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CITATION.cff
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# Citation File Format (cff).
# See https://citation-file-format.github.io/
cff-version: "1.2.0"
message: "If you use this software, please cite it using these metadata."
# Keep project metadata in sync with `pyproject.toml`!
type: "software"
title: "transfer_Li"
abstract: "Transfer Li ions from cathode to anode in MD simulations."
authors:
- given-names: "Andreas"
family-names: "Thum"
alias: "andthum"
email: "[email protected]"
tel: "+49 251 83-29179"
fax: "+49 251 83-29159"
affiliation: "University of Münster, Institute for Physical Chemistry"
address: "Corrensstraße 28/30"
city: "Münster"
post-code: 48149
country: "DE"
region: "North Rhine-Westphalia"
orcid: "https://orcid.org/0000-0002-2262-8507"
contact:
- given-names: "Andreas"
family-names: "Thum"
email: "[email protected]"
identifiers:
- description: "The concept DOI of the software."
type: "doi"
value: "10.5281/zenodo.10155117"
url: "https://github.com/andthum/transfer_Li"
repository-code: "https://github.com/andthum/transfer_Li"
license: "MIT"
license-url: "https://mit-license.org/"
keywords:
- "Python Scripts"
- "Science"
- "Scientific Computing"
- "Computational Science"
- "Materials Science"
- "Molecular Simulation"
- "Molecular Modeling"
- "Molecular Mechanics"
- "Molecular Dynamics"
- "Molecular Dynamics Simulations"
- "Gromacs"
- "MDAnalysis"
- "NumPy"
# Keep references in sync with pyproject.toml.
references:
- type: "software"
title: "MDTools"
abstract: "Scripts to prepare and analyze molecular dynamics simulations."
authors:
- given-names: "Andreas"
family-names: "Thum"
- given-names: "Len"
family-names: "Kimms"
- name: "All Contributors to MDTools"
url: "https://github.com/andthum/mdtools"
repository-code: "https://github.com/andthum/mdtools"
license: "GPL-3.0-or-later"
license-url: "https://www.gnu.org/licenses/gpl-3.0.html"
keywords:
- "Scripts Collection"
- "Python Scripts"
- "Science"
- "Scientific Computing"
- "Computational Science"
- "Computational Biology"
- "Computational Chemistry"
- "Computational Physics"
- "Materials Science"
- "Molecular Simulation"
- "Molecular Modeling"
- "Molecular Mechanics"
- "Molecular Dynamics"
- "Molecular Dynamics Simulation"
- "Trajectory Analysis"
- "MDAnalysis"
- "NumPy"
- "Python3"
- "GPLv3"
- type: "software"
title: "MDAnalysis"
abstract: >-
MDAnalysis is a Python library to analyze molecular dynamics simulations.
authors:
- given-names: "Naveen"
family-names: "Michaud-Agrawal"
- name: "The MDAnalysis Core Developer Team"
- name: "All Contributors to MDAnalysis"
url: "https://www.mdanalysis.org"
repository-code: "https://github.com/MDAnalysis/mdanalysis"
license: "GPL-2.0-or-later"
license-url: "https://www.gnu.org/licenses/gpl-2.0.html"
keywords:
- "python"
- "science"
- "chemistry"
- "biophysics"
- "molecular-dynamics"
- "computational-chemistry"
- "molecular-simulation"
- "analysis"
- "trajectory-analysis"
- type: "proceedings"
title: >-
MDAnalysis: A Python Package for the Rapid Analysis of Molecular Dynamics
Simulations
abstract: >-
MDAnalysis (http://mdanalysis.org) is a library for structural and
temporal analysis of molecular dynamics (MD) simulation trajectories and
individual protein structures. MD simulations of biological molecules
have become an important tool to elucidate the relationship between
molecular structure and physiological function. Simulations are performed
with highly optimized software packages on HPC resources but most codes
generate output trajectories in their own formats so that the development
of new trajectory analysis algorithms is confined to specific user
communities and widespread adoption and further development is delayed.
MDAnalysis addresses this problem by abstracting access to the raw
simulation data and presenting a uniform object-oriented Python interface
to the user. It thus enables users to rapidly write code that is portable
and immediately usable in virtually all biomolecular simulation
communities. The user interface and modular design work equally well in
complex scripted work flows, as foundations for other packages, and for
interactive and rapid prototyping work in IPython / Jupyter notebooks,
especially together with molecular visualization provided by nglview and
time series analysis with pandas. MDAnalysis is written in Python and
Cython and uses NumPy arrays for easy interoperability with the wider
scientific Python ecosystem. It is widely used and forms the foundation
for more specialized biomolecular simulation tools. MDAnalysis is
available under the GNU General Public License v2.
authors:
- given-names: "Richard J."
family-names: "Gowers"
- given-names: "Max"
family-names: "Linke"
- given-names: "Jonathan"
family-names: "Barnoud"
- given-names: "Tyler John Edward"
family-names: "Reddy"
- given-names: "Manuel N."
family-names: "Melo"
- given-names: "Sean L."
family-names: "Seyler"
- given-names: "Jan"
family-names: "Domanski"
- given-names: "David L."
family-names: "Dotson"
- given-names: "Sebastien"
family-names: "Buchoux"
- given-names: "Ian M."
