SBML Import Export Plug-In

The SBML Import/Export Plug-In allows to import and export files in the Systems Biology Markup Language (SBML).

After installation, the plug-in functionality is available during opening files as well as when importing or exporting the network model. The corresponding file dialogs allow to select Systems Biology Markup Language files (file name suffix *.sbml, *.xml).

Model Export

During export, the SBML plug-in saves the network stoichiometry to file, i.e. each compartment is represented by a <compartment> object, each metabolite is represented by a <species> object and each reaction is represented by a <reaction> object in the SBML file. The <species> objects reference the <compartment> they are located in. The same metabolite in different compartments is exported as different <species> objects in SBML. For all metabolites that are not located in a compartment, the plug-in generates a default compartment in the SBML model.

Each reaction references its educt and product metabolites in <speciesReference> objects in their list of reactants and list of products. The attribute "stoichiometry" of <speciesReference> carries the stoichiometric coefficient of the flux edge. All effector edges of a reaction are represented in the list of modifiers. Furthermore, the "reversibility" attribute of the reaction is exported. Basically, all mandatory attributes are assigned with default values like <reaction fast="false">.

Each network component has an ID that follows the rules of valid SBML identifiers. Usually, the object ID is derived from the components name in the Omix diagram. The name attribute, furthermore, carries the actual name of the network component.

The layout of the Omix network is saved by using the layout package of SBML.

When the Network Constraints Plug-In is active in the exported Omix document, the constraints are also exported to SBML. However, this does not apply for exchange flux constraints, since the SBML specification does not include any concept for exchange fluxes.

When the Kinetic Modeling Plug-In is active in the exported Omix document, the kinetic properties of the model and model components are also exported to SBML. This includes the kinetic laws, global parameters, user-defined functions, kinetic metabolite and compartment properties, initial assignments, rules and events; or easy said, everything that has been specified in the kinetic model. The Kinetic Modeling Plug-In realizes the modeling concept of network kinetics as it is inherent in SBML.

The exported SBML files correspond to the SBML level 3 version 1.

Model Import

The SBML plug-in is also capable to import SBML including kinetics, constraints and layout. Each <species> object in an SBML file is realized as Omix metabolite. Each <reaction> object is interpreted as metabolic reaction in Omix. Also compartments are supported.

Unless no layout information is provided in the SBML file, all reactions and metabolites are not drawn on the drawing area after importing from SBML, but listed in the component view (highlighted red) because, no positioning information is available for the components. You can place the individual items on the drawing area by drag and drop, you can use the layout pattern and motif stamp feature of Omix (see User Manual) and/or you can use the AutoLayout Plug-In in order to arrange the network on the drawing area.

Non-positioned network nodes available in the component view
Non-positioned network nodes available in the component view