fjclark / biosimspace-openbiosim

An interoperable Python framework for biomolecular simulation.

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 Mambaforge.

To create a new environment:

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

To install the latest development version you can use:

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

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

mamba 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:

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

Installing from source

Alternatively, to install BioSimSpace from source:

(Before starting, you'll need a working Git installation.)

BioSimSpace is built on top of the Sire molecular simulation framework. To download and install Sire, follow the instructions here, making sure that BioSimSpace's dependencies are installed into the Sire conda environment at the point at which Sire is installed.

Next you will need to download BioSimSpace and install it into your Sire Conda environment.

git clone https://github.com/openbiosim/biosimspace
cd biosimspace/python
python setup.py install

If you plan to develop and want an editable install, use:

python setup.py develop

If you want to skip the installation of BioSimSpace dependencies, e.g. if they are already installed, then you can use:

BSS_SKIP_DEPENDENCIES=1 python setup.py develop

Once finished, you can test the installation by running:

python

Then try importing the BioSimSpace package:

import BioSimSpace as BSS

If you don't want to install Sire from source, an alternative is to create a conda environment containing only the dependencies of BioSimSpace, then install the latest development code into that.

mamba create -n openbiosim-dev -c conda-forge -c openbiosim/label/dev biosimspace --only-deps
mamba activate openbiosim-dev
git clone https://github.com/openbiosim/biosimspace
cd biosimspace/python
BSS_SKIP_DEPENDENCIES=1 python setup.py develop

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

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__)