http://precedings.nature.com/tags/SBML Recently posted documents tagged with 'SBML' 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.2009.3124.1 BioModels Database (http://www.ebi.ac.uk/biomodels/) is a free resource for storing, viewing and retrieving published, peer-reviewed, quantitative models of biochemical and cellular systems. As a storage format, BioModels Database uses the Systems Biology Markup Language (SBML), but also allows submission and export of models in various other commonly used formats.To offer scientists reliable information, models are curated to comply with the MIRIAM (Minimal Information Requested In the Annotation of biochemical Models) standard. This curation process involves verification of the model structure, the parameter and variable values and its mathematical relations. Furthermore reproduction of results in the reference publication is checked.The different elements of the models are extensively annotated with references to controlled vocabularies and links to other databases, to allow for identification and search. Those references and links are provided in the exported SBML files as a URN (Uniform Resource Name), identifying the data-type and the data-set, and a qualifier, indicating the relation between the element and the referenced data-set. The URNs follow the MIRIAM scheme and are resolved, for instance to URLs, using the Web Services of MIRIAM Resources (http://www.ebi.ac.uk/miriam/). http://dx.doi.org/10.1038/npre.2009.3124.1 Wed, 22 Apr 2009 12:58:44 UTC Curation and annotation for BioModels Database, a resource of published quantitative kinetic models doi:10.1038/npre.2009.3124.1 2009-05-06 Lukas Endler Nature Precedings 2009-04-22T12:58:44Z Poster Bioinformatics http://creativecommons.org/licenses/by/3.0/ http://dx.doi.org/10.1038/npre.2009.3093.1 Semantic annotations in SBML (systems biology markup language) enable computer programs to check and process biochemical models based on their biochemical meaning. Annotations are an important prerequisite for model merging, which would be a major step towards the construction of large-scale cell models. The software tool semanticSBML allows users to check and edit MIRIAM annotations and SBO terms, the most common forms of annotation in SBML models. It uses a large collection of biochemical names and database identifiers to support modellers in finding the right annotations. Annotated SBML models can also be built from lists of chemical reactions. In model merging, semanticSBML suggests a preliminary merged model based on MIRIAM annotations in the original models. This model provides a starting point for manually aligning the elements of all input models. To resolve conflicting element properties, conflicts are highlighted and categorised. The user can navigate through the models, change the matching of model elements, check the conflicts between them and decide how they should be resolved. Alternatively, the software can resolve all conflicts automatically, selecting each time the attribute value from the input model with highest priority.URL: http://www.semanticsbml.org/ http://dx.doi.org/10.1038/npre.2009.3093.1 Mon, 20 Apr 2009 18:02:26 UTC SemanticSBML: a tool for annotating, checking, and merging of biochemical models in SBML format doi:10.1038/npre.2009.3093.1 2009-04-20 Wolfram Liebermeister Nature Precedings 2009-04-20T18:02:26Z Poster Bioinformatics http://creativecommons.org/licenses/by/3.0/ http://dx.doi.org/10.1038/npre.2009.3085.1 SABIO-RK (http://sabio.villa-bosch.de/SABIORK/) is a curated, web-accessible database for modellers and wet-lab scientists to get comprehensive information about biochemical reactions and their kinetic properties. It integrates data from different origin in order to facilitate the access to reaction kinetics data and corresponding information. Since most of the kinetic data is exclusively found in the literature SABIO-RK offers data manually extracted from the literature and related information obtained from other publicly available biological databases. For instance, the kinetic data are related to reactions, organisms, tissues and cellular locations. The type of the kinetic mechanism and corresponding rate equations are presented together with their parameters and experimental conditions. Additionally, SABIO-RK also includes data about the detailed mechanism for some of the reactions based on literature information. This not only includes the graphical representation of the mechanism but also the single reaction steps with their corresponding kinetic data.The data in SABIO-RK are extracted manually from literature and the selection of articles is not restricted to any biological source (e.g. organisms or organism classifications). All the data are curated and annotated by biological experts using a web-based input interface. To support the curation process and data integration we have implemented different constraints in the input interface and offer several controlled vocabularies as lists of values, as well as additional semi-automatic consistency checks to avoid errors and inconsistencies in the database. Controlled vocabularies and annotations to external resources and ontologies were used to identify and relate the data to their biological context. All these efforts to unify and integrate the data augment the content and the semantics of the SABIO-RK database entries