http://precedings.nature.com/tags/structured%20data%20formats Recently posted documents tagged with 'structured data formats' 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.2007.21.1 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 format, different software tools can operate on the same representation of a model, removing chances 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 over 100 software systems supporting it today.In this presentation, I will discuss the current state of SBML, including recent developments such as this year’s finalization of Version 2 of SBML Level 2. I will also survey some of the software tools that support SBML, and related projects that have arisen to support more effective use of computational models. Lastly, I will discuss expected future developments in SBML. http://dx.doi.org/10.1038/npre.2007.21.1 Mon, 22 Jan 2007 01:52:11 UTC The Systems Biology Markup Language (SBML): Where It’s Been and Where It’s Going doi:10.1038/npre.2007.21.1 2007-01-22 Michael Hucka Nature Precedings 2007-01-22T01:52:11Z Presentation Biotechnology Bioinformatics http://creativecommons.org/licenses/by/2.5/ 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/ http://dx.doi.org/10.1038/npre.2007.19.1 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 researchers to build upon each other’s work with greater ease and accuracy.SBML can encode models consisting of biochemical entities (species) linked by reactions to form networks. An important principle is that models are decomposed into explicitly-labeled constituent elements, the set of which resembles a verbose rendition of chemical reaction equations. The representation deliberately does not cast the model directly into a set of differential equations or other specific interpretation of the model. The formalisms in SBML allows a wide range of biological phenomena to be modeled, including metabolism, cell signaling, gene regulation, and more. Significant flexibility and power comes from the ability to define arbitrary formulae for the rates of change of variables as well as the ability to express other constraints mathematically.This tutorial covered the latest edition of SBML, which is Level 2 Version 2, finalized in September 2006. Topics covered include the basic common principles in SBML as well the changes introduced in Level 2 Version 2. We also discussed software tools for programmers, in particular libSBML. http://dx.doi.org/10.1038/npre.2007.19.1 Mon, 22 Jan 2007 01:48:17 UTC The Systems Biology Markup Language (SBML) Level 2 Version 2 doi:10.1038/npre.2007.19.1 2007-01-22 Michael Hucka Nature Precedings 2007-01-22T01:48:17Z Presentation Biotechnology Bioinformatics http://creativecommons.org/licenses/by/2.5/