Benjamin Kormeier

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For the implementation of the virtual cell, the fundamental question is how to model and simulate complex biological networks. During the last 15 years, Petri nets have attracted more and more attention to help to solve this key problem. Regarding the published papers, it seems clear that hybrid functional Petri nets are the adequate method to model complex(More)
This paper presents a novel bioinformatics data warehouse software kit that integrates biological information from multiple public life science data sources into a local database management system. It stands out from other approaches by providing up-to-date integrated knowledge, platform and database independence as well as high usability and customization.(More)
The understanding of the molecular mechanism of cell-to-cell communication is fundamental for system biology. Up to now, the main objectives of bioinformatics have been reconstruction, modeling and analysis of metabolic, regulatory and signaling processes, based on data generated from high-throughput technologies. Cell-to-cell communication or quorum(More)
BACKGROUND Adverse drug reactions are one of the most common causes of death in industrialized Western countries. Nowadays, empirical data from clinical studies for the approval and monitoring of drugs and molecular databases is available. METHODS The integration of database information is a promising method for providing well-based knowledge to avoid(More)
Drugs are essential for the prevention and treatment of diseases. However, co-administration of multiple drugs may cause serious adverse drug reactions, which are usually known but sometimes unknown. Package inserts of prescription drugs are supposed to contain risks and side effects, but such information is not necessarily complete. At the core of efforts(More)
Detailed investigation of socially important diseases with modern experimental methods has resulted in the generation of large volume of valuable data. However, analysis and interpretation of this data needs application of efficient computational techniques and systems biology approaches. In particular, the techniques allowing the reconstruction of(More)
Standards shape our everyday life. From nuts and bolts to electronic devices and technological processes, standardised products and processes are all around us. Standards have technological and economic benefits, such as making information exchange, production, and services more efficient. However, novel, innovative areas often either lack proper standards,(More)
The CELLmicrocosmos PathwayIntegration (CmPI) was developed to support and visualize the subcellular localization prediction of protein-related data such as protein-interaction networks. From the start it was possible to manually analyze the localizations by using an interactive table. It was, however, quite complicated to compare and analyze the different(More)
VANESA is a modeling software for the automatic reconstruction and analysis of biological networks based on life-science database information. Using VANESA, scientists are able to model any kind of biological processes and systems as biological networks. It is now possible for scientists to automatically reconstruct important molecular systems with(More)