IAlibay / BioSimSpace-MDRquery

Code and resources for the EPSRC BioSimSpace project.

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.
• Interact with molecular-simulation processes in real time.

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 biosimspace -c conda-forge -c michellab biosimspace
conda activate biosimspace

To install the latest development version you can use:

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

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

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

If you plan on using BioSimSpace interactively via Jupyter, then you might also need to enable the required notebook extensions within your Conda environment:

jupyter-nbextension enable nglview --py --sys-prefix

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 michellab/label/dev biosimspace

If you find that Conda is particularly slow to install or upgrade BioSimSpace, then we advise using mamba:

conda install -c conda-forge mamba

You can then replace all conda commands with mamba, e.g.:

mamba create -n biosimspace -c conda-forge -c michellab 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:

git clone https://github.com/michellab/Sire
cd Sire
./compile_sire.sh

Assuming the default installation path, this will install Sire into $HOME/sire.app.

(Note that the installation is slow and can take in excess of an hour.)

Next you will need to download BioSimSpace and install it into your Sire application. (The following assumes the default Sire installation path.)

git clone https://github.com/michellab/BioSimSpace
cd BioSimSpace/python
$HOME/sire.app/bin/python setup.py install

Once finished, you can test the installation by running:

$HOME/sire.app/bin/ipython

Then try importing the BioSimSpace package:

import BioSimSpace as BSS

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__)