Experiences from the Joint MuG-BioExcel Workshop: Multiscale Nucleic Acids Simulations


On Friday 22nd of June, BioExcel joined forces with Multiscale Complex Genomics (MuG) project running a workshop on Multiscale Nucleic Acids Simulations. The workshop was presented as a co-located event with the International Society of Quantum Biology and Pharmacology (ISQBP) meeting, in the fantastic city of Barcelona. It was a great opportunity for students attending to the conference to enlarge their stay in the city, and at the same time learn about Multiscale Nucleic Acids simulation tools: how to run them and the methods behind. The workshop started with a one-hour introduction to the two projects by professor Modesto Orozco, president and organizer of the ISQBP conference, and member of the Institute for Research in Biomedicine (IRB Barcelona), which is a partner in BioExcel CoE and the coordinator of MuG.

The workshop was split in two different blocks. During the morning, the different tools to be used during the day were presented: Mesoscopic simulations (MCDNA and Chromatin Dynamics, coarse-grained algorithms to simulate large DNA fibers and Chromatin, respectively); Atomistic simulations (biobb: bio-building blocks to build workflows to prepare and run atomistic MD simulations); and Nucleic Acids Flexibility (NAFlex, to extract a set of flexibility analysis from a coarse-grained or atomistic nucleic acids trajectory). Students had the possibility to individually deploy a Virtual Machine (VM) for each of the tools (with all libraries needed by the tools already installed), connect to them using Command Line Interface (CLI) and directly run a test example. VM deployment was done using the BioExcel Cloud Portal. During the afternoon, the same examples were run, but in this case using the MuG Virtual Research Environment, a graphical workspace integrating the navigation in genomics data from sequence to 3D/4D dynamics.

To have a break between sessions, an opportunity to do networking and relax a bit, we all went to the Torre Girona Chapel, where we had a finger-food lunch, and a guided visit to the Marenostrum IV supercomputer, including a premiere view to the recently installed POWER9 cluster, Europe’s greenest supercomputer . Thanks @Oriol!

This event was the first real test for our BioExcel Cloud Portal. It was able to deploy and sustain 20 VMs at the same time, one per student. Moreover, all the VMs were connected to an external shared disk, using a single NFS server, allowing big file sizes (as the ones generated from atomistic MD simulations) to be generated by the students, or to be used to store pre-generated examples, avoiding the well-known VMs disk size restraints. All in all, our cloud portal proved to be a powerful tool for training events, as we envisaged.

It was a long week in Barcelona, starting from the ISQBP meeting and finishing with the Joint MuG-BioExcel workshop on multiscale nucleic acids simulation. For some of the students attending to the workshop, the week wasn’t still finished, as they were staying for the Sant Joan celebration, full of light, firecrackers and fireworks. We hope they had a nice and entertaining week, and we are already looking forward to organize new BioExcel events!

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