Multi-scale study of 3D Chromatin structure

Date: Wednesday 15th November (14:30 – 18:30h)

Venue: Sala Nicolau d’Olwer, Institut d’Estudis Catalans,
C. del Carme, 47. 08001 Barcelona

This MuG workshop is co-located with the Barcelona BioMed Conference Multidimensional Genomics: The 3D/4D organization of chromatin.




This short workshop will introduce delegates to the Virtual Research Environment (VRE), created by the Multi-scale complex Genomics project (MuG), to facilitate the analysis and interpretation of the 3D and 4D structure genome.

The MuG VRE integrates a range of data from genome annotation to 3D folding and DNA flexibility. Recent studies have shown the role that genome organisation can play in gene expression and the VRE has been designed to provide a way of analysing such data.

The workshop will demonstrate how to use the multi-scale features of the VRE through integrated tools for the study of Nucleosome dynamics and for the analysis of Hi-C data and visualization of 3D models.


he workshop is aimed at both experimental (bench-based) researchers and bioinformaticians; additionally it may be of interest to tool developers who wish to integrate their tools into the VRE.

Participants should have knowledge of genome organisation and the role it can play within the nucleus.

Syllabus, tools and resources

During this workshop participants will learn about:

  • The MuG Virtual Research Environment (VRE) initiative for 3D genomics
  • Nucleosome architecture. NucleR and Nucleosome Dynamics
  • Global chromatin structure from Hi-C, interaction matrices and TADs (topologically associating domains)


Time Topic Speakers
14:30-15:00 MuG VRE presentation Josep Lluis Gelpí (BSC)
15:00-16:00 TADbit and TADkit: Generation of Hi-C interaction matrices from Hi-C data and visualization of 3D models David Castillo (CNAG-CRG)
16:00-16:30 Coffee break
16:30-17:30 Nucleosome Dynamics Ricard Illa (IRB Barcelona)
Jürgen Walther (IRB Barcelona)
17:30-18:30 Conclusions and feedback