BioSimSpace <http://biosimspace.org>__

.. image:: https://github.com/michellab/BioSimSpace/workflows/Build/badge.svg :target: https://github.com/michellab/BioSimSpace/actions?query=workflow%3ABuild) :alt: Build status

.. image:: https://anaconda.org/michellab/biosimspace/badges/downloads.svg :target: https://anaconda.org/michellab/biosimspace :alt: Conda Downloads

.. image:: https://img.shields.io/badge/License-GPL%20v2-blue.svg :target: https://www.gnu.org/licenses/old-licenses/gpl-2.0.en.html :alt: License

.. image:: https://joss.theoj.org/papers/4ba84ad443693b5dded90e35bf5f8225/status.svg :target: https://joss.theoj.org/papers/4ba84ad443693b5dded90e35bf5f8225 :alt: Paper

About

BioSimSpace <https://biosimspace.org>__ 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 <https://jupyter.org>__.
• Interact with molecular-simulation processes in real time.

Citation |DOI for Citing BioSimSpace|

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}
}

.. |DOI for Citing BioSimSpace| image:: https://joss.theoj.org/papers/4ba84ad443693b5dded90e35bf5f8225/status.svg :target: https://joss.theoj.org/papers/4ba84ad443693b5dded90e35bf5f8225

Documentation

Full documentation can be found here <https://biosimspace.org>__.

Installation

Conda package ^^^^^^^^^^^^^

The easiest way to install BioSimSpace is using our conda channel <https://anaconda.org/michellab/repo>. BioSimSpace is built using dependencies from conda-forge <https://conda-forge.org/>, so please ensure that the channel takes strict priority. We recommend using Miniforge <https://github.com/conda-forge/miniforge>__.

To create a new environment:

.. code-block:: bash

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

To install the latest development version you can use:

.. code-block:: bash

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 <https://github.com/michellab/Sire>_ at the same time:

.. code-block:: bash

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:

.. code-block:: bash

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:

.. code-block:: bash

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 <https://github.com/TheSnakePit/mamba>__:

.. code-block:: bash

conda install -c conda-forge mamba

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

.. code-block:: bash

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 <https://git-scm.com>__ installation.)

BioSimSpace is built on top of the Sire <https://github.com/michellab/Sire>__ molecular simulation framework. To download and install Sire:

.. code-block:: bash

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.)

.. code-block:: bash

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:

.. code-block:: bash

$HOME/sire.app/bin/ipython

Then try importing the BioSimSpace package:

.. code-block:: python

import BioSimSpace as BSS

Developers

Please follow the developer's guide <https://biosimspace.org/development.html>__.

Issues

Please report bugs and other issues using the GitHub issue tracker <https://github.com/michellab/BioSimSpace/issues>__. 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:

.. code-block:: python

import BioSimSpace as BSS print(BSS.version)