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semanticSBML 2.0

Advanced user interface for SBML models

Quick Feature Overview

The services on this web site are organised as follows: you can upload your annotated SBML models and load models from the BioModels Database into your model list at the bottom of this page.
The links in each row allow you to display the XML code and the network structure of your model, to add SBO terms for kinetic laws and parameters, to insert standard rate laws with balanced parameters, and to find similar models in BioModels Database, and to download the model again.


Further services are accessible in the sidebar. The link LIBSBANNOTATION allows you to browse our internal biological database libSBAnnotation. The CLUSTER link (requires at least 2 models in the model list) takes you to a page displaying the pairwise similarities of all models in your model list. SHORTHAND SBML allows you to build models easily using the Shorthand SBML notation. REST API links to a documentation of our RESTful web services, NON-SBML leads to an annotation tool for non-SBML models and data sets.

Model Search

screenshot model similarity Search the model repository BioModels Database for models that resemble your query model. Query and target models are compared by their MIRIAM-compliant element annotations.

Usage: Add model to model list, use the 'similar models' link in the Model List overview

Model Clustering

screenshot clustering of models All models from the model list are clustered by their annotation similarities and arranged in a graph. Clustering is disabled if the model list contains less than two models.

Usage: Add models to model list, use the 'CLUSTER' link in the left navigation bar

Model Diff

[screenshot model diff] Align several models in a tree view and detect similarities and conflicts between their elements. Note that this feature is still in an experimental stage.

Usage: Add models to model list, use the 'diff/merge/split selected' button above the Model List overview

Network Graphics

[screenshot display] View network structure of models.

Usage: Add model to model list; for a static network grapghics, click the 'view' icon in the Model List overview. For a flexible network graphics, click the 'SBML Wobble' icon.

Parameter Balancing

screenshot parameter balancing of a model Metabolic network models can be populated with modular rate laws (Liebermeister et al, 2010). Kinetic constants are uploaded in the form of a data table, mapped to the model, and completed or balanced to obtain a full set of kinetic constants appearing in the rate laws. Parameter balancing (Liebermeister and Klipp, 2006) helps to ensure the thermodynamic consistency of the parameter set. Note that this feature is still in an experimental stage.

See the short introduction to parameter balancing
Usage: Add model to model list, use the 'balance parameters' link in the Model List overview

SBML Browse

screenshot html view of a model Export an SBML model and add a link to the SBML Browse stylesheet. This will enable browsers to display your model in a neat and practical way. Courtesy of Neil Swainston and Kieran Smallbone, MCISB.

Usage: Add model to model list, use the show html icon ("SBML Browse") link in the Model List overview

Assignment of SBO Terms

screenshot SBO terms SBO annotations are assigned automatically to kinetic rate laws and the local parameters representing kinetic constants.

Usage: Add model to model list, use the 'add terms' link in the Model List overview

libSBAnnotation

screenshot libSBAnnotation SemanticSBML 2.0 is based on the libSBAnnotation, an internal database of biological entities and relations. You can browse the libSBAnnotation ontology and discover synonyms, cross-references, and chemical relations for your favourite organisms, processes, and chemical entities.

Usage: use the 'LIBSBANNOTATION' link in the left navigation bar

REST API

screenshot REST API Documentation You can access many features of semanticSBML 2.0 through a RESTful interface. This allows you to easily integrate semanticSBML2.0 in your software application or web site.

Usage: use the 'REST API' link in the left navigation bar