Date: The training will consist of three sessions and participants are expected to attend all three of them:

  • Monday 9th November 2020
  • Wednesday 11th November 2020
  • Friday 13th November 2020

 Time: 14:00 – 16:00 GMT / 15:00 – 17:00 CET

Session times will be 2 hours, but the trainer can stay a bit longer if anyone has specific questions about the session, the library, or about how they could apply it in their research.


Are you interested in computational biomolecular simulation methods such as Molecular Dynamics simulations, but scared to make the first step? What if you could start smoothly using interactive, graphical user interfaces like Jupyter Notebooks? What if you could easily build pipelines chaining different programs using a single, interoperable library with a unique syntax?

In this session we will introduce the BioExcel building blocks, a fully interoperable software library comprising a collection of Python wrappers on top of biomolecular simulation tools such as GROMACS, Ambertools, Openbabel or ACPYPE. The philosophy behind its design, following best practices and FAIR principles for software development makes it easy to find, install and use, increasing reproducibility and (re)usability. Demonstration workflows implemented in Jupyter notebooks using the library will be presented and explained step by step (e.g. protein-ligand complex GROMACS MD setup). The first steps on how to build and run complex workflows in command-line will be explored.


This session is aimed at people interested in:

  • Starting with computational biomolecular simulations, and more specifically Molecular Dynamics simulations.
  • Building computational biomolecular simulations workflows, ensuring reproducibility.

No expertise in Molecular Dynamics is needed to attend the training, although some knowledge and familiarity with this method is recommended to properly follow the course.

Minimum Linux skills are also required.

This is an interactive session that is presented remotely using GoToTraining.

Technical requirements:

  • To participate in the online interactive sessions:
    • Google Chrome or Firefox (if you are using Linux). Try to avoid Firefox if you are using a Mac, as there might be audio problems
    • A microphone and (ideally) a webcam.
  • To perform the hands-on tasks during and after the sessions:
    • Web browser
    • GitHub account (
    • Unix shell terminal (Linux / MacOS)
    • Conda package management system
  • Note: Instructions about what to install and how to do it will be sent out after registration

Learning outcomes:

At the end of these sessions you will be able to…

  • Interactively work with computational biomolecular simulation demonstration workflows built using the BioExcel building blocks library in Jupyter Notebooks sessions: change input structure, modify parameters, add/remove steps, etc.
  • Write a new computational biomolecular simulation workflow using the BioExcel building blocks library from scratch.
  • Launch computational biomolecular simulation workflows built using the BioExcel building blocks library in a command-line interface.

Trainers: Adam Hospital (IRB Barcelona, BioExcel), Genís Bayarri (IRB Barcelona, BioExcel) and Pau Andrio (BSC, BioExcel)

Limit: 20 participants

Interested to apply? Contact Marta Lloret explaining briefly why you want to attend the course. You will then receive instructions on how to register.