to enable a comprehensive understanding and comparison of the data for the user.SABIO-RK can be accessed via a web-based user interface or via web-services. The user interface allows the definition of complex queries by specifying reactions and reaction participants, kinetic parameters, environmental conditions or literature sources. Links to other databases based on the annotations of thedata enable the user to gather further information for example for compounds, reactions or proteins. Selected data about reactions and their kinetics, together with their annotations, can be exported in SBML (Systems Biology Mark-up Language), a widely used standard exchange format in systems biology. http://dx.doi.org/10.1038/npre.2009.3085.1 Mon, 20 Apr 2009 09:32:22 UTC SABIO-RK: Curated Kinetic Data of Biochemical Reactions doi:10.1038/npre.2009.3085.1 2009-04-21 Ulrike Wittig Nature Precedings 2009-04-20T09:32:22Z Presentation Chemistry Bioinformatics http://creativecommons.org/licenses/by/3.0/ http://dx.doi.org/10.1038/npre.2008.2715.1 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 regulation etc., SBML can also be used to encode any kinetic model. SBML offers mechanisms to describe biological components by means of compartments and reacting species, as well as their dynamic behaviour, using reactions, events and arbitrary mathematical rules. SBML also offers all the housekeeping structures needed to ensure an unambiguous understanding of quantitative descriptions.This is Release 1 of the specification for SBML Level 2 Version 4, describing the structures of the language and the rules used to build a valid model. SBML XML Schema and other related documents and software are also available from the SBML project web site, http://sbml.org/. http://dx.doi.org/10.1038/npre.2008.2715.1 Wed, 24 Dec 2008 15:41:15 UTC Systems Biology Markup Language (SBML) Level 2: Structures and Facilities for Model Definitions doi:10.1038/npre.2008.2715.1 2008-12-24 Nicolas Le Novère Nature Precedings 2008-12-24T15:41:15Z Manuscript Bioinformatics http://creativecommons.org/licenses/by/3.0/ http://precedings.nature.com/documents/58/version/2 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 regulation etc., SBML can also be used to encode any kinetic model. SBML offers mechanisms to describe biological components by means of compartments and reacting species, as well as their dynamic behaviour, using reactions, events and arbitrary mathematical rules. SBML also offers all the housekeeping structures needed to ensure an unambiguous understanding of quantitative descriptions.This specification presents the structures of the language and the rules used to build a valid model. SBML XML Schema and other related documents and software are also available from the SBML project web site, http://sbml.org/. http://precedings.nature.com/documents/58/version/2 Mon, 05 Nov 2007 16:05:47 UTC Systems Biology Markup Language (SBML) Level 2: Structures and Facilities for Model Definitions hdl:10101/npre.2007.58.2 2009-01-10 Nicolas Le Novere Nature Precedings 2007-11-05T16:05:47Z Manuscript Bioinformatics http://creativecommons.org/licenses/by/2.5/ http://dx.doi.org/10.1038/npre.2007.1281.1 Pathway curation is a powerful tool for systematically associating gene products with functions. Reactome (www.reactome.org) is a manually curated human pathway knowledgebase describing a wide range of biological processes in a computationally accessible manner. The core unit of the Reactome data model is the Reaction, whose instances form a network of biological interactions through entities that are consumed, produced, or act as catalysts. Entities are distinguished by their molecular identities and cellular locations. Set objects allow grouping of related entities. Curation is based on communication between expert authors and staff curators, facilitated by freely available data entry tools. Manually curated data are subjected to quality control and peer review by a second expert. Reactome data are released quarterly. At release time, electronic orthology inference performed on human data produces reaction predictions in 22 species ranging from mouse to bacteria. Cross-references to a large number of publicly available databases are attached, providing multiple entry points into the database. The Reactome Mart allows query submission and data retrieval from Reactome and across other databases. The SkyPainter tool provides visualization and statistical analysis of user supplied data, e.g. from microarray experiments. Reactome data are freely available in a number of data formats (e.g. BioPax, SBML). http://dx.doi.org/10.1038/npre.2007.1281.1 Wed, 31 Oct 2007 21:20:37 UTC Reactome – a knowledgebase of human biological pathways doi:10.1038/npre.2007.1281.1 2009-05-07 Peter D'Eustachio Nature Precedings 2007-10-31T21:20:37Z Poster Molecular Cell Biology Bioinformatics http://creativecommons.org/licenses/by/2.5/ http://precedings.nature.com/documents/58/version/1 Not applicable http://precedings.nature.com/documents/58/version/1 Mon, 18 Jun 2007 08:52:34 UTC Systems Biology Markup Language (SBML) Level 2: Structures and Facilities for Model Definitions hdl:10101/npre.2007.58.1 2007-06-18 Nicolas Le Novere Nature Precedings 2007-06-18T08:52:34Z Manuscript Bioinformatics http://creativecommons.org/licenses/by/2.5/ 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/