Notebook server

Visit our online notebook server here. This will launch a Jupyter hub running inside of a Docker container. This includes all of the software that is required, allowing you to play around with BioSimSpace and learn how it works without needing to install anything yourself.

Demos

The notebook server has a set of example nodes to get you started. To run any of these, simply navigate to the demo directory from the landing page. A description of each node is given below:

  • conversion.ipynb: Convert between common molecular file formats.

  • input_files.ipynb: Generate molecular dynamics input files for a range of protocols and molecular dynamics engines.

  • molecular_setup.ipynb: Parameterise and solvate a molecule ready for simulation.

  • minimisation.ipynb: Minimise a molecular configuration.

Workshops

The server also contains several BioSimSpace training workshops. Navigate to the workshops directory from the landing page.

  • python: A basic Python programing workshop.

  • introduction: An introduction to the core concepts of BioSimSpace.

  • advanced: Using BioSimSpace to set up and run advanced sampling simulations, such as free energy pertubation and metadynamics.