NDLI: Genome3D: A viewer-model framework for integrating and visualizing multi-scale epigenomic information within a three-dimensional genome

Content Provider	IEEE Xplore Digital Library
Author	Arndt, W. Asbury, T.M. Zheng, W.J. Mitman, M. Jijun Tang
Copyright Year	2011
Description	Author affiliation: Bioinformatics Division, Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC (Arndt, W.; Asbury, T.M.; Zheng, W.J.) \|\| Department of Computer Science Engineering, University of South Carolina, Columbia, SC (Mitman, M.; Jijun Tang)
Abstract	New technologies permit the measurement of many types of genomic and epigenomic information at scales ranging from the atomic to nuclear. Much of this new data is structural in nature and challenging to coordinate with existing data formats. There is an increasing need to integrate and visualize disparate data sets in order to reveal structural relationships not apparent when viewing these data formats separately. We have developed the Genome3D software package in order to integrate and display epigenomic data within the context of a three-dimensional physical model of the human genome. To our knowledge, this is the first such tool developed to visualize human genome in three dimensions. Here we describe the major features of Genome3D and discuss our multi-scale data framework using a representative basic physical model. Additionally, utilities to generate demonstration models of common chromosome interaction scenarios derived from High-C or CHIA-PET analysis are under development. These models are compatible with existing annotation data formats and can demonstrate common situations where one or more chromosomes are arranged such that two or more interaction sites appear in close proximity. These models can be used to directly create publication images without resorting to intermediate use of image editing software. Availability: http://genomebioinfo.musc.edu/Genome3D/Index.html
Starting Page	936
Ending Page	938
File Size	755511
Page Count	3
File Format	PDF
ISBN	9781457716126
e-ISBN	9781457716133
DOI	10.1109/BIBMW.2011.6112510
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2011-11-12
Publisher Place	USA
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Genomics DNA Data visualization Data models Three dimensional displays Bioinformatics Biological cells
Content Type	Text
Resource Type	Article

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
6	Contents and Copyright Issues	Queries related to content curation and copyright issues	content@ndl.gov.in
7	National Digital Library of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
8	Digital Preservation Centre (DPC)	Assistance with digitizing and archiving copyright-free printed books	dpc@ndl.gov.in
9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

Genome3D: A viewer-model framework for integrating and visualizing multi-scale epigenomic information within a three-dimensional genome

Genome3D: A viewer-model framework for integrating and visualizing multi-scale epigenomic information within a three-dimensional genome

VisCHAINER: Visualizing Genome Comparison

A Color Visualization Method to the Isochores of DNA Sequences

Exploring genomes with a game engine

Immersive Visualization for Genome Exploration and Analysis

The Development of Urban Landscape Three-Dimensional Visualization System

ABySS-Explorer: Visualizing Genome Sequence Assemblies

Bacterial gene neighborhood investigation environment: A large-scale genome visualization for big displays

Genome3D: A viewer-model framework for integrating and visualizing multi-scale epigenomic information within a three-dimensional genome

Similar Documents

Genome3D: A viewer-model framework for integrating and visualizing multi-scale epigenomic information within a three-dimensional genome

Genome3D: A viewer-model framework for integrating and visualizing multi-scale epigenomic information within a three-dimensional genome

VisCHAINER: Visualizing Genome Comparison

A Color Visualization Method to the Isochores of DNA Sequences

Exploring genomes with a game engine

Immersive Visualization for Genome Exploration and Analysis

The Development of Urban Landscape Three-Dimensional Visualization System

ABySS-Explorer: Visualizing Genome Sequence Assemblies

Bacterial gene neighborhood investigation environment: A large-scale genome visualization for big displays

Genome3D: A viewer-model framework for integrating and visualizing multi-scale epigenomic information within a three-dimensional genome