BioSimSpace

About

BioSimSpace is an interoperable Python framework for biomolecular simulation. With it you can:

• Write robust and portable biomolecular workflow components that work on different hardware, with different software packages, and that can be run in different ways, e.g. command-line, Jupyter.
• Start, stop, and monitor molecular simulation processes within interactive Python environments.

Citation

If you use BioSimSpace in any scientific software, please cite the following paper:

@article{Hedges2019,
  doi = {10.21105/joss.01831},
  url = {https://doi.org/10.21105/joss.01831},
  year = {2019},
  publisher = {The Open Journal},
  volume = {4},
  number = {43},
  pages = {1831},
  author = {Lester Hedges and Antonia Mey and Charles Laughton and Francesco Gervasio and Adrian Mulholland and Christopher Woods and Julien Michel},
  title = {BioSimSpace: An interoperable Python framework for biomolecular simulation},
  journal = {Journal of Open Source Software}
}

Documentation

Full documentation can be found here.

Installation

Conda package

The easiest way to install BioSimSpace is using our conda channel. BioSimSpace is built using dependencies from conda-forge, so please ensure that the channel takes strict priority. We recommend using Miniforge.

To create a new environment:

conda create -n openbiosim -c conda-forge -c openbiosim biosimspace
conda activate openbiosim

To install the latest development version you can use:

conda create -n openbiosim-dev -c conda-forge -c openbiosim/label/dev biosimspace
conda activate openbiosim-dev

When updating the development version it is generally advised to update Sire at the same time:

conda update -c conda-forge -c openbiosim/label/dev biosimspace sire

Unless you add the required channels to your Conda configuration, then you'll need to add them when updating, e.g., for the development package:

conda update -c conda-forge -c openbiosim/label/dev biosimspace

Installing from source (standalone)

To install from source using pixi, which will automatically create an environment with all required dependencies (including pre-built Sire):

git clone https://github.com/openbiosim/biosimspace
cd biosimspace
pixi install
pixi shell
pip install -e .

Installing from source (full OpenBioSim development)

If you are developing across the full OpenBioSim stack, first install Sire from source by following the instructions here, then activate its pixi environment:

pixi shell --manifest-path /path/to/sire/pixi.toml -e dev

Next, clone and install BioSimSpace:

git clone https://github.com/openbiosim/biosimspace
cd biosimspace
pip install -e .

You may also want to install optional dependencies, such as ambertools and gromacs into the environment.

Once finished, you can test the installation by running:

import BioSimSpace as BSS

Development

Pre-commit hooks are used to ensure consistent code formatting and linting. To set up pre-commit in your development environment:

pixi shell -e dev
pre-commit install

This will run ruff formatting and linting checks automatically on each commit. To run the checks manually against all files:

pre-commit run --all-files

Developers

Please follow the developer's guide.

Issues

Please report bugs and other issues using the GitHub issue tracker. When reporting issues please try to include a minimal code snippet that reproduces the problem. Additional files can be also be uploaded as an archive, e.g. a zip file. Please also report the branch on which you are experiencing the issue, along with the BioSimSpace version number. This can be found by running:

import BioSimSpace as BSS
print(BSS.__version__)