Anyone interested in learning how to use the new CCP-BioSim BioSimSpace Python environment for easy setup, running, management and analysis of biomolecular simulations.
Knowledge of Python, e.g. as gained from the Python for Biomolecular Modellers workshop.
BioSimSpace is the new flagship software being produced in partnership with CCP-BioSim/HEC-BioSim. The software provides an easy-to-use Python environment for manipulating biomolecules, running simulations, and analysing / visualising outputs. BioSimSpace hides the details of using individual simulation and analysis packages behind a common, simple Python interface. This enables you to setup, run and analyse simulations using, e.g. Amber, NAMD or Gromacs, all from the same Python script or Jupyter Python interface.
The workshop consists of a series of Jupyter notebooks. To run these, you will first need to create a BioSimSpace conda environment:
conda create -n openbiosim -c conda-forge -c openbiosim biosimspace=2023.1.0
conda activate openbiosim
These training materials will teach you more about BioSimSpace, including how to write your own BioSimSpace code. The material is split into two parts.
- 01_introduction.ipynb : This notebook introduces the goals of BioSimSpace and shows you how to easily configure and run molecular-dynamics simulations and interact with them in real time.
- 02_writing_nodes.ipynb : This notebook shows you how to use BioSimSpace to write an interoperable workflow component, called a node. This node is independent of the underlying software packages.
- 03_running_nodes.ipynb : This notebook shows you the various ways of running BioSimSpace nodes.
- Excercises
- 04_molecular_setup.ipynb : This notebook shows you how to use BioSimSpace to parameterise and solvate molecules.
- Excercise