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Workshop 1: Distributed, High-Performance and Grid Computing in Computational Biology (GCCB 2006)

Workshop 2:
Genome Annotation: a BioSapiens Network of Excellence Initiative

Workshop 1: Distributed, High-Performance and Grid Computing in Computational Biology (GCCB 2006)

Werner Dubitzky, University of Ulster
Assaf Schuster, Technion - Israel Institute of Technology
Peter Sloot, University of Amsterdam
Michael Schroeder, Dresden University of Technology
Mathilde Romberg, University of Ulster

Click here for the detailed program.

Click here to submit a paper to the workshop.

Context. Biology and biotechnology encompass research and development in areas such as biophysics, biochemistry, biology, neuroscience, biomedicine, and environmental sciences. A common theme among biology and biotechnology disciplines is the desire to understand the stimuli-response mechanisms of biological entities, systems and processes at different levels of organization (molecular, sub-cellular, cellular, inter-cellular, tissue, organism, population, environment, ecosystem). As natural phenomena are being probed and mapped in ever-greater detail, life scientists and biotechnologists are generating an increasingly growing amount of data and information in electronic format.

To organize, share, integrate and analyze these data and information, and to use them in order to model and simulate the underlying biological systems and processes has become an essential part of modern life science research and development. The conceptual and technical challenges involved in these tasks are considerable, so much that an entire discipline, computational biology and bioinformatics, has emerged to address these challenges. Increasingly, the tasks, applications and computer systems involved are characterized by large and complex-structured data and by considerable requirements for compute power and storage (primary and secondary memory). In addition, since many of the relevant communities, systems, instruments and (computing) resources are geographically widely distributed, it has become necessary to seamlessly share such computing resources through computer networks.

In order to tackle the arising computational challenges, computational biologists and bioinformaticians need to leverage, develop and deploy distributed, high-performance and grid computing technologies. While certain distributed, high-performance and grid computing technologies and methodologies can be used and applied in a context-independent way across many disciplines, the unique features and characteristics encountered in biology and biotechnology poses additional constraints and challenges; some of these are listed below.

Challenges. However, distributed, high-performance and grid computing approaches in biology and biotechnology are faced with a number of challenges that render such endeavors much more complex and intricate than development and deployment of these technologies in classical application areas such as physics, engineering, manufacturing, transport, construction, automotive, etc., and conventional business areas (retail, marketing, customer relationship management and finance). Some of the added complexities arise from the

Conceptual complexity of biological knowledge and the methodologies used in biology and biotechnology;
Need to understand biological systems and processes at a detailed mechanistic, systemic and quantitative level across several levels of organization (ranging from molecules, to cells, populations, and the environment);
Growing availability of high-throughput data from genomics, transcriptomics, proteomics and metabolomics;
Widespread use of image data in biological research and development (microscopy, NMR, MRI, PET, X-ray, CT, etc.)
Increasing number of investigations studying the properties and dynamic behavior of biological systems and processes using computational techniques (molecular dynamics, QSAR/QSPR, simulation of gene-regulatory, signaling and metabolic networks, protein folding/unfolding, etc);
Requirement to combine (in an ad hoc fashion) data, information and compute services (e.g., sequence alignments) residing on systems geographically distributed around the world;
Variety of different technologies, instruments, infrastructures and systems used in life science R&D;
Huge variety of information formats and frequent addition of new formats arising from new experimental protocols, instruments and phenomena to be studied;
Large and growing number of investigated biological and biomedical phenomena;
Fact that life science R&D is based heavily on the use of distributed and globally accessible computing resources (databases, knowledge bases, model bases, instruments, text repositories, compute-intensive services).

Topics. The GCCB Workshop will bring together computational biologists, bioinformaticians and life scientists who have researched and applied distributed, high-performance and grid computing technologies in the context of computational biology and bioinformatics. The Workshop will discuss innovative work in progress and important new directions. Contributions of interest will address topics related to the development, deployment, application and evaluation of distributed, high-performance and grid computing technologies in the context of the following computational biology and bioinformatics areas:

Analysis, modeling and simulation of processes like pathways, biological networks, pharmacodynamics, pharmacokinetics, protein-protein interaction, transcription initiation, and whole systems;
Computational approaches to biological entities and processes, e.g. to functional genomics, proteomics, metabolomics, epidemiology, epigenetics, biodiversity, ecosystems, neuroscience;
Linkage and sequence analysis;
Molecule design;
Prediction of protein-, DNA-, and RNA-structure, toxicity, AMDE (absorption, distribution, metabolism and excretion), etc.;
Protein folding and unfolding;
Information retrieval and knowledge discovery including data and text mining;
Management and integration of biological data and information;
Distributed ontologies and semantic Web/grid approaches;
Visualization and image management and processing of biological data;
Grid tools for computational biology and bioinformatics;
Distributed systems and databases;
Development of diagnostic, prognostic and therapeutic (drugs) technologies;
Large-scale (storage, computation, components/systems) studies in computational biology and bioinformatics.

Workshop 2: Genome Annotation: a BioSapiens Network of Excellence Initiative
This one-day workshop will bring together an international group of experts to discuss functional aspects of genome annotation. The workshop goals are to create an open forum to discuss current problems on function annotation, to foster the analysis of key scientific issues in function prediction, and to promote collaboration among scientists interested in the development of computational methods in this key area of molecular biology.

Click here for the detailed program.

Click here to submit a paper to the workshop.

Nir Ben-Tal
Department of Biochemistry
George S. Wise Faculty of Life Sciences
Tel Aviv University, Israel
Tel. +972 3 640-6709
Fax +972 3 640-6834