Demos A2 - Bioinformatics Semantic Web

Type inference in the Biochemical Abstract Machine BIOCHAM

Type checking and type inference are important concepts and methods of programming languages and software engineering. In this demonstration, we illustrate the application of these concepts to systems biology. More specifically, we consider the Systems Biology Markup Language SBML and the Biochemical Abstract Machine BIOCHAM with their repositories of models of biochemical systems. We study three type systems: one for checking or inferring the functions of proteins in a reaction model, one for checking or inferring the activation and inhibition effects of proteins in a reaction model, and another one for checking or inferring the topology of compartments or locations. Through some examples, we show that the analysis of biochemical models by type inference provides accurate and useful information. In particular, we are currently developing an interface between SBML/BIOCHAM objects and the ontologies on the web, that uses the protein function types.

The demo has been developed in co-operation with I3.

http://contraintes.inria.fr/BIOCHAM

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Home Contact Participants Members Working Groups Rule Markup Policies Composition & Typing Query Evolution Time & Location Bioinformatics Personalisation Activities Education Technology Transfer Assessment Standardization Network Organisation Search on	Demos A2 - Bioinformatics Semantic Web Type inference in the Biochemical Abstract Machine BIOCHAM Type checking and type inference are important concepts and methods of programming languages and software engineering. In this demonstration, we illustrate the application of these concepts to systems biology. More specifically, we consider the Systems Biology Markup Language SBML and the Biochemical Abstract Machine BIOCHAM with their repositories of models of biochemical systems. We study three type systems: one for checking or inferring the functions of proteins in a reaction model, one for checking or inferring the activation and inhibition effects of proteins in a reaction model, and another one for checking or inferring the topology of compartments or locations. Through some examples, we show that the analysis of biochemical models by type inference provides accurate and useful information. In particular, we are currently developing an interface between SBML/BIOCHAM objects and the ontologies on the web, that uses the protein function types. The demo has been developed in co-operation with I3. http://contraintes.inria.fr/BIOCHAM Printer friendly version [html] go to top of page	Annual Meeting 2007 Welcome Programme Demos Check In Accommodation
last modification : Tue Oct 14 19:04:29 2008