3D-GNOME specifications

Unique identifier:
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:
3D GeNOme Modeling Engine
Restrictions to use:
Programming languages:
C++, Javascript, PHP, Python, R
Computer skills:

3D-GNOME support



  • Przemek Szałaj <>


tutorial arrow
Communicate with other users
Participate in the forum to get support for using tools. Ask questions about technical specifications.
Take part in the discussion
Sign up for free to ask question and share your advices

No open topic.


tutorial arrow
Promote your skills
Define all the tasks you managed and assign your profile the appropriate badges. Become an active member.
Promote your work
Sign up for free to badge your contributorship



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

User review

tutorial arrow
Vote up tools and offer feedback
Give value to tools and make your expertise visible
Give your feedback on this tool
Sign up for free to join and share with the community

0 user reviews

star_border star_border star_border star_border star_border
star star star star star

0 user reviews

star_border star_border star_border star_border star_border
star star star star star

No review has been posted.

Related Tools