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CITATION.cff
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# -*- coding: utf-8 -*-
# This CITATION.cff file was initially generated with cffinit.
# Visit https://bit.ly/cffinit to generate yours today!
cff-version: 1.2.0
title: 'alchemlyb: the simple alchemistry library'
message: >-
If you use this software, please cite it using the
preferred citation (JOSS DOI 10.21105/joss.06934) together
with any other references.
type: software
authors:
- email: david@datryllic.com
given-names: David L.
family-names: Dotson
orcid: 'https://orcid.org/0000-0001-5879-2942'
affiliation: Datryllic LLC
- given-names: Ian M.
family-names: Kenney
orcid: 'https://orcid.org/0000-0002-9749-8866'
affiliation: Kenney Consulting, LLC
- given-names: Oliver
family-names: Beckstein
email: obeckste@asu.edu
affiliation: Arizona State University
orcid: 'https://orcid.org/0000-0003-1340-0831'
- given-names: Shuai
family-names: Liu
orcid: 'https://orcid.org/0000-0002-8632-633X'
affiliation: Silicon Therapeutics LLC
- given-names: Travis
family-names: Jensen
- given-names: Bryce
family-names: Allen
orcid: 'https://orcid.org/0000-0002-0804-8127'
affiliation: Differentiated Therapeutics
- given-names: Dominik
family-names: Wille
affiliation: Freie Universität Berlin
- given-names: Victoria
family-names: Lim
orcid: 'https://orcid.org/0000-0003-4030-9312'
affiliation: University of California Irvine
- given-names: Hyungro
family-names: Lee
orcid: 'https://orcid.org/0000-0002-4221-7094'
affiliation: Pacific Northwest National Laboratory
- given-names: Mohammad Soroush
family-names: Barhaghi
orcid: 'https://orcid.org/0000-0001-8226-7347'
affiliation: Wayne State University
- given-names: Zhiyi
family-names: Wu
affiliation: Exscientia plc
orcid: 'https://orcid.org/0000-0002-7615-7851'
email: william@zhiyiwu.me
- given-names: Wei-Tse
family-names: Hsu
orcid: https://orcid.org/0000-0001-6167-5480
affiliation: University of Colorado Boulder
- given-names: Alexander
family-names: Schlaich
orcid: 'https://orcid.org/0000-0002-4250-363X'
affiliation: University of Stuttgart
- given-names: Jérôme
family-names: Hénin
orcid: 'https://orcid.org/0000-0003-2540-4098'
affiliation: CNRS
- given-names: Thomas T.
family-names: Joseph
orcid: 'https://orcid.org/0000-0003-1323-3244'
affiliation: University of Pennsylvania
- given-names: Irfan
family-names: Alibay
orcid: 'https://orcid.org/0000-0001-5787-9130'
affiliation: Open Molecular Software Foundation
- given-names: Pascal T.
family-names: Merz
affiliation: PM Scientific Consulting
orcid: 'https://orcid.org/0000-0002-7045-8725'
- given-names: Domenico
family-names: Marson
orcid: 'https://orcid.org/0000-0003-1839-9868'
affiliation: University of Trieste
- given-names: Shujie
family-names: Fan
orcid: 'https://orcid.org/0000-0002-0271-2760'
affiliation: Arizona State University
- given-names: Jan
family-names: Janssen
affiliation: Max-Planck-Institut for Sustainable Materials
orcid: 'https://orcid.org/0000-0001-9948-7119'
- given-names: Haoxi
family-names: Li
orcid: 'https://orcid.org/0009-0004-8369-1042'
affiliation: University of North Carolina
- given-names: Helmut
family-names: Carter
orcid: https://orcid.org/0000-0003-0273-4107
affiliation: City University of New York
- given-names: David
family-names: Mobley
orcid: 'https://orcid.org/0000-0002-1083-5533'
affiliation: University of California Irvine
- given-names: Michael R.
family-names: Shirts
orcid: 'https://orcid.org/0000-0003-3249-1097'
affiliation: University of Colorado Boulder
- given-names: Jennifer A.
family-names: Clark
orcid: https://orcid.org/0000-0003-4897-5651
affiliation: National Institute of Standards and Technology
identifiers:
- type: swh
value: 'swh:1:dir:4cd266754be413312ee7ef3f1f7fbe05b38192cf'
description: >-
The Software Heritage identifier for the top level
directory of the repository.
