Commercial Uses and Applications for Bioinformatics Companies
BioUML technology can be both a tool for your in-house development as well as a basis for a possible cooperation. BioUML is Java framework for systems biology. It spans a comprehensive range of capabilities including access to databases with experimental data, tools for formalized description of biological systems structure and functioning, as well as tools for their visualization and simulations. BioUML technology also can be extended for solving your particular bioinformatics tasks, for example, metabolic pathway or signal transduction pathways simulation. We are currently completing a new version of the BioUML workbench. This workbench is open source software that is distributed under a GNU LGPL license. We have made this decision to popularize BioUML and make it a standard tool for modeling biological or other complex systems. The main change to the BioUML architecture is the use of the Eclipse platform to provide the BioUML workbench extensibility as well as a seamless integration with other tools for systems biology. Thus the BioUML workbench is now a plug-in-based application framework. It consists of a core runtime kernel that supports 'plug-ins' and a set of plug-ins that support database access, diagram editing, and simulation for different complex systems. While the BioUML workbench is free and open source, some plug-ins will be commercial and we hope to develop a commercial plug-in that provides integration between the SRS system developed by LION Bioscience and BioUML. The plug-in will allow customers to use SRS for database search, while BioUML will provide a client interface for database search and to store results in a customer database. More importantly, search results can be visualized as a graph to allow the user to navigate via database hyperlinks.
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Framework for Systems Biology
