms a scientist can represent any network of biochemical interactions, which can then be interpreted in an unambiguous way. The set of symbols used is limited, and the grammar quite simple, to allow its usage in textbooks and its teaching directly in high schools. The first level of the SBGN Entity Relationship language has been publicly released. Shared by the communities of biochemists, genomicians, theoreticians and computational biologists, SBGN languages will foster efficient storage, exchange and reuse of information on signalling pathways, metabolic networks and gene regulatory maps. http://dx.doi.org/10.1038/npre.2009.3719.1 Fri, 04 Sep 2009 15:21:22 UTC Systems Biology Graphical Notation: Entity Relationship language Level 1 doi:10.1038/npre.2009.3719.1 2009-09-04 Nicolas Le Novère Nature Precedings 2009-09-04T15:21:22Z Manuscript Bioinformatics http://creativecommons.org/licenses/by/3.0/ http://dx.doi.org/10.1038/npre.2007.20.1 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. In this presentation, I will discuss several international projects (SBML, SBGN, and BioModels.net) aimed at addressing the last issue.An important prerequisite for effective sharing of computational models is reaching agreement on how to communicate them, both between software and between humans. The Systems Biology Markup Language (SBML) project is an effort to create a machine-readable format for representing computational models at the biochemical reaction level. By supporting SBML as an input and output format, different software tools can operate on the same representation of a model, removing chance for errors in translation and assuring a common starting point for analyses and simulations. SBML has become the most successful effort in this direction so far, with nearly 100 software tools supporting it today.A recently-created sister project is the Systems Biology Graphical Notation (SBGN) project. It addresses the issue of consistent human communication, by attempting to add more rigor and consistency to the graphical network diagrams that often accompany published research on models of biological reaction systems. The real payoff will come when more people and software adopt such a common visual notation and it becomes as familiar to them as circuit schematics are to electronics engineers.Finally, when developing and publishing computational models, it is only natural to want to put them into a database. The BioModels.net project is an effort to (1) provide a free, centralized, publicly-accessible database of human-curated computational models in SBML and other structured formats; (2) define agreed-upon standards for model curation; and (2) define agreed-upon vocabularies for annotating models with connections to biological data resources. http://dx.doi.org/10.1038/npre.2007.20.1 Mon, 22 Jan 2007 01:50:17 UTC Evolving standards and infrastructure for systems biology: SBML, SBGN, and BioModels.net doi:10.1038/npre.2007.20.1 2007-01-22 Michael Hucka Nature Precedings 2007-01-22T01:50:17Z Presentation Biotechnology Bioinformatics http://creativecommons.org/licenses/by/2.5/