Date: The online training will consist of two sessions:

  • Monday 9th December 2019
  • Thursday 12th December 2019 

Time: 10:00 – 13:00 GMT / 11:00 – 14:00 CET
 (Session times will be 2 to 3 hours, depending on the level of interactivity)


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?

Join the online training session where 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

  • Interactive session:
    Google Chrome, Safari or Firefox. Try to avoid Firefox if you are using a Mac, as there might be audio problems
    A microphone and (ideally) a webcam.
  • Hands-on:
    Unix shell terminal (Linux / MacOS)
    Conda package management system
    Web browser (Jupyter Notebooks)
    Note: Instructions about what to install and how to do it will be sent out after registration

Learning outcomes

At the end of this session 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.

Register here:

Contact: Marta Lloret

Note: This session has been created in the context of the BioExcel virtual training programme. Our pilot sessions are free to attend but we ask that you provide us with feedback after the session to help us optimise the session.