SBML Level Research Articles

Updates to the SBML Level 3 Flux Balance Constraints (FBC) package

Updates to the SBML Level 3 Flux Balance Constraints (FBC) package

A generic approach for representing complex structures in biological models

AbstractIncreasingly, the biological modelling community is looking for ways of handling complex and possibly dynamic structures in their models. On the one hand, the pathway-modelling groups (SBML and CellML) seek to move up levels of organisation, while on the other hand the "Virtual X" communities (where X is some organism or organ) need to represent the organisational structure within their object of study. To date, various approaches have been proposed, such as the SBML Level 3 'comp', 'spatial', 'array' and 'dyn' extension packages, and domain-specific elements in languages such as NeuroML, but there is no generic approach intended to be adopted by the various communities.We have designed and implemented such a generic approach in the Simile modelling environment ("http://www.simulistics.com":http://www.simulistics.com). Simile combines a diagrammatic notation for ODEs (in terms of stocks, flows and subsidiary equations), combined with a UML-like notation for representing classes of object and associations between them. No domain-specific concepts are built in, so the object classes can represent anything from molecules to planets, and the associations are specified by the modeller. For example, Simile has no spatial concepts built in, but the modeller can create a class called (perhaps) 'spatial unit', and specify a regular (2- or 4-neighbour) square grid, a 3D array, a hexagonal grid or arbitrary polygons, simply by changing the expression which defines when the association exists between any pair of spatial units. Containership is represented simply by drawing one class inside another (so you can easily show that molecules are inside cells, and cells are inside organs), and objects can be dynamically created and destroyed during the simulation. Because Simile generates compiled C++ code for simulating model behaviour, it is capable of handling very complex models (1 million+ objects).We thus consider that Simile demonstrates the feasibility of a generic approach for handling disaggregation in biological models. We suggest that the widespread adoption of such an approach across the various biological modelling communities would greatly improve the efficiency and effectiveness of future model development as the models become increasingly complex.

SBML Level 3 Hierarchical Model Composition

AbstractA new proposal for incorporating modularity (or 'model composition') into SBML Level 3.

Progress report: SBML Level 3 package FBA

AbstractThe SBML Level 3 "FBA" package is a proposal for an extension to the current Level 3 Core specification that allows for the description and annotation of constraint based models.This allows one to e.g. store information related to flux balance analysis in SBML Level 3 models.

Progress report: SBML Level 3 package FBA

The SBML Level 3 "FBA" package is a proposal for an extension to the current Level 3 Core specification that allows for the description and annotation of constraint based models.This allows one to e.g. store information related to flux balance analysis in SBML Level 3 models.

SBML Level 3 Brief Update

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.The evolution of SBML continues. The latest iteration is SBML Level 3, a modular language consisting of a Core and optional packages that add topic-specific features to the Core to support more specialized models and application areas. In this presentation, I provide a very brief overview of SBML Level 3 activity areas.

The SBML Level 3 Annotation package: an initial proposal

AbstractThe SBML Level 3 Annotation package proposal intends to extend the current Level 3 Core annotations by increasing the range of RDF features supported.Such an extension will support RDF Reification, annotation of SBML attributes, specification of relationships between annotations, negation of annotations and cross-references and cross-element annotations.

Implementation of SBML Level 3 Support within iBioSim

AbstractThis presentation gives details about our experiences when adding SBML Level 3 support to our iBioSim tool.

Implementation of SBML Level 3 Support within iBioSim

Implementation of SBML Level 3 Support within iBioSim

The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core

AbstractThis is the final specification for Release 1 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/":http://sbml.org/Documents/Specifications/.

The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core

This is the final specification for Release 1 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/":http://sbml.org/Documents/Specifications/.

A Unified Approach for Representing Structurally-Complex Models in SBML Level 3

AbstractThe aim of this document is to explore a unified approach to handling several of the proposed extensions to the SBML Level 3 Core specification. The approach is illustrated with reference to Simile, a modelling environment which appears to have most of the capabilities of the various SBML Level 3 package proposals which deal with model structure. Simile (http://www.simulistics.com) is a visual modelling environment for continuous systems modelling which includes the ability to handle complex disaggregation of model structure, by allowing the modeller to specify classes of object and the relationships between them.The note is organised around the 6 packages listed on the SBML Level 3 Proposals web page (http://sbml.org/Community/Wiki/SBML_Level_3_Proposals) which deal with model structure, namely comp, arrays, spatial, geom, dyn and multi. For each one, I consider how the requirements which motivated the package can be handled using Simile's unified approach. Although Simile has a declarative model-representation language (in both Prolog and XML syntax), I use Simile diagrams and equation syntax throughout, since this is more compact and readable than large chunks of XML.The conclusion is that Simile can indeed meet most of the requirements of these various packages, using a generic set of constructs - basically, the multiple-instance submodel, the concept of a relationship (association) between submodels, and array variables. This suggests the possibility of having a single SBML Level 3 extension package similar to the Simile data model, rather than a series of separate packages. Such an approach has a number of potential advantages and disadvantages compared with having the current set of discrete packages: these are discussed in this paper.

A Unified Approach for Representing Structurally-Complex Models in SBML Level 3

The aim of this document is to explore a unified approach to handling several of the proposed extensions to the SBML Level 3 Core specification. The approach is illustrated with reference to Simile, a modelling environment which appears to have most of the capabilities of the various SBML Level 3 package proposals which deal with model structure. Simile (http://www.simulistics.com) is a visual modelling environment for continuous systems modelling which includes the ability to handle complex disaggregation of model structure, by allowing the modeller to specify classes of object and the relationships between them.The note is organised around the 6 packages listed on the SBML Level 3 Proposals web page (http://sbml.org/Community/Wiki/SBML_Level_3_Proposals) which deal with model structure, namely comp, arrays, spatial, geom, dyn and multi. For each one, I consider how the requirements which motivated the package can be handled using Simile's unified approach. Although Simile has a declarative model-representation language (in both Prolog and XML syntax), I use Simile diagrams and equation syntax throughout, since this is more compact and readable than large chunks of XML.The conclusion is that Simile can indeed meet most of the requirements of these various packages, using a generic set of constructs - basically, the multiple-instance submodel, the concept of a relationship (association) between submodels, and array variables. This suggests the possibility of having a single SBML Level 3 extension package similar to the Simile data model, rather than a series of separate packages. Such an approach has a number of potential advantages and disadvantages compared with having the current set of discrete packages: these are discussed in this paper.

SBML Level 3 Package Proposal: Flux

AbstractThis 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.

The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core (Release 1 Candidate)

AbstractThis 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/ ":http://sbml.org/Documents/Specifications/.

CellML2SBML: conversion of CellML into SBML

CellML and SBML are XML-based languages for storage and exchange of molecular biological and physiological reaction models. They use very similar subsets of MathML to specify the mathematical aspects of the models. CellML2SBML is implemented as a suite of XSLT stylesheets that, when applied consecutively, convert models expressed in CellML into SBML without significant loss of information. The converter is based on the most recent stable versions of the languages (CellML version 1.1; SBML Level 2 Version 1), and the XSLT used in the stylesheets adheres to the XSLT version 1.0 specification. Of all 306 models in the CellML repository in April 2005, CellML2SBML converted 91% automatically into SBML. Minor manual changes to the unit definitions in the originals raised the percentage of successful conversions to 96%. http://sbml.org/software/cellml2sbml/. Instructions for use and further documentation available on http://sbml.org/software/cellml2sbml/