family-names: "Kenney"
- given-names: "Oliver"
family-names: "Beckstein"
editors:
- given-names: "Sebastian"
family-names: "Benthall"
- given-names: "Scott"
family-names: "Rostrup"
conference:
name: "Proceedings of the 15th Python in Science Conference"
city: "Austin"
region: "Texas"
country: "US"
year: 2016
pages: 98-105
doi: "10.25080/Majora-629e541a-00e"
url: "https://www.osti.gov/biblio/1565806"
keywords:
- "software"
- "molecular dynamics simulations"
- "science"
- "chemistry"
- "physics"
- "biology"
- type: "article"
title: >-
MDAnalysis: A toolkit for the analysis of molecular dynamics simulations
abstract: >-
Abstract MDAnalysis is an object-oriented library for structural and
temporal analysis of molecular dynamics (MD) simulation trajectories and
individual protein structures. It is written in the Python language with
some performance-critical code in C. It uses the powerful NumPy package
to expose trajectory data as fast and efficient NumPy arrays. It has been
tested on systems of millions of particles. Many common file formats of
simulation packages including CHARMM, Gromacs, Amber, and NAMD and the
Protein Data Bank format can be read and written. Atoms can be selected
with a syntax similar to CHARMM's powerful selection commands. MDAnalysis
enables both novice and experienced programmers to rapidly write their
own analytical tools and access data stored in trajectories in an easily
accessible manner that facilitates interactive explorative analysis.
MDAnalysis has been tested on and works for most Unix-based platforms
such as Linux and Mac OS X. It is freely available under the GNU General
Public License from http://mdanalysis.googlecode.com.
authors:
- given-names: "Naveen"
family-names: "Michaud-Agrawal"
- given-names: "Elizabeth J."
family-names: "Denning"
- given-names: "Thomas B."
family-names: "Woolf"
- given-names: "Oliver"
family-names: "Beckstein"
journal: "Journal of Computational Chemistry"
volume: 32
number: 10
pages: "2319-2327"
year: 2011
doi: "10.1002/jcc.21787"
url: "https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.21787"
keywords:
- "molecular dynamics simulations"
- "analysis"
- "proteins"
- "object-oriented design"
- "software"
- "membrane systems"
- "Python programming language"
- type: "software"
title: "NumPy"
abstract: "The fundamental package for scientific computing with Python."
authors:
- name: "All Contributors to NumPy"
url: "https://numpy.org"
repository-code: "https://github.com/numpy/numpy"
license: "BSD-3-Clause"
license-url: "https://opensource.org/licenses/BSD-3-Clause"
keywords:
- "python"
- "numpy"
- "closember"
- type: "article"
title: "Array programming with NumPy"
abstract: >-
Array programming provides a powerful, compact and expressive syntax for
accessing, manipulating and operating on data in vectors, matrices and
higher-dimensional arrays. NumPy is the primary array programming library
for the Python language. It has an essential role in research analysis
pipelines in fields as diverse as physics, chemistry, astronomy,
geoscience, biology, psychology, materials science, engineering, finance
and economics. For example, in astronomy, NumPy was an important part of
the software stack used in the discovery of gravitational waves and in
the first imaging of a black hole. Here we review how a few fundamental
array concepts lead to a simple and powerful programming paradigm for
organizing, exploring and analysing scientific data. NumPy is the
foundation upon which the scientific Python ecosystem is constructed. It
is so pervasive that several projects, targeting audiences with
specialized needs, have developed their own NumPy-like interfaces and
array objects. Owing to its central position in the ecosystem, NumPy
increasingly acts as an interoperability layer between such array
computation libraries and, together with its application programming
interface (API), provides a flexible framework to support the next decade
of scientific and industrial analysis.
authors:
- given-names: "Charles R."
family-names: "Harris"
- given-names: "K. Jarrod"
family-names: "Millman"
- given-names: "Stéfan J."
family-names: "van der Walt"
- given-names: "Ralf"
family-names: "Gommers"
- given-names: "Pauli"
family-names: "Virtanen"
- given-names: "David"
family-names: "Cournapeau"
- given-names: "Eric"
family-names: "Wieser"
- given-names: "Julian"
family-names: "Taylor"
- given-names: "Sebastian"
family-names: "Berg"
- given-names: "Nathaniel J."
family-names: "Smith"
- given-names: "Robert"
family-names: "Kern"
- given-names: "Matti"
family-names: "Picus"
- given-names: "Stephan"
family-names: "Hoyer"
- given-names: "Marten H."
family-names: "van Kerkwijk"
- given-names: "Matthew"
family-names: "Brett"
- given-names: "Allan"
family-names: "Haldane"
- given-names: "Jaime Fernández"
family-names: "del Río"
- given-names: "Mark"
family-names: "Wiebe"
- given-names: "Pearu"
family-names: "Peterson"
- given-names: "Pierre"
family-names: "Gérard-Marchant"
- given-names: "Kevin"
family-names: "Sheppard"
- given-names: "Tyler"
family-names: "Reddy"
- given-names: "Warren"
family-names: "Weckesser"
- given-names: "Hameer"
family-names: "Abbasi"
- given-names: "Christoph"
family-names: "Gohlke"
- given-names: "Travis E."
family-names: "Oliphant"
journal: "Nature"
volume: 585
number: 7825
pages: "357-362"
year: 2020
month: 9
publisher:
name: "Springer Science and Business Media LLC"
doi: "10.1038/s41586-020-2649-2"
url: "https://doi.org/10.1038/s41586-020-2649-2"