What is CSynth?

CSynth is a physics based interactive visualisation platform for visualizing the 3D structure of the biological molecules. It is primarily designed to provide an engaging way to explore and understand the complex structure of the genome in 3D by integrating data from next generation sequencing (Hi-C) and modelling. For example, it allows the user to see a traditional Hi-C heat map overlaid with dynamically generated or precomputed 3D structures.

Part of chr16 from white and red blood cells, modelled using CSynth:


It is possible for a reasonably powered desktop or laptop computer to compute potential structures in real-time for a variety of molecule scales, with a high degree of interactivity. The display of 3D structures and overlaying of features (such as gene or enhancer locations) and quantitative signals (such as the results of ChIP-seq experiments) provides a novel way of hypothesis generation and to understand potential effects of chromatin folding in the cell.

CSynth visualizations may also be viewed in Virtual Reality, so we can look at these 3D structures in a completely immersive environment to help gain new insights into complex data sets.

Csynth is published: CSynth: an interactive modelling and visualization tool for 3D chromatin structure (Bioinformatics 2021, 37(7):951-955). CSynth has been exhibited at the Royal Society, schools and various public festivals and is fantastic tool for getting across concepts about the complexities of genome structure.