Irfan Alibay
Open Molecular Software Foundation, Irvine, CA, USA

Lily Wang
Open Molecular Software Foundation, Irvine, CA, USA

Fiona Naughton
Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, USA

Ian Kenney
Arizona State University, Tempe, AZ, USA

Jonathan Barnoud
Centro Singular de Investigación en Tecnoloxías Intelixentes, Santiago de Compostela, Spain

Richard J Gowers
Open Molecular Software Foundation, Irvine, CA, USA

Oliver Beckstein
Arizona State University, Tempe, AZ, USA

Abstract

The reproducibility and transparency of scientific findings are widely recognized as crucial for promoting scientific progress. However, when it comes to scientific software, researchers face many barriers and few incentives to ensure that their software is open to the community, thoroughly tested, and easily accessible. To address this issue, the MDAKits framework has been developed, which simplifies the process of creating toolkits for the MDAnalysis simulation analysis package (https://www.mdanalysis.org/) that follow the basic principles of FAIR (findability, accessibility, interoperability, and reusability). The MDAKit framework provides a cookiecutter template, best practices documentation, and a continually validated registry. Registered kits are continually tested against the latest release and development version of the MDAnalysis library and their code health is indicated with badges. Users can browse the registry frontend (https://mdakits.mdanalysis.org/) to find new packages, learn about associated publications, and assess the package health in order to make informed decisions about using a MDAKit in their own research. The criteria for registering an MDAKit (open source, version control, documentation, tests) are similar to the criteria required for publishing a paper in a software journal, so we encourage and support publication in, e.g., the Journal of Open Source Software, creating further academic incentive for researchers to publish code. Through the MDAKits framework, we aim to foster the creation of a diverse ecosystem of sustainable community-driven downstream tools for MDAnalysis and hope to provide a blueprint for a model for growing communities around other scientific packages.

Keywords

Molecular Dynamics Simulations, Python, MDAnalysis, eco-system

DOI

10.25080/gerudo-f2bc6f59-00a

Bibtex entry

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Copyright © 2023 Irfan Alibay et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.