BioSimSpace <http:/biosimspace.openbiosim.org>__

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

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

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

Note

BioSimSpace <https://biosimspace.openbiosim.org> is now supported and maintained by OpenBioSim <https://www.openbiosim.org> and is available through their GitHub organisation <https://github.com/OpenBioSim/biosimspace>__. This repository will only be maintained for legacy development work, with bug-fixes back-ported periodically. Developers can update their remote to point to the new location.

About

BioSimSpace <https:/biosimspace.openbiosim.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.openbiosim.org>__.

Installation

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

The easiest way to install BioSimSpace is using our conda channel <https://anaconda.org/openbiosim/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 Mambaforge <https://github.com/conda-forge/miniforge#mambaforge>__.

To create a new environment:

.. code-block:: bash

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

To install the latest development version you can use:

.. code-block:: bash

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 <https://github.com/openbiosim/sire>_ at the same time:

.. code-block:: bash

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:

.. code-block:: bash

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

BioSimSpace is built on top of the Sire <https://github.com/openbiosim/sire> molecular simulation framework. To download and install Sire, follow the instructions here <https://github.com/openbiosim/sire#installation>, 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.

.. code-block:: bash

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

Once finished, you can test the installation by running:

.. code-block:: bash

python

Then try importing the BioSimSpace package:

.. code-block:: python

import BioSimSpace as BSS

Developers

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

Issues

Please report bugs and other issues using the GitHub issue tracker <https://github.com/openbiosim/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)