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tmp survey information

layout - Ralph Gauges

  • Latest URL: http://otto.bioquant.uni-heidelberg.de/sbml/level2/20050425/SBMLLayoutExtension-20050425.pdf
  • Need: While SBML provides programs with the possibility to reliably exchange the mathematical description of chemical reaction networks, there is currently no general way to encode graphical information on the described models. However, often it is easier and more intuitive to provide an overview of a reaction model using some type of diagram instead of a list of reactions. To be able to store arbitrary types of diagrams together with the mathematical description, the layout (and render) extension(s) have been developed.
  • Approach: The current approach of the layout extension is very simple: the user can specify one or more graphs consisting of nodes (bounding boxes) and edges (curves). These nodes and edges in the layout can be associated with elements from the core SBML model which enable programs to display analysis results, e.g. elementary flux modes, from a model using the diagrams provided by the layout extension.
    The layout extension is supplemented by the render extension (separate package) which provides ways of associating style information with the elements in a layout. This way arbitrary types of diagrams on models can be encoded and stored within SBML files.

render - Ralph Gauges

  • Latest URL: http://otto.bioquant.uni-heidelberg.de/sbml/level2/20110525/sbml-render-specification-20110525.pdf
  • Need: As described in the proposal for the layout extension (above), core SBML does not provide a way to encode diagrams on reaction networks. While the layout extension provides a way to encode the general layout of such a reaction network using nodes and edges, it does not provide a way to encode how the individual nodes and edges are to be displayed. However, in a lot of diagrams important information elements associated with the nodes and edges is provided by the way they are rendered, SBGN being a prominent example of such a diagram. With the render extension we provide ways of specifying style information on nodes and edges of a layout in a very general way, allowing users to store arbitrary diagrams within SBML files.
  • Approach: The render extension provides a set of simple graphical primitives (rectangles, curves, ellipses, images and text elements) which can be combined in arbitrary ways and supplemented with additional information like stroke color, fill color etc. to form styles which can be associated with elements from the layout extension. Each layout can be associated with several styles allowing the user to render one layout in several different ways, e.g. highlighting different elements of the layout.

multi - Nicolas Le Novere

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comp - Lucian Smith

  • Latest URL: http://sbml.org/Community/Wiki/SBML_Level_3_Proposals/Hierarchical_Model_Composition
  • Need: For the last ten years, people have discussed and proposed ideas for how best to nest SBML models and link them together. The ability to do this would promote model re-use and the development of model libraries designed to be used as parts of larger models. It would also allow the creation of models along semantic and physical modular lines to promote understanding by end users of the model.
  • Approach: This current proposal divides the SBML document into a model to be instantiated, and model definitons which can themselves be instantated as submodels within other models. It also contains rules for connecting elements within those models hierarchically, with elements in containing models overridding elements in submodels.

qual - Claudine Chaouiya and Denis Thieffry

  • Latest URL: http://sbml.org/Community/Wiki/SBML_Level_3_Proposals/Qualitative_Models
  • Need: Quantitative methods for modelling biological networks require an in-depth knowledge of the biochemical reactions and their stoichiometric and kinetic parameters. In many cases, this knowledge is missing. This has led to the development of several qualitative modelling methods using information such as gene expression data coming from functional genomic experiments. Qualitative models are typically based on the definition of regulatory or influence graph. The components of these models differ from species and reactions used in current SBML models. For example, qualitative models typically associate discrete levels of activities with entity pools; the processes involving them cannot be described as reactions per se but rather as transitions between states. Boolean networks, logical models and some Petri nets are the most used qualitative formalisms in biology. Despite differences from traditional SBML models, it is desirable to bring these classes of models under a common format scheme. The purpose of this Qualitative Models package for SBML Level 3 is to support qualitative models into SBML.
  • Approach: This current proposal defines new elements for SBML models to account for the specificities of qualitative species and associated transitions. It was defined mainly to allow the representation of logical models (Boolean or multi-valued), but it should also cover the needs for Petri nets and symbolic qualitative

models.

distrib - Darren Wilkinson

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spatial - Jim Schaff

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fbc - Brett Olivier

  • Need: Constraint based modelling is a widely used methodology used to analyse and study biological networks on both a small and whole organism (genome) scale. As constraint based models are generally underdetermined, i.e. few or none of the kinetic rate equations and related parameters are known, it is important that such a model definition includes a mechanism to define parameters such as model objective functions, flux bounds and constraints ... this is, currently, not possible in SBML Level 2 or Level 3 core.

