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Sharing data from molecular simulations

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Abraham, Mark, Apostolov, Rossen, Barnoud, Jonathan, Bauer, Paul, Blau, Christian, Bonvin, Alexandre M.J.J., Chavent, Matthieu, Chodera, John, Čondić-Jurkić, Karmen, Delemotte, Lucie et al.
(2019) Sharing data from molecular simulations. Journal of Chemical Information and Modeling, 59 (10). pp. 4093-4099. doi:10.1021/acs.jcim.9b00665

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Official URL: http://dx.doi.org/10.1021/acs.jcim.9b00665

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Abstract

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 has 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, 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 toward more open, interoperable, and reproducible outputs coming from research studies using MD simulations.

Item Type: Journal Article
Subjects: Q Science > QA Mathematics
Q Science > QP Physiology
T Technology > T Technology (General)
Divisions: Faculty of Science > Life Sciences (2010- )
Library of Congress Subject Headings (LCSH): Molecular dynamics -- Simulation methods, Molecular dynamics -- Computer simulation, Modecular dynamics -- Data processing
Journal or Publication Title: Journal of Chemical Information and Modeling
Publisher: American Chemical Society
ISSN: 1549-9596
Official Date: 28 October 2019
Dates:
DateEvent
28 October 2019Published
17 September 2019Available
3 September 2019Accepted
Date of first compliant deposit: 5 November 2019
Volume: 59
Number: 10
Page Range: pp. 4093-4099
DOI: 10.1021/acs.jcim.9b00665
Status: Peer Reviewed
Publication Status: Published
Publisher Statement: This document is the Accepted Manuscript version of a Published Work that appeared in final form in Journal of Chemical Information and Modeling, copyright © American Chemical Society after peer review and technical editing by the publisher. To access the final edited and published work see: http://dx.doi.org/10.1021/acs.jcim.9b00665
Access rights to Published version: Restricted or Subscription Access
RIOXX Funder/Project Grant:
Project/Grant IDRIOXX Funder NameFunder ID
H2020-INFRAEDI-02-2018-823830BioExcel Centre of Excellencehttps://bioexcel.eu/
H2020-EINFRA-2015-1- 675728BioExcel Centre of Excellencehttps://bioexcel.eu/
UNSPECIFIEDScience for Life Laboratoryhttp://dx.doi.org/10.13039/501100009252
315596Academy of Finlandhttp://dx.doi.org/10.13039/501100002341
ACI-1547580National Science Foundationhttp://dx.doi.org/10.13039/100000001
208361/Z/17/ZWellcome Trusthttp://dx.doi.org/10.13039/100010269
MR/S009213/1[MRC] Medical Research Councilhttp://dx.doi.org/10.13039/501100000265
HI1502/1-2[DFG] Deutsche Forschungsgemeinschafthttp://dx.doi.org/10.13039/501100001659
Priority programmes 1648, 755, and 803[DFG] Deutsche Forschungsgemeinschafthttp://dx.doi.org/10.13039/501100001659
EP/N018591/1[EPSRC] Engineering and Physical Sciences Research Councilhttp://dx.doi.org/10.13039/501100000266
Cluster of excellence Multiscale ImagingMax-Planck-Gesellschafthttp://dx.doi.org/10.13039/501100004189
PEPS MPI 2018[CNRS] Centre National de la Recherche Scientifiquehttp://dx.doi.org/10.13039/501100004794
“Modélisation du vivant” 2019[CNRS] Centre National de la Recherche Scientifiquehttp://dx.doi.org/10.13039/501100004794
BB/P01948X/1 [BBSRC] Biotechnology and Biological Sciences Research Councilhttp://dx.doi.org/10.13039/501100000268
BB/R002517/1 [BBSRC] Biotechnology and Biological Sciences Research Councilhttp://dx.doi.org/10.13039/501100000268
BB/S003339/1[BBSRC] Biotechnology and Biological Sciences Research Councilhttp://dx.doi.org/10.13039/501100000268
BB/I019855/1[BBSRC] Biotechnology and Biological Sciences Research Councilhttp://dx.doi.org/10.13039/501100000268
UNSPECIFIEDGöran Gustafssons Stiftelse för Naturvetenskaplig och Medicinsk Forskninghttps://search.crossref.org/funding?q=501100003426

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