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

  • Monday 22nd November 2021
  • Tuesday 23rd November 2021
  • Wednesday 24th November 2021

 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.

Registrant capacity: 20 participants

Overview: 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.

Audience: 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 are recommended to properly follow the course. Minimum Linux skills are also required. This is an interactive session that is presented remotely using Zoom.

Technical requirements:

  • To participate in the online interactive sessions:
    • We recommend using the Zoom desktop app.
    • 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: Technical instructions for the course 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.

Trainer: Adam Hospital (IRB Barcelona, BioExcel)

Interested? Contact Marta Lloret (marta.lloret@ebi.ac.uk) explaining briefly why you want to attend the course. You will then receive instructions on how to register.