Scientists in the Multiscale Complex Genomics (MuG) Consortium are working on new cloud-based computational infrastructure to support and improve the existing genome analysis tools. The beta-version of the Virtual Research Environment (VRE) was presented for the first time in Cambridge in April. MuG is a Horizon 2020 project coordinated by IRB Barcelona Group Leader Modesto Orozco.
Genomics is not what it used to be. At the beginning of the century, the challenge for scientists was to obtain the genome sequence of an organism, the so-called “1D code.” Today, scientists have a more dynamic 3D vision of genomes.
Their new focus is on the spatial organisation of the genome, and how this time-dependent organisation affects gene regulation and expression. This field of research is called 3D/4D genomics, and its protagonist is called chromatin—the complex of DNA, RNA and proteins that chromosomes are made of.
Chromatin and the study of its folded states lie at the heart of the Horizon 2020 MuG (Multiscale Complex Genomics) Project, which was launched in 2016 and is coordinated by UB Professor and Group Leader Modesto Orozco.
The estimated 3,000 scientists worldwide working in the field consider 3D/4D genomics “one of the biggest challenges for biology and biomedicine in the next decade,” as the MuG team explains on their website. But to guarantee significant advances, they need to overcome the differences in data formats, lack of standardisation in data analysis and simulation tools.
Orozco and members of his Molecular Modelling and Bioinformatics Lab are working to develop a Virtual Research Environment (VRE), a cloud-based computational infrastructure to support the deployment of software tools for genome analysis. 3D/4D genomics experts had the opportunity to test the potential of the beta version of the MuG VRE computer platform in a training workshop held in Cambridge, UK, on 10-11 April, called “Multi-scale study of 3D chromatin structure.”
“One of the main objectives of MuG is to provide the 3D/4D genomics community with a useful compilation of all the tools that scientists currently use at different scales (from DNA to nucleus structures), and with workflows that help connect them,” explains Anna Montras, the MuG project officer.
At the workshop, the prototype was applied to real biological cases, and the VRE developers and end users discussed how it was working and the next steps of its development. “It is great to see highly talented researchers in various disciplines working together towards the same objective and even more to see that the results will facilitate the work of many other researchers in the field in the future,” says Montras.
Among the participants in the meeting, were PhD students Jürgen Walther and Ricard Illa and Postdoctoral Fellow Federica Battistini. Walther appreciates the interest that lab scientists have shown in the VRE. “This is a good sign because it reflects a synergy between theory and experiment,” he says. The Experimental Bioinformatics Laboratory Director Isabelle Brun-Heath, Postdoc Adam Hospital, PhD student Diana Buitrago, and web developer Genís Bayarri are also working on the development of VRE.
Scientists in the MuG Consortium are currently channelling efforts into improving the prototype to achieve the stability and functionality required for public release to end users, which is expected later this year.
In the meantime, Orozco is busy co-organising a Barcelona BioMed Conference on Multidimensional Genomics: The 3D/4D organization of chromatin, with Marc Martí-Renom (CNAG-CRG/ICREA, Barcelona) and Giacomo Cavalli (IGH-CNRS, Montpellier, France). To be held on 13–15 November and in collaboration with the BBVA Foundation, the conference will bring together 20 speakers and 150 selected young international scientists. The deadline for applications is 31 July.
If you are interested in joining the MuG community, you can find more information on the consortium’s website.