Todd, Stephen; Todd, Peter; McGowan, Simon J; Hughes, James R; Kakui, Yasutaka; Leymarie, Frederic Fol; Latham, William and Taylor, Stephen. 2021. CSynth: An Interactive Modelling and Visualisation Tool for 3D Chromatin Structure. Bioinformatics, 37(7), pp. 951-955. ISSN 1367-4803 [Article]

	Text btaa757.pdf - Accepted Version Permissions: Administrator Access Only Available under License Creative Commons Attribution Non-commercial. Download (424kB)
Preview	Text btaa757.pdf - Published Version Available under License Creative Commons Attribution Non-commercial. Download (269kB) | Preview

Abstract or Description

Motivation
The 3D structure of chromatin in the nucleus is important for gene expression and regulation. Chromosome conformation capture techniques, such as Hi-C, generate large amounts of data showing interaction points on the genome but these are hard to interpret using standard tools.

Results
We have developed CSynth, an interactive 3D genome browser and real-time chromatin restraint-based modeller to visualise models of any chromosome conformation capture (3C) data. Unlike other modelling systems CSynth allows dynamic interaction with the modelling parameters to allow experimentation and effects on the model. It also allows comparison of models generated from data in different tissues / cell states and the results of third-party 3D modelling outputs. In addition, we include an option to view and manipulate these complicated structures using Virtual Reality (VR) so scientists can immerse themselves in the models for further understanding. This VR component has also proven to be a valuable teaching and public engagement tool.

Availability
CSynth is web based and available to use at https://csynth.org.

Item Type:	Article
Identification Number (DOI):	https://doi.org/10.1093/bioinformatics/btaa757
Additional Information:	Supplementary information Supplementary data are available at Bioinformatics online. Funding: Medical Research Council (MC_UU_12025) and Wellcome Trust (106130/Z/14/B).
Departments, Centres and Research Units:	Computing
Dates:	Date Event 19 August 2020 Accepted 31 August 2020 Published Online April 2021 Published
Item ID:	29368
Date Deposited:	26 Oct 2020 09:10
Last Modified:	28 Apr 2022 12:42
Peer Reviewed:	Yes, this version has been peer-reviewed.
URI:	https://research.gold.ac.uk/id/eprint/29368

View statistics for this item...

Edit Record (login required)