    The question of how to encode constraint based (historically stoichiometric/FBA/steady-state) models in SBML is not new. However, with the advances in the methods used to construct GSR scale models and the wider adoption of constraint based modelling in biotechnological/medical applications has led to a rapid increase in both the number of models being constructed and the tools used to analyse them. Faced with such rapidly growing diversity, the need for a standardised model description and exchange format is vital.

    As the core model components (e.g. species, reactions, stoichiometry) can already be effectively described in SBML it seems prudent to use as a basis for such an extension. In addition, the modularised extension mechanism now available in SBML Level 3 provides an ideal platform for such an implementation.
  • Approach: The current proposal extends Level 3 core with the addition of new model elements such as 'fluxBounds' and 'objectives' that allows bounds to be set on the model fluxes at steady state and allows definition of pre-defined objective functions in addition we (re)introduce species attributes such as 'charge' and 'chemicalFormula' which allows the incorporation of reaction balancing information.


groups - Mike Hucka

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annot - Neil Swainston

  • Latest URL: http://precedings.nature.com/documents/5610/version/1
  • Need: The ability to assign semantic annotations to elements within SBML documents, essentially through use of the Resource Descriptor Framework (RDF) was introduced in Level 2. Since then, there has been some uptake of this approach, with curated models in Biomodels and recent genome-scale metabolic networks applying annotations to unambiguously identify SBML elements with Unique Resource Identifiers (URIs) as specified by the MIRIAM standard. However, it is recognised that the existing Level 2 and Level 3 Core annotation recommendations contain a number of limitations that prevent the full functionality of RDF to be used. The Annotation proposal attempts to correct some of these limitations by fully supporting RDF, while also providing the facility to extend the current level of annotations from SBML elements to SBML attributes.
  • Approach: This current proposal suggests the use of "new" annotation elements (in a new namespace, to distinguish them from existing L2 and L3 Core annotations) in which unrestricted collections of RDF statements may be specified. These new annotation elements can be assigned to any SBML element, and can be used to refer to either the element itself or any of its attributes. Due to the lifting of restrictions on the RDF statements permitted, existing methods such as RDF Reification, allowing the chaining of RDF statements to encode more complex concepts, will be supported. While all valid RDF will be supported, it is intended that a simplified libSBML API package extension will be provided, allowing the use of the Level 3 Annotation package by non-expert users.

req - Lucian Smith

  • Latest URL: http://sbml.org/Community/Wiki/SBML_Level_3_Proposals/Required_Elements
  • Need: When a package declares that it is 'required', the model reader knows that the math of the model has changed, but not how, without understanding the specification of the package itself. If the <math> subelement of something in the SBML core has been overridden by something in a package, the 'required elements' package can tell the model consumer what specifically has been overridden, and whether the original math can be used to create a reasonable alternative model.
  • Approach: Attaching two attributes to any element in the SBML core with a <math> subelement.

arrays - [open--Bruce or Mike?]

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dyn - Chris Meyers

  • Latest URL: http://sbml.org/Community/Wiki/SBML_Level_3_Proposals/Dynamic_Structures
  • Need: SBML's structural constructs are currently fixed: it is not possible to define the creation or removal of species, compartments, reactions or other components from within a model definition. To simulate the creation or destruction of compartments, one currently has to use tricks. For example, a model could define all the compartments it could ever need and use variables to indicate which compartments are actually "active" at any given timeā€”but this would only work if the total number needed is known at the beginning of a simulation. In defense of SBML's limitation in this area, it should be pointed out that we only know of perhaps two or three software tools that support dynamic structures today. Still, it is clear that some modeling problems would benefit from this capability. Dynamic structures would be used to encapsulate portions of a model that need to change dynamically during a simulation. Within SBML this may correspond to adding, modifying or removing some collection of compartments, species, reactions, rules, etc. Biologically, this might correspond to cell birth, differentiation, cell death, as well as exocytosis and endocytosis; experimentally this might correspond to the administration of a protocol during a simulation, such as turning a laser or the application of a hormone or toxin.
  • Approach: Dynamic structures are usually associated with compound structures such as lists, sets, and arrays. For example, cell division might be represented by adding a new cell to a list or set of cells, or increasing the dimension of an array of compartments. In SBML, if the compartment is of a particular compartment type structure and has associated with it a collection of basic SBML elements, such as species and reactions, these should be automatically added to the model. Similarly, cell death might be represented by the removal of a cell from a set. We have already made preliminary proposals for both arrays and (separately) sets in SBML. Arrays and sets are alternative proposals for roughly the same kind of capability, and it is likely that only one will ultimately be chosen as a supported SBML Level 3 language extension.

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