The GLOBE 3D Genome Platform
Towards a novel System-Biological Paper-Tool to integrate the Huge Complexity of Genome Organization and Function - Presentation
The combination of genome sequence and structure, its annotation and experimental data in an accessible and comprehensible way is a major challenge. Increasingly, there are a large number of extremely divergent data sets: the sequence itself, genes, regulatory regions, various forms of reoccurring sequence features and clone sets etc. Currently, one possibility to represent this information in a visual form - and thus to reveal its scientific meaning - is to use genome browsers such as "Ensembl" or "The UCSC Genome Browser". These browsers have been beneficial in the understanding of the complex organization of genomes. However, there are also huge limitations concerning their focus on linear presentation, standardized input and data bank accessibility. Also customisability by a remote user with special requirements is difficult. Therefore, the GLOBE-Consortium has developed the next generation genome viewer - the GLOBE 3D-Viewer - to visualize multi-dimensional data sets from various sources in an easy intuitive manor while accounting for the complexity of genome organization. Together with an easily accessible data-warehouse for archiving (un- )published experimental data and the Erasmus Computing Grid (ECG) for fast interactive large-scale (correlative) analysis the GLOBE-Consortium creates an intuitive holistic environment for genome research. Thus, the GLOBE 3D-Viewer sets the new standard to integrate complex genomic data sets within a single holistic display system and thus is major advance for scientific and clinical genome research.
|Keywords||Genome, genomics, genome organization, genome architecture, structural sequencing, architectural sequencing, systems genomics, coevolution, holistic genetics, genome mechanics, genome function, genetics, gene, regulation, replication, transcription, repair, homologous recombination, simultaneous co-transfection, cell, division, mitosis, metaphase, interphase, cell nucleus, nuclear structure, nuclear organization, chromatin density, distribution, nuclear morphology, chromosome territories, subchromosomal domains, chromatin loop, aggregates, chromatin rosettes, chromatin loops, chromatin fibre, chromatin density, persistence length, spatial, distance measurement, histones, H1.0, H2A, H2B, H3, H4, mH2A1.2, DNA sequence, complete sequenced, genomes, molecular transport, obstructed diffusion, anomalous diffusion, percolation, long-range correlations, fractal analysis, scaling analysis, exact yard-stick dimension, box-counting dimension, lacunarity dimension, local nuclear dimension, nuclear diffuseness, parallel super computing, grid computing, volunteer computing, Brownian Dynamics, Monte Carlo, fluorescence in situ hybridization, confocal laser scanning microscopy, fluorescence correlation spectroscopy, super resolution microscopy, spatial precision distance microscopy, auto-, fluorescent proteins, CFP, GFP, YFP, DsRed, fusion protein, in vivo labelling, information browser, visual data, base access, holistic viewing system, integrative data management, extreme visualization, three-dimensional, virtual environment, virtual paper tool|
|Conference||HealthGRID 2009, International Health Grid Organization, dbb Forum Berlin, 29th June - 1st July, 2009.|
Knoch, T.A, Lesnussa, M, Kepper, F.N, Eussen, H.J.F.M.M, & Grosveld, F.G. (2009, June 29). The GLOBE 3D Genome Platform. Presented at the HealthGRID 2009, International Health Grid Organization, dbb Forum Berlin, 29th June - 1st July, 2009. Retrieved from http://hdl.handle.net/1765/78198