Challenges for Modeling and Simulation Methods in Systems Biology

Systems Biology is aimed at analyzing the behavior and interrelationships of biological systems and is characterized by combining experimentation, theory, and computation. Dedicated to exploring current challenges, the panel brings together people from a variety of disciplines whose perspectives illuminate diverse facets of Systems Biology and the challenges for modeling and simulation methods

System zur Erfassung und Verarbeitung von Parametern im Rahmen des arbeitsphysiologischen Belastungs-Beanspruchungs-Konzeptes

Das automatisierungstechnische System medLIMS führt zu einer erheblichen Verbesserung in der Versuchsdurchführung und -auswertung in der arbeitsphysiologischen Forschung und Diagnose. Arbeitsabschnitte, Tätigkeiten und Fragebögen werden mit einem Protokollierungssystem (Mobilfunktelefon) erfasst. Physiologische Daten wie Herzfrequenz, EKG, Blutdruck, Atemgasparameter werden von Messgeräten geladen. Die Datenaufbereitung ermöglicht die Visualisierung, die Datenauswertung und -ausgabe. Die Praxistauglichkeit des Systems wurde in mehreren Untersuchungsreihen und Forschungsprojekten bestätigt.Research and practice of occupational medicine is highly improved by the automation system medLIMS (universal structures for data acquisition, management and analysis). A mobile-phone-based logging system is used for self-monitoring of working tasks, activity and questionnaires. Physiological parameters as heart rate, ECG, blood pressure and respiratory parameters could be uploaded. A visualization function and special routines and algorithms for data analysis could be used for analysis. The medLIMS system has been successfully used during several studies and research projects

An evaluation of the Use of XML for Representation, Querying, and Analysis of Molecular Interactions, In: T. Grust et. al. (Eds) Current Trends

Abstract. Currently, biology researchers rapidly generate new information on how genes, proteins and other molecules interact in living organisms. To completely understand the machinery underlying life it is necessary to integrate and analyze these large quantities of data. As one step in this direction, new standards for describing molecular interactions have been defined based on XML. This work evaluates the usage of the XML Query language XQuery for molecular interactions, as it would be of great benefit to the user to work directly on data represented in the new standards. We use and compare a set of available XQuery implementations, eXist, X-Hive, Sedna and QizX/open for querying and analysis on data exported from available databases. Our conclusion is that XQuery can easily be used for the most common queries in this domain but is not feasible for more complex analyses. In particular, for queries containing path analysis the available XQuery implementations have poor performance and an extension of the GTL package clearly outperforms XQuery. The paper ends with a discussion regarding the usability of XQuery in this domain. In particular we point out the need for more efficient graph handling and that XQuery also requires the user to understand the exact XML format of each dataset