3D-GNOME specifications

Unique identifier:
OMICS_11874
Interface:
Web user interface
Input data:
Users submit a bedpe (paired-end BED format) file containing the locations and strengths of long range contact points, and 3D-GNOME simulates the structure and provides a convenient user interface for further analysis. Alternatively, a user may generate structures using published ChIA-PET data for the GM12878 cell line by simply specifying a genomic region of interest.
Database management system:
MySQL
Stability:
Stable
Name:
3D GeNOme Modeling Engine
Restrictions to use:
None
Programming languages:
C++, Javascript, PHP, Python, R
Computer skills:
Basic
Maintained:
Yes

3D-GNOME support

Documentation

Maintainer

  • Przemek Szałaj <>

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Publications

Institution(s)

Centre of New Technologies, University of Warsaw, Warsaw, Poland; Center for Bioinformatics and Data Analysis, Medical University of Bialystok, Bialystok, Poland; I-BioStat, Hasselt University, Hasselt, Belgium; The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA; Department of Genetics and Genome Sciences, UConn Health, Farmington, CT, USA; Faculty of Pharmacy, Medical University of Warsaw, Warsaw, Poland

Funding source(s)

National Leading Research Centre in Bialystok; European Union under the European Social Fund; Polish National Science Centre [2014/15/B/ST6/05082, 2013/09/B/NZ2/00121]; European Cooperation in Science and Technology action [COST BM1405, BM1408]; Director Innovation Fund from Jackson Laboratory and NCI [R01 CA186714]; The Roux family as a Florine Roux Endowed Chair and Professor in Genomics and Computational Biology

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