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Sharing Data from Molecular Simulations

preprint
submitted on 05.09.2019 and posted on 09.09.2019 by Mark J. Abraham, Rossen Apostolov, Jonathan Barnoud, Paul Bauer, Christian Blau, Alexandre M.J.J. Bonvin, matthieu chavent, John Chodera, Karmen Condic-Jurkic, Lucie Delemotte, Helmut Grubmüller, Rebecca J. Howard, E joseph jordan, Erik Lindahl, Samuli Ollila, Jana Selent, Daniel Smith, Phillip J. Stansfeld, Johanna Tiemann, Mikael Trellet, Christopher Woods, Artem Zhmurov
Given the need for modern researchers to produce open, reproducible scientific output, the lack of standards and best practices for sharing data and workflows used to produce and analyze molecular dynamics (MD) simulations have become an important issue in the field. There are now multiple well-established packages to perform molecular dynamics simulations, often highly tuned for exploiting specific classes of hardware, and each with strong communities surrounding them, but with very limited interoperability/transferability options. Thus, the choice of the software package often dictates the workflow for both simulation production and analysis. The level of detail in documenting the workflows and analysis code varies greatly in published work, hindering reproducibility of the reported results and the ability for other researchers to build on these studies. An increasing number of researchers are motivated to make their data available, but many challenges remain in order to effectively share and reuse simulation data. To discuss these and other issues related to best practices in the field in general, we organized a workshop in November 2018 ( https://bioexcel.eu/events/workshop-on-sharing-data-from-molecular-simulations/). Here, we present a brief overview of this workshop and topics discussed. We hope this effort will spark further conversation in the MD community to pave the way towards more open, interoperable and reproducible outputs coming from research studies using MD simulations.

History

Email Address of Submitting Author

matthieu.chavent@ipbs.fr

Institution

IPBS, Université Paul Sabatier, Toulouse, France

Country

France

ORCID For Submitting Author

0000-0003-4524-4773

Declaration of Conflict of Interest

no conflict of interest

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in Journal of Chemical Information and Modeling

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