Multi-resolution Nucleic Acids Simulations. A joint MuG-BioExcel workshop.

Workshop co-located with the International Society of Quantum Biology and Pharmacology (ISQBP) President’s meeting.

Date:  Friday 22nd June 2018

Venue: Barcelona Supercomputing Center, Computer Architecture Department at Universitat Politècnica de Catalunya, Barcelona, Spain.

Room: Vertex Building.

Application open: February 20th, 2018.

Extended deadline: June 10th, 2018. Inscription closed.

Participation: Open application with selection. We will review applications as they come in.

Contact: Adam Hospital (

Registration fee: Registration for the course is free. Attendees need to cover their own travel and accommodation expenses.



Nucleic acids (NAs) are biomolecules essential to all known forms of life that exhibit a remarkable structural and functional diversity. NAs are studied through several different techniques, including experimental and theoretical methods. The notorious improvements of the latter, together with the increased computation power, explain their widespread use in improving our understanding of their structure and function. Giving the multiscale nature of NAs, different theoretical disciplines like quantum chemistry, molecular mechanics and mesoscopic biophysical approaches are considered.

Multiscale Complex Genomics (MuG) project was conceived to tackle the latest computational challenges on the multiscale nature of NAs, connecting this community to the HPC and Big Data world and providing a suitable set of tools and infrastructure to integrate the navigation in genomics data from sequence (1D) to 3D/4D chromatin dynamics.

BioExcel Center of Excelence is as a central hub for biomolecular modelling and simulations, with a mission to enable scientists to fully exploit the power of data and computing e-infrastructure by providing support to non-experts and advanced users.

The purpose of this workshop is to:

  • Discover the set of multiscale genomics modelling and simulation tools used in the MuG project.
  • Learn how to easily run them through the BioExcel Cloud Portal infrastructure.
  • Have a first contact with the MuG Virtual Research Environment (VRE), a GUI integrating the set of tools with an interactive and graphical interface.


The workshop is aimed at both experimental researchers and bioinformaticians; additionally it may be of interest to tool developers who wish to integrate their tools into the MuG VRE.

No software installation will be necessary, Virtual Machines (VMs) will be deployed on-line through the BioExcel Cloud Portal. The room is equipped with computers.


After this course you should be able to:

  • Prepare and simulate NAs mesoscopic and atomistic models, both in a High-Throughput way (workflows, command-line executions) as well as using a user-friendly GUI interface.
  • Obtain flexibility parameters out of the NAs simulations: PCA, Helical Parameters, Distance Contact Maps, NMR observables, etc.


  • Introducing BioExcel & MuG
  • Mesoscopic Models:
    • Simulating Chromatin
    • Coarse-Grained DNA
  • Atomistic Models:
    • Automatic tools for MD simulations
  • Ensemble/Trajectories Analysis tools
  • MuG VRE: Integrating tools and genomics data


Draft Programme – subject to slight change

Friday 22 June 2018  

Start End Title (Presenter name)
09:00 10:00 Welcome & Introduction: BioExcel & MuG

(Modesto Orozco, MuG project coordinator – IRB Barcelona,
Josep Lluís Gelpí, BSC; Adam Hospital, IRB Barcelona)

10:00 11:00 Mesoscopic Models

(Jürgen Walther, IRB Barcelona)

11:00 11:30 Coffee Break
11:30 12:30 MD Atomistic Models

(Pau Andrio, BSC Barcelona)

12:30 13:30 Ensemble/Trajectory Analysis

(Adam Hospital, IRB Barcelona)

13:30 15:00 Lunch / MareNostrum IV Supercomputer Visit
15:00 15:30 Multi-resolution Nucleic Acids Simulations Integration VRE

Chromatin Dynamics (ChromDyn)

(Jürgen Walther, IRB Barcelona)

15:30 16:00 Multi-resolution Nucleic Acids Simulations Integration VRE

MonteCarlo DNA (MCDNA)

(Jürgen Walther, IRB Barcelona)

16:00 16:30 Multi-resolution Nucleic Acids Simulations Integration VRE

Python Molecular Dynamics library (PyMD)

(Pau Andrio, BSC Barcelona)

16:30 17:00 Multi-resolution Nucleic Acids Simulations Integration VRE

Nucleic Acids Flexibility (NAFlex)

(Adam Hospital, IRB Barcelona)

17:00 18:00 Q & A + Wrap Up Session

(All speakers)


How to apply

  • To attend to the Workshop exclusively, please send an e-mail to this direction, including your personal info (name, affiliation, country, e-mail) and a motivation letter (max 1 page).

Extended deadline
June 10th, 2018

Number of places
20 places

Apply now (ISQBP combined)

Apply now (Just Workshop)


This training course is a joint MuGBioExcel workshop.

This training course is powered by the BioExcel Cloud Portal interface. 

The BioExcel Cloud Portal has been developed by the Technology and Science Integration team at EMBL-EBI to simplify the experience for researchers when running their workloads across different cloud providers.

The portal enables cloud providers and research teams to package and share their BioExcel applications and environments with their respective users. That way, these key applications can be deployed on demand onto the cloud providers the user is able to access.


  • Adam Hospital
  • Anna Montras


  • Modesto Orozco – IRB Barcelona
  • Josep Lluís Gelpí – BSC Barcelona Supercomputing Center
  • Pau Andrio – BSC Barcelona Supercomputing Center
  • Adam Hospital – IRB Barcelona
  • Jürgen Walther – IRB Barcelona

22 Jun, 2018
All Day

Barcelona Supercomputing Center