Bioinformatics Laboratory
Medical Bioinformatics and e-Bioscience

Department of Clinical Epidemiology,
Biostatistics and Bioinformatics

Academic Medical Center


University of Amsterdam


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e-Bioscience People
Advances in molecular biology provided us with advanced experimental techniques to determine complete genomic sequences, measure gene, protein, and metabolite profiles, determine gene mutations, SNPs, protein interactions and epigenetic effects. Many of these techniques measure on a genome-wide scale and thereby provide a basis for understand the (dynamics of) living organisms. However, if we want to be really able to understand living systems as a basis to develop novel clinical applications we necessarily must go beyond the molecular level. Microscopic and imaging technologies such as microscopy and MRI are used to visualize the (sub)cellular and tissue level. In situ hybridization in combination with microscopy allows the determination of the spatial distribution of expressed proteins. Medical techniques such as electrocardiography provide further information about organ structure and function. Finally, for patients (and healthy persons) a wealth of information about life style, disease history, genetics, plasma metabolite levels, clinical parameters and cell counts is generally stored in hospital databases and (electronic) patient files.

The radical increase of biological and clinical data creates completely new challenges and opportunities in life sciences and transforms life science research in an information science. Heterogeneous (real-time) data from living organisms combined with new and more powerful ways of exploiting this wealth of data, will lead to major advances in our knowledge of the multi-level organisation (and dynamics) of living systems. This requires (i) access and integration of databases, (ii) access and integration of computational models, and (iii) new ways of searching, re-using, communicating and processing this information and models.

E-bioscience
E-bioscience refers to scientific projects within the domain of life sciences that are carried out in distributed collaborations using technologies from the informatics and ICT fields. E-bioscience objectives include the seamless incorporation in biosciences of (large data generating) research facilities such as measurement devices (e.g. mass spectrometers, MRI), of (very) large biological and medical data collections, of compute power and data storage, as well as facilities for scientific visualization and data analysis. Sharing facilities is one of the essential components of e-bioscience. Thus, in contrast to traditional collaborations, e-bioscience makes use of new technologies from informatics in order to increase the efficiency of data (generating) facilities within existing collaborations, and it safeguards access to these facilities and to the associated scientific expertise. When combined with rigorous data modelling and standardization (e.g., by making use of agreed ontologies and data analysis protocols) e-bioscience will increases the quality and reproducibility of the research. The Web and GRID technology will enable e-bioscience. The requirement for a research infrastructure to support large-scale data and computing requirements is not limited to the biological sciences, and the necessary IT research activity has resulted in a global research effort to develop what is termed cyberinfrastructure in the USA, and e-Science in Europe, built upon ‘grid’ technologies.

Experimentation platforms One approach towards implementing the e-bioscience paradigm for life sciences involves the development of so-called experimentation platforms. Such platform comprises a collaborative effort to:

  • Make genomics and bioinformatics expertise available to the whole platform;
  • Import, use and define standards and ontologies;
  • Implement software/databases using those standards and ontologies;
  • Set up comprehensive yet flexible data storage / databases.
  • Integrate databases and computational models

Typically, an experimentation platform comprises collaborating researchers from different disciplines and different institutes. Together they will:

  • Help define standardized and generic approaches (e.g., protocols) for management, processing, analysis and interpretation of (genomics) data;
  • Enlarge consensus and coherence in the field with respect to the use and selection of computational models and data sources;
  • Provide access to research facilities and resources including compute power, storage facilities, computational models and databases;
  • Use generic state-of-the-art Web and GRID based mechanisms to make experimentation platforms accessible to systems biology researchers.

The e-Bioscience research is led by Silvia Olabarriaga .


Grid related stuff: GridBioLab

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Topic revision: r10 - 2010-01-22 - 22:52:11 - PerryMoerland