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| Nick Juty; Nicolas Le Novère; Dagmar Waltemath; Christian Knuepfer. |
| The use of computational modelling in the description and analysis of biological systems is at the heart of Systems Biology. Besides the information stored in a core model, there is increasingly a need to provide additional semantic information: to identify model components, to assist in biological interpretation of models, to define simulation conditions and to describe simulation results. This information deficit can be addressed through the use of ontologies. We describe here three ontologies created specifically to address the needs of the Systems Biology community in each sub-division, and illustrate their practical use with the 'Repressilator' model (Elowitz and Leibler, 2000). |
| Tipo: Poster |
Palavras-chave: Bioinformatics; Data Standards. |
| Ano: 2010 |
URL: http://precedings.nature.com/documents/5122/version/1 |
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| Ron Henkel; Dagmar Waltemath; Olaf Wolkenhauer. |
| In this poster, we present our experience with techniques for the management of bio-models (i.e. XML-encoded computational models of biological systems) in repositories. These techniques support users to find, access, adapt and then re-submit models - tasks which are essential for the reuse of models in systems biology. Here, we focus on model retrieval, the ranking of search results and concepts to track the history of a model through version control. These concepts have so far not been sufficiently addressed in existing systems.
To validate our techniques, we have been implemented a framework called Sombi. The underlying database called mDB is tailored towards a fine-grained storage of the model and its annotations. The design is... |
| Tipo: Poster |
Palavras-chave: Bioinformatics; Data Standards. |
| Ano: 2011 |
URL: http://precedings.nature.com/documents/6325/version/1 |
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| Anna Zhukova; Dagmar Waltemath; Nick Juty; Camille Laibe; Nicolas Le Novère. |
| To enable the accurate and repeatable execution of a computational simulation task, it is important to identify both the algorithm used and the initial setup. These minimum information requirements are described by the MIASE guidelines. Since the details of some algorithms are not always publicly available, and many are implemented only in a limited number of simulation tools, it is crucial to identify alternative algorithms with similar characteristics that may be used to provide comparable results in an equivalent simulation experiment. The Kinetic Simulation Algorithm Ontology (KiSAO) was developed to address this issue by describing existing algorithms and their inter-relationships through their characteristics and parameters. The use of KiSAO in... |
| Tipo: Presentation |
Palavras-chave: Bioinformatics; Data Standards. |
| Ano: 2011 |
URL: http://precedings.nature.com/documents/6330/version/1 |
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| Ron Henkel; Dagmar Waltemath; Andre Peters; Lukas Endler; Nicolas le Novère. |
| *Aim*

The increasing number of computational models of biological systems demands a better support for search facilities. One possible improvement is to enable ranked retrieval of models based on existing model annotation. 
 
Applying existing Information Retrieval (IR) techniques to computational models, we have implemented a new search strategy in BioModels Database. In this search strategy the index of search terms contains not only the model descriptions in the database, but is expanded by including ontological and textual information about a model and its constituents retrieved from external sources. To add more background knowledge, we additionally index the abstracts of... |
| Tipo: Poster |
Palavras-chave: Bioinformatics. |
| Ano: 2010 |
URL: http://precedings.nature.com/documents/4985/version/1 |
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