The Library
Sharing data from molecular simulations
Tools
Tools
Tools
(2019) Sharing data from molecular simulations. Journal of Chemical Information and Modeling, 59 (10). pp. 4093-4099. doi:10.1021/acs.jcim.9b00665
|
PDF
WRAP-sharing-data-molecular-simulations-Stansfeld-2019.pdf - Accepted Version - Requires a PDF viewer. Download (703Kb) | Preview |
Official URL: http://dx.doi.org/10.1021/acs.jcim.9b00665
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, Engineering and Medicine > 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: |
|
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Volume: | 59 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Number: | 10 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Page Range: | pp. 4093-4099 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| DOI: | 10.1021/acs.jcim.9b00665 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Status: | Peer Reviewed | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Publication Status: | Published | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Reuse Statement (publisher, data, author rights): | 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: |
|
Request changes or add full text files to a record
Repository staff actions (login required)
 |
View Item |
Downloads
Downloads per month over past year
