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6月17日Dr. Björn Sommer (Monash University)学术报告预告

发布时间:2015-06-16 09:34:11    浏览量:1503


  目:ELLmicrocosmos PathwayIntegration: Basics and New Approaches

报告人:Dr. Björn Sommer (Monash University)

  间:617(周三)15:00

  点:郁文B309

  要:

The CELLmicrocosmos 4.2 PathwayIntegration (CmPI) is a tool for localizing and visualizing biological networks in the context of a virtual cell environment. It consists of two major components.

The first one can be used to import biological networks, such as metabolic pathways and protein-protein interaction networks. Then, a connection to a Bio data warehouse is used to localize the protein- or gene- related data, containing databases like UniProt or Reactome [Cons13, COWH11, TKKH08]. Usually, for each protein a number of subcellular localizations are found. CmPI provides now different analysis methods to predict the subcellular localization in a specific context [SKDA13]. This process can be used to analyze specific metabolic reactions or to predict the localization of disease-related data.

The second major component represents a virtual cell environment which can be used to interactively explore the result of the previous localization process [SKSH10]. It consists of a number of three- dimensional, multi-layered cell component models which were generated based on microscopic data sets.

Moreover, new approaches were integrated to visualize and explore this environment in three dimensions. The underlying Java-based framework can be used for scientific as well as educational purposes.

A new version of this framework will be released soon at:

http://Cm4.CELLmicrocosmos.org

报告人简介:

Björn Sommer received his B.Sc. in Media Informatics and Design in 2004. He extended his experience in the field of cell visualization during his study of Interdisciplinary Media Sciences which he finished with the M.A. in 2006. At that time, he started to establish the CELLmicrocosmos project which was extended by a number of student projects and theses in the last few years. In 2007, he joined the DFG Graduate College Bioinformatics (GK635). From 2009 to 2015 he was working and teaching as a research assistant in the Bio-/Medical Informatics Department at Bielefeld University, giving lectures on Interdisciplinary Cell Visualization and Modeling of Biological Networks. In 2012/2013 he finished his PhD thesis on Integrative Cell Modeling. Currently, he is working as a Research Fellow at Monash University in Melbourne, Australia. Participating in the Immersive Analytics initiative, he is working on the establishment of new analysis and visualization methods for biological data.