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Humboldt-Universitaet zu Berlin - Collaborative Research Center for Theoretical Biology

Upcoming Round Table Discussion

ROUND TABLE DISCUSSIONS AT THE ITB Invalidenstr. 43, Nordwestfluegel des Naturkundemuseums, first floor

NEXT SESSION: November 28th, 14:00

F.A.Kolpakov: "BioUML - open source extensible workbench for systems biology"
(Biosoft.Ru, Institutskaya 6, Novosibirsk, Russia. Laboratory of Bioinformatics, Design Technological Institute of Digital Techniques, Institutskaya 6, Novosibirsk, Russia.)

BioUML - Biological Universal Modeling Language – is open source extensible Java workbench for systems biology. BioUML meta model provides a formalism for comprehensive description, visualization and simulation of wide range of biological and other complex systems. It splits the system description into three interconnected levels: 1) graph structure - the system structure is described as compartmentalized graph; 2) database level - each graph element can contains reference to database object, additionally arbitrary attributes can be associated with graph element; 3) executable model - any graph element can be element of executable (mathematical) model, for example it can be variable or equation. BioUML workbench is a plugin-based application framework that provides its extensibility and possibility of seamless integration of other tools for systems biology. It consists from a Eclipse platform runtime kernel that supports 'plug-ins' and a set of plug-ins that support database access, diagram editing, and biological systems simulation.

Availability: http://www.biouml.org or http://groups.yahoo.com/group/biouml