repository-code: 'https://github.com/alchemistry/alchemlyb'
url: 'https://alchemlyb.readthedocs.io'
abstract: >-
alchemlyb is an open-source Python software package for
the analysis of alchemical free energy calculations. Its
functionality contains individual composable building
blocks for all aspects of a full typical free energy
analysis workflow, starting with the extraction of raw
data from the output of diverse molecular simulation
packages, moving on to data preprocessing tasks such as
decorrelation of time series, using various estimators to
derive free energy estimates from simulation samples, and
finally providing quality analysis tools for data
convergence checking and visualization. alchemlyb also
contains high-level end-to-end workflows that combine
multiple building blocks into a user-friendly analysis
pipeline from the initial data input stage to the final
results.
keywords:
- Python
- free energy
- molecular dynamics
- alchemistry
license: BSD-3-Clause
preferred-citation:
title: 'alchemlyb: the simple alchemistry library'
authors:
- given-names: Zhiyi
family-names: Wu
affiliation: Exscientia plc
orcid: 'https://orcid.org/0000-0002-7615-7851'
email: william@zhiyiwu.me
- given-names: David L.
family-names: Dotson
orcid: 'https://orcid.org/0000-0001-5879-2942'
affiliation: Arizona State University
- given-names: Irfan
family-names: Alibay
orcid: 'https://orcid.org/0000-0001-5787-9130'
affiliation: Open Molecular Software Foundation
- given-names: Bryce
family-names: Allen
orcid: 'https://orcid.org/0000-0002-0804-8127'
affiliation: Differentiated Therapeutics
- given-names: Mohammad Soroush
family-names: Barhaghi
orcid: 'https://orcid.org/0000-0001-8226-7347'
affiliation: Wayne State University
- given-names: Jérôme
family-names: Hénin
orcid: 'https://orcid.org/0000-0003-2540-4098'
affiliation: CNRS
- given-names: Thomas T.
family-names: Joseph
orcid: 'https://orcid.org/0000-0003-1323-3244'
affiliation: University of Pennsylvania
- given-names: Ian M.
family-names: Kenney
orcid: 'https://orcid.org/0000-0002-9749-8866'
affiliation: Arizona State University
- given-names: Hyungro
family-names: Lee
orcid: 'https://orcid.org/0000-0002-4221-7094'
affiliation: Pacific Northwest National Laboratory
- given-names: Haoxi
family-names: Li
orcid: 'https://orcid.org/0009-0004-8369-1042'
affiliation: University of North Carolina
- given-names: Victoria
family-names: Lim
orcid: 'https://orcid.org/0000-0003-4030-9312'
affiliation: University of California Irvine
- given-names: Shuai
family-names: Liu
orcid: 'https://orcid.org/0000-0002-8632-633X'
affiliation: Silicon Therapeutics LLC
- given-names: Domenico
family-names: Marson
orcid: 'https://orcid.org/0000-0003-1839-9868'
affiliation: University of Trieste
- given-names: Pascal T.
family-names: Merz
affiliation: PM Scientific Consulting
orcid: 'https://orcid.org/0000-0002-7045-8725'
- given-names: Alexander
family-names: Schlaich
orcid: 'https://orcid.org/0000-0002-4250-363X'
affiliation: University of Stuttgart
- given-names: David
family-names: Mobley
orcid: 'https://orcid.org/0000-0002-1083-5533'
affiliation: University of California Irvine
- given-names: Michael R.
family-names: Shirts
orcid: 'https://orcid.org/0000-0003-3249-1097'
affiliation: University of Colorado Boulder
- given-names: Oliver
family-names: Beckstein
email: obeckste@asu.edu
affiliation: Arizona State University
orcid: 'https://orcid.org/0000-0003-1340-0831'
type: 'article'
year: 2024
journal: 'Journal of Open Source Software'
doi: '10.21105/joss.06934'
references:
- title: Statistically optimal analysis of samples from multiple equilibrium states
authors:
- family-names: Shirts
given-names: Michael R
- family-names: Chodera
given-names: John D
type: 'article'
pages: '124105'
year: '2008'
journal: Journal of Chemical Physics
doi: '10.1063/1.2978177'
- title: A Simple Method for Automated Equilibration Detection in Molecular Simulations
authors:
- family-names: Chodera
given-names: John D.
type: 'article'
pages: '1799–1805'
year: '2016'
journal: 'Journal of Chemical Theory and Computation'
doi: '10.1021/acs.jctc.5b00784'