G3DV: A new 3D genome browser and experimental data viewer.

2006-01-21

Genomes are tremendous co-evolutionary holistic systems for molecular storage, processing and fabrication of information. Their system-biological complexity remains, however, still largely mysterious, despite immense sequencing achievements and huge advances in the understanding of the general sequential, three-dimensional and regulatory organization. Here, we present the GLOBE 3D Genome Platform a completely novel grid based virtual “paper” tool and in fact the first system-biological genome browser integrating the holistic complexity of genomes in a single easy comprehensible platform: Based on a detailed study of biophysical and IT requirements, every architectural level from sequence to morphology of one or several genomes can be approached in a real and in a symbolic representation simultaneously and navigated by continuous scale-free zooming within a unique three-dimensional OpenGL and grid driven environment. In principle an unlimited number of multi-dimensional data sets can be visualized, customized in terms of arrangement, shape, colour, and texture etc. as well as accessed and annotated individually or in groups using internal or external data bases/facilities. Any information can be searched and correlated by importing or calculating simple relations in real-time using grid resources. A general correlation and application platform for more complex correlative analysis and a front-end for system-biological simulations both using again the huge capabilities of grid infrastructures is currently under development. Hence, the GLOBE 3D Genome Platform is an example of a grid based approach towards a virtual desktop for genomic work combining the three fundamental distributed resources: i) visual data representation, ii) data access and management, and iii) data analysis and creation. Thus, the GLOBE 3D Genome Platform is the novel system-biology oriented information system urgently needed to access, present, annotate, and to simulate the holistic genome comple

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; 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; autofluorescent; proteins; CFP; GFP; YFP; DsRed; fusion protein; in vivo labelling; info:eu-repo/semantics/other

Open access content. Open access content
info:eu-repo/semantics/openAccess

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QGQ oai:repub.eur.nl:77547
urn:hdl:1765/77547
929963652

ERASMUS UNIVERSITEIT ROTTERDAM
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