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Update joss_paper/paper.md
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Co-authored-by: Pascal Merz <[email protected]>
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xiki-tempula and ptmerz authored Jun 3, 2024
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Expand Up @@ -111,7 +111,7 @@ Statistical mechanical estimators are available to extract free energies and the
*alchemlyb* implements modular building blocks to simplify the process of extracting crucial thermodynamic insights from molecular simulations in a uniform manner.

*alchemlyb* succeeds the widely-used but now deprecated [`alchemical-analysis.py` tool](https://github.com/MobleyLab/alchemical-analysis) [@klimovich2015guidelines], which combined pre-processing, free energy estimation, and plotting in a single script.
`alchemical-analysis.py` was not thoroughly tested and hard to integrate into modern workflows due to its monolithic design, and only supported outdated Python 2.
`alchemical-analysis.py` was not thoroughly tested and hard to integrate into modern workflows due to its monolithic design, and only supported (now outdated) Python 2.
*alchemlyb* improves over its predecessor with a modular, function based design and thorough testing of all components using continuous integration.
Thus, *alchemlyb* is a library that enables users to easily use well-tested building blocks within their own tools while additionally providing examples of complete end-to-end workflows.
This innovation enables consistent processing of free energy data from diverse simulation packages, facilitating streamlined comparison and combination of